<article>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#article10_02_09_1336250</id>
	<title>Call For Scientific Research Code To Be Released</title>
	<author>Soulskill</author>
	<datestamp>1265726460000</datestamp>
	<htmltext>Pentagram writes <i>"Professor Ince, writing in the Guardian, has issued a call for scientists to <a href="http://www.guardian.co.uk/technology/2010/feb/05/science-climate-emails-code-release">make the code they use in the course of their research publicly available</a>. He focuses specifically on the <a href="http://science.slashdot.org/story/09/12/05/137203/Scientific-Journal-emNatureem-Finds-Nothing-Notable-In-CRU-Leak">topical controversies</a> in climate science, and concludes with the view that researchers who are able but unwilling to release programs they use should not be regarded as scientists. Quoting: 'There is enough evidence for us to regard a lot of scientific software with worry. For example Professor Les Hatton, an international expert in software testing resident in the Universities of Kent and Kingston, carried out <a href="http://www.leshatton.org/IEEE\_CSE\_297.html">an extensive analysis of several million lines of scientific code</a>. He showed that the software had an unacceptably high level of detectable inconsistencies. For example, interface inconsistencies between software modules which pass data from one part of a program to another occurred at the rate of one in every seven interfaces on average in the programming language Fortran, and one in every 37 interfaces in the language C. This is hugely worrying when you realise that just one error &mdash; just one &mdash; will usually invalidate a computer program. What he also discovered, even more worryingly, is that the accuracy of results declined from six significant figures to one significant figure during the running of programs.'"</i></htmltext>
<tokenext>Pentagram writes " Professor Ince , writing in the Guardian , has issued a call for scientists to make the code they use in the course of their research publicly available .
He focuses specifically on the topical controversies in climate science , and concludes with the view that researchers who are able but unwilling to release programs they use should not be regarded as scientists .
Quoting : 'There is enough evidence for us to regard a lot of scientific software with worry .
For example Professor Les Hatton , an international expert in software testing resident in the Universities of Kent and Kingston , carried out an extensive analysis of several million lines of scientific code .
He showed that the software had an unacceptably high level of detectable inconsistencies .
For example , interface inconsistencies between software modules which pass data from one part of a program to another occurred at the rate of one in every seven interfaces on average in the programming language Fortran , and one in every 37 interfaces in the language C. This is hugely worrying when you realise that just one error    just one    will usually invalidate a computer program .
What he also discovered , even more worryingly , is that the accuracy of results declined from six significant figures to one significant figure during the running of programs .
' "</tokentext>
<sentencetext>Pentagram writes "Professor Ince, writing in the Guardian, has issued a call for scientists to make the code they use in the course of their research publicly available.
He focuses specifically on the topical controversies in climate science, and concludes with the view that researchers who are able but unwilling to release programs they use should not be regarded as scientists.
Quoting: 'There is enough evidence for us to regard a lot of scientific software with worry.
For example Professor Les Hatton, an international expert in software testing resident in the Universities of Kent and Kingston, carried out an extensive analysis of several million lines of scientific code.
He showed that the software had an unacceptably high level of detectable inconsistencies.
For example, interface inconsistencies between software modules which pass data from one part of a program to another occurred at the rate of one in every seven interfaces on average in the programming language Fortran, and one in every 37 interfaces in the language C. This is hugely worrying when you realise that just one error — just one — will usually invalidate a computer program.
What he also discovered, even more worryingly, is that the accuracy of results declined from six significant figures to one significant figure during the running of programs.
'"</sentencetext>
</article>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072784</id>
	<title>Re:Engineering Course Grade = F</title>
	<author>khayman80</author>
	<datestamp>1265734380000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>2</modscore>
	<htmltext>Yes, sounds like someone didn't read <a href="http://docs.sun.com/source/806-3568/ncg\_goldberg.html" title="sun.com">What Every Computer Scientist Should Know About Floating-Point Arithmetic</a> [sun.com].</htmltext>
<tokenext>Yes , sounds like someone did n't read What Every Computer Scientist Should Know About Floating-Point Arithmetic [ sun.com ] .</tokentext>
<sentencetext>Yes, sounds like someone didn't read What Every Computer Scientist Should Know About Floating-Point Arithmetic [sun.com].</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071980</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072886</id>
	<title>Accuracy decreasing during execution?</title>
	<author>Bromskloss</author>
	<datestamp>1265734740000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><blockquote><div><p>the accuracy of results declined from six significant figures to one significant figure during the running of programs</p></div></blockquote><p>What is that supposed to mean?</p></div>
	</htmltext>
<tokenext>the accuracy of results declined from six significant figures to one significant figure during the running of programsWhat is that supposed to mean ?</tokentext>
<sentencetext>the accuracy of results declined from six significant figures to one significant figure during the running of programsWhat is that supposed to mean?
	</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072196</id>
	<title>one error will invalidate a computer program?!?!?</title>
	<author>Anonymous</author>
	<datestamp>1265731860000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext><p>As it is written, the editorial is saying that if there is any error at all in a scientific computer program, the science is usually invalid. What a lot of bull hunky! If this were true, then scientific computing would be impossible, especially with regards to programs that run on Windows.</p><p>Scientists have been doing great science with software for decades. The editorial is full of it.</p><p>Not that it would be bad for scientists to make their software open source. And not that it would be bad for scientists to benefit from some extra QA.</p></htmltext>
<tokenext>As it is written , the editorial is saying that if there is any error at all in a scientific computer program , the science is usually invalid .
What a lot of bull hunky !
If this were true , then scientific computing would be impossible , especially with regards to programs that run on Windows.Scientists have been doing great science with software for decades .
The editorial is full of it.Not that it would be bad for scientists to make their software open source .
And not that it would be bad for scientists to benefit from some extra QA .</tokentext>
<sentencetext>As it is written, the editorial is saying that if there is any error at all in a scientific computer program, the science is usually invalid.
What a lot of bull hunky!
If this were true, then scientific computing would be impossible, especially with regards to programs that run on Windows.Scientists have been doing great science with software for decades.
The editorial is full of it.Not that it would be bad for scientists to make their software open source.
And not that it would be bad for scientists to benefit from some extra QA.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073112</id>
	<title>Re:I concur</title>
	<author>Rising Ape</author>
	<datestamp>1265735580000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext><p>&gt; 600 lines of code in the main, no functions, no comments</p><p>Does that make it function incorrectly?</p><p>Looking pretty and being correct are orthogonal issues. Code can be well-structured but wrong, after all.</p></htmltext>
<tokenext>&gt; 600 lines of code in the main , no functions , no commentsDoes that make it function incorrectly ? Looking pretty and being correct are orthogonal issues .
Code can be well-structured but wrong , after all .</tokentext>
<sentencetext>&gt; 600 lines of code in the main, no functions, no commentsDoes that make it function incorrectly?Looking pretty and being correct are orthogonal issues.
Code can be well-structured but wrong, after all.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072260</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073214</id>
	<title>Re:Not a good idea</title>
	<author>shabtai87</author>
	<datestamp>1265736000000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>What about comparison? Sometimes the goal isn't to reprove the same concept but to test speed/efficiency etc. In these cases the results should be able to be cloned so that one person can say "A is better than B" without the person who proposed "B" sitting up and saying, "well you must have run that on a bad machine" or "your code for our algorithm was obviously not as optimized as ours". Even so in some cases at least the raw data should be provided (garbage in/garbage out).</htmltext>
<tokenext>What about comparison ?
Sometimes the goal is n't to reprove the same concept but to test speed/efficiency etc .
In these cases the results should be able to be cloned so that one person can say " A is better than B " without the person who proposed " B " sitting up and saying , " well you must have run that on a bad machine " or " your code for our algorithm was obviously not as optimized as ours " .
Even so in some cases at least the raw data should be provided ( garbage in/garbage out ) .</tokentext>
<sentencetext>What about comparison?
Sometimes the goal isn't to reprove the same concept but to test speed/efficiency etc.
In these cases the results should be able to be cloned so that one person can say "A is better than B" without the person who proposed "B" sitting up and saying, "well you must have run that on a bad machine" or "your code for our algorithm was obviously not as optimized as ours".
Even so in some cases at least the raw data should be provided (garbage in/garbage out).</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072364</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31075740</id>
	<title>Dirty Laundry</title>
	<author>ThatsNotPudding</author>
	<datestamp>1265744940000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>No one likes their And\_Then\_A\_Miracle\_Occurs() subroutines aired out in public.</htmltext>
<tokenext>No one likes their And \ _Then \ _A \ _Miracle \ _Occurs ( ) subroutines aired out in public .</tokentext>
<sentencetext>No one likes their And\_Then\_A\_Miracle\_Occurs() subroutines aired out in public.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074878</id>
	<title>Re:Not a good idea</title>
	<author>petes\_PoV</author>
	<datestamp>1265742000000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext><p><div class="quote"><p>Experiments produce results</p></div><p>Errrm, experiments produce data. It's the analysis of that data plus the insight and knowledge of the analysts and scientists that turn it into results. The problem is that if everyone uses the same software they'll never notice any systemic failures in the processing it performs.</p></div>
	</htmltext>
<tokenext>Experiments produce resultsErrrm , experiments produce data .
It 's the analysis of that data plus the insight and knowledge of the analysts and scientists that turn it into results .
The problem is that if everyone uses the same software they 'll never notice any systemic failures in the processing it performs .</tokentext>
<sentencetext>Experiments produce resultsErrrm, experiments produce data.
It's the analysis of that data plus the insight and knowledge of the analysts and scientists that turn it into results.
The problem is that if everyone uses the same software they'll never notice any systemic failures in the processing it performs.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073218</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072296</id>
	<title>all</title>
	<author>rossdee</author>
	<datestamp>1265732340000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>1</modscore>
	<htmltext><p>So if scientists use MS Excel for part of their data analysis, MS should release the source code of Excel to prove that there's no bugs in it (that may favour one conclusion over another)<br>Soumds fair to me.</p><p>And if MS doesnt comply then all scientists have to switch to OO.org ?</p></htmltext>
<tokenext>So if scientists use MS Excel for part of their data analysis , MS should release the source code of Excel to prove that there 's no bugs in it ( that may favour one conclusion over another ) Soumds fair to me.And if MS doesnt comply then all scientists have to switch to OO.org ?</tokentext>
<sentencetext>So if scientists use MS Excel for part of their data analysis, MS should release the source code of Excel to prove that there's no bugs in it (that may favour one conclusion over another)Soumds fair to me.And if MS doesnt comply then all scientists have to switch to OO.org ?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072364</id>
	<title>Not a good idea</title>
	<author>Anonymous</author>
	<datestamp>1265732580000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>5</modscore>
	<htmltext>The point about reproducible experiments is not to provide your peers with the exact same equipment you used - then they'd get (probably / hopefully) the exact same results. The idea is to provide them with enough information so that they can design their own experiements to [b]measure the same things[/b] and then to analyze their results to confirm or disprove your conclusions.
<p>
If all scientists run their results through the same analytical software, using the same code as the first researcher, they are not providing confirmation, they are merely cloning the results. That doesn't give the original results either the confidence that they've been independently validated, or that they have been refuted.
</p><p>
What you end up with is no-one having any confidence in the results - as they have only ever been produced in one way and arguments thatt descend into a slanging match between individuals and groups of vested interests who try to "prove" that the same results show they are right and everyone else is wrong.</p></htmltext>
<tokenext>The point about reproducible experiments is not to provide your peers with the exact same equipment you used - then they 'd get ( probably / hopefully ) the exact same results .
The idea is to provide them with enough information so that they can design their own experiements to [ b ] measure the same things [ /b ] and then to analyze their results to confirm or disprove your conclusions .
If all scientists run their results through the same analytical software , using the same code as the first researcher , they are not providing confirmation , they are merely cloning the results .
That does n't give the original results either the confidence that they 've been independently validated , or that they have been refuted .
What you end up with is no-one having any confidence in the results - as they have only ever been produced in one way and arguments thatt descend into a slanging match between individuals and groups of vested interests who try to " prove " that the same results show they are right and everyone else is wrong .</tokentext>
<sentencetext>The point about reproducible experiments is not to provide your peers with the exact same equipment you used - then they'd get (probably / hopefully) the exact same results.
The idea is to provide them with enough information so that they can design their own experiements to [b]measure the same things[/b] and then to analyze their results to confirm or disprove your conclusions.
If all scientists run their results through the same analytical software, using the same code as the first researcher, they are not providing confirmation, they are merely cloning the results.
That doesn't give the original results either the confidence that they've been independently validated, or that they have been refuted.
What you end up with is no-one having any confidence in the results - as they have only ever been produced in one way and arguments thatt descend into a slanging match between individuals and groups of vested interests who try to "prove" that the same results show they are right and everyone else is wrong.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072040</id>
	<title>I'd like to see the code...</title>
	<author>argent</author>
	<datestamp>1265731140000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>I'd like to see actual examples of the code failures mentioned in the T experiments paper.</p><p>Or at least Figure 9.</p></htmltext>
<tokenext>I 'd like to see actual examples of the code failures mentioned in the T experiments paper.Or at least Figure 9 .</tokentext>
<sentencetext>I'd like to see actual examples of the code failures mentioned in the T experiments paper.Or at least Figure 9.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31076538</id>
	<title>Re:Engineering Course Grade = F</title>
	<author>Anonymous</author>
	<datestamp>1265747700000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><blockquote><div><p>When you use floats to do the arithmetic, you lose precision in each operation</p></div></blockquote><p>
This is false.  You may lose precision, but not always.  For example, using IEEE floating point, you can add 2+2 and get exactly 4.</p><blockquote><div><p>But, if you don't use those algorithms, or don't use them correctly and carefully, you really cannot assert \_any\_ precision in the result.</p></div></blockquote><p>
This is also false.  There are plenty of problems which are simple enough to be implemented by a naive programmer and have no trouble with precision.
<br> <br>On the other hand, there are some operations that are very hard to get right.  Large sums is a common problem.  I'd also like to say how much I agree with your confidence interval and wish it was standard practice to compute and store that along with the actual data value.</p></div>
	</htmltext>
<tokenext>When you use floats to do the arithmetic , you lose precision in each operation This is false .
You may lose precision , but not always .
For example , using IEEE floating point , you can add 2 + 2 and get exactly 4.But , if you do n't use those algorithms , or do n't use them correctly and carefully , you really can not assert \ _any \ _ precision in the result .
This is also false .
There are plenty of problems which are simple enough to be implemented by a naive programmer and have no trouble with precision .
On the other hand , there are some operations that are very hard to get right .
Large sums is a common problem .
I 'd also like to say how much I agree with your confidence interval and wish it was standard practice to compute and store that along with the actual data value .</tokentext>
<sentencetext>When you use floats to do the arithmetic, you lose precision in each operation
This is false.
You may lose precision, but not always.
For example, using IEEE floating point, you can add 2+2 and get exactly 4.But, if you don't use those algorithms, or don't use them correctly and carefully, you really cannot assert \_any\_ precision in the result.
This is also false.
There are plenty of problems which are simple enough to be implemented by a naive programmer and have no trouble with precision.
On the other hand, there are some operations that are very hard to get right.
Large sums is a common problem.
I'd also like to say how much I agree with your confidence interval and wish it was standard practice to compute and store that along with the actual data value.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072452</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31077500</id>
	<title>Seems to me that there are several issues here...</title>
	<author>wfolta</author>
	<datestamp>1265708340000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Seems to me that there are several issues here:</p><p>1. Making code available. What do we mean by "code"? Do we mean 100K lines of f77 that's been hacked for 30 years? Or do we mean R, SAS, or Mathematica code? The former is probably not so useful to others, though the latter may well be incredibly illuminating, even for non-experts in the specific field.</p><p>2. Making DATA available. Yes, in the leaked climate emails, there was some amateurish code. But the big issue there was actually sharing DATA, not code. In fact, emails indicated that there were threats of deleting data, and data that was never actually confirmed, hence a scandal.</p><p>3. Unqualified people using your data/code to attack your position. Seems to me that unqualified people are already attacking positions without data/code access, so it's not really a winning position to refuse to share. In fact, it's quite legitimate to suspect someone who is unwilling to share their data/method for arriving at a conclusion. The 1950's "according to scientists" simply doesn't fly anymore.</p><p>4. Unqualified wasting your time answering questions about your data/code. The open source movement has had to deal with this for quite some time. Not only that, the presentation of a question or objection: a) can often be judged by its own statement, and b) may be a common question that needs to be answered. In the first case, someone writing to a climatologist and saying "I downloaded your data and put it in excel and used that curve fitting thing and my curve shows temperatures peaking and going down" needs nothing beyond a canned reply, whether in public or private. (And a public discussion of why this is NOT a scientific objection would actually advance the overall state of education and science in the world.)</p><p>I'm not sure that 300K of crufty f77 code would be very useful to anyone to see. Though I'd also say that knowing someone's conclusions were based on 300K lines of crufty f77 code would be a point in the "not so sure" column. Which I think is much of the objection of releasing code: it takes guts to put not only your conclusions on the line, but also your assumptions and reasoning and most people are simply not willing to do this. Scientists (capital "S") should be willing to do this, but it would be pretty embarrassing to say, "My conclusions are based on a model that involves 400K lines of fortran code that has been tweaked for the last 30 years and which no one living actually understands. It seems to interpolate data very well, and we have reasons X, Y, and Z to believe that it extrapolates well also."</p><p>You may be right, but how many people are willing to say this? Easier to say, "Our proprietary model, developed by [Cue authoritative music] the most EMINENT SCIENTISTS on the PLANET, says A, B, and C," and then Appeal To Authority (tm).</p></htmltext>
<tokenext>Seems to me that there are several issues here : 1 .
Making code available .
What do we mean by " code " ?
Do we mean 100K lines of f77 that 's been hacked for 30 years ?
Or do we mean R , SAS , or Mathematica code ?
The former is probably not so useful to others , though the latter may well be incredibly illuminating , even for non-experts in the specific field.2 .
Making DATA available .
Yes , in the leaked climate emails , there was some amateurish code .
But the big issue there was actually sharing DATA , not code .
In fact , emails indicated that there were threats of deleting data , and data that was never actually confirmed , hence a scandal.3 .
Unqualified people using your data/code to attack your position .
Seems to me that unqualified people are already attacking positions without data/code access , so it 's not really a winning position to refuse to share .
In fact , it 's quite legitimate to suspect someone who is unwilling to share their data/method for arriving at a conclusion .
The 1950 's " according to scientists " simply does n't fly anymore.4 .
Unqualified wasting your time answering questions about your data/code .
The open source movement has had to deal with this for quite some time .
Not only that , the presentation of a question or objection : a ) can often be judged by its own statement , and b ) may be a common question that needs to be answered .
In the first case , someone writing to a climatologist and saying " I downloaded your data and put it in excel and used that curve fitting thing and my curve shows temperatures peaking and going down " needs nothing beyond a canned reply , whether in public or private .
( And a public discussion of why this is NOT a scientific objection would actually advance the overall state of education and science in the world .
) I 'm not sure that 300K of crufty f77 code would be very useful to anyone to see .
Though I 'd also say that knowing someone 's conclusions were based on 300K lines of crufty f77 code would be a point in the " not so sure " column .
Which I think is much of the objection of releasing code : it takes guts to put not only your conclusions on the line , but also your assumptions and reasoning and most people are simply not willing to do this .
Scientists ( capital " S " ) should be willing to do this , but it would be pretty embarrassing to say , " My conclusions are based on a model that involves 400K lines of fortran code that has been tweaked for the last 30 years and which no one living actually understands .
It seems to interpolate data very well , and we have reasons X , Y , and Z to believe that it extrapolates well also .
" You may be right , but how many people are willing to say this ?
Easier to say , " Our proprietary model , developed by [ Cue authoritative music ] the most EMINENT SCIENTISTS on the PLANET , says A , B , and C , " and then Appeal To Authority ( tm ) .</tokentext>
<sentencetext>Seems to me that there are several issues here:1.
Making code available.
What do we mean by "code"?
Do we mean 100K lines of f77 that's been hacked for 30 years?
Or do we mean R, SAS, or Mathematica code?
The former is probably not so useful to others, though the latter may well be incredibly illuminating, even for non-experts in the specific field.2.
Making DATA available.
Yes, in the leaked climate emails, there was some amateurish code.
But the big issue there was actually sharing DATA, not code.
In fact, emails indicated that there were threats of deleting data, and data that was never actually confirmed, hence a scandal.3.
Unqualified people using your data/code to attack your position.
Seems to me that unqualified people are already attacking positions without data/code access, so it's not really a winning position to refuse to share.
In fact, it's quite legitimate to suspect someone who is unwilling to share their data/method for arriving at a conclusion.
The 1950's "according to scientists" simply doesn't fly anymore.4.
Unqualified wasting your time answering questions about your data/code.
The open source movement has had to deal with this for quite some time.
Not only that, the presentation of a question or objection: a) can often be judged by its own statement, and b) may be a common question that needs to be answered.
In the first case, someone writing to a climatologist and saying "I downloaded your data and put it in excel and used that curve fitting thing and my curve shows temperatures peaking and going down" needs nothing beyond a canned reply, whether in public or private.
(And a public discussion of why this is NOT a scientific objection would actually advance the overall state of education and science in the world.
)I'm not sure that 300K of crufty f77 code would be very useful to anyone to see.
Though I'd also say that knowing someone's conclusions were based on 300K lines of crufty f77 code would be a point in the "not so sure" column.
Which I think is much of the objection of releasing code: it takes guts to put not only your conclusions on the line, but also your assumptions and reasoning and most people are simply not willing to do this.
Scientists (capital "S") should be willing to do this, but it would be pretty embarrassing to say, "My conclusions are based on a model that involves 400K lines of fortran code that has been tweaked for the last 30 years and which no one living actually understands.
It seems to interpolate data very well, and we have reasons X, Y, and Z to believe that it extrapolates well also.
"You may be right, but how many people are willing to say this?
Easier to say, "Our proprietary model, developed by [Cue authoritative music] the most EMINENT SCIENTISTS on the PLANET, says A, B, and C," and then Appeal To Authority (tm).</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072564</id>
	<title>Re:Why release it?</title>
	<author>jgtg32a</author>
	<datestamp>1265733480000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Who said it was a conspiracy of a thousand people?  Isn't the claim that the ipcc reports are written by thousand people?  That's not exactly true.  The actual report was written by something like 50 people the thousand number comes from the supporting data.  There were a lot of groups of people who did independent research that showed "whatever", and the "whatever" supports the "conclusion" so it is used, and things that don't support the "conclusion" are suppressed.<br>
&nbsp; <br>Now we have a fancy report, we pass that around, and it is solid and everyone agrees with what they see</p></htmltext>
<tokenext>Who said it was a conspiracy of a thousand people ?
Is n't the claim that the ipcc reports are written by thousand people ?
That 's not exactly true .
The actual report was written by something like 50 people the thousand number comes from the supporting data .
There were a lot of groups of people who did independent research that showed " whatever " , and the " whatever " supports the " conclusion " so it is used , and things that do n't support the " conclusion " are suppressed .
  Now we have a fancy report , we pass that around , and it is solid and everyone agrees with what they see</tokentext>
<sentencetext>Who said it was a conspiracy of a thousand people?
Isn't the claim that the ipcc reports are written by thousand people?
That's not exactly true.
The actual report was written by something like 50 people the thousand number comes from the supporting data.
There were a lot of groups of people who did independent research that showed "whatever", and the "whatever" supports the "conclusion" so it is used, and things that don't support the "conclusion" are suppressed.
  Now we have a fancy report, we pass that around, and it is solid and everyone agrees with what they see</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071954</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31080248</id>
	<title>The actual paper is not quite as convincing</title>
	<author>Krahar</author>
	<datestamp>1265720820000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>From reading the actual paper, the analysis of source code is based on automatic static analysis, NOT on humans actually reading the code. Static analysis software can generate a high amount of false positives, so knowing that lots of software triggers the static analysis criteria for a fault doesn't necessarily mean anything at all about number of bugs or quality of the software. It does mildly suggest that there might be a problem, though.
<br> <br>
The second part of the paper is about comparing different commercial software for doing calculations on seismic data. The results of this is that even though the operations that these software systems are supposed to carry out are completely mathematically stringently defined algorithms, the answers you get in the end differ wildly, and in some cases the different packages agree on only 1 figure! There is no one package that seems to generate better output than the others. As the paper states, this could result in drilling a 20 million dollar oil well in the wrong place, since up to three significant figures can be needed for that purpose.
<br> <br>
To sum up, this is absolutely scandalous, and there is no reason to suspect that software for seismic calculations is any worse than for lots of other areas.</htmltext>
<tokenext>From reading the actual paper , the analysis of source code is based on automatic static analysis , NOT on humans actually reading the code .
Static analysis software can generate a high amount of false positives , so knowing that lots of software triggers the static analysis criteria for a fault does n't necessarily mean anything at all about number of bugs or quality of the software .
It does mildly suggest that there might be a problem , though .
The second part of the paper is about comparing different commercial software for doing calculations on seismic data .
The results of this is that even though the operations that these software systems are supposed to carry out are completely mathematically stringently defined algorithms , the answers you get in the end differ wildly , and in some cases the different packages agree on only 1 figure !
There is no one package that seems to generate better output than the others .
As the paper states , this could result in drilling a 20 million dollar oil well in the wrong place , since up to three significant figures can be needed for that purpose .
To sum up , this is absolutely scandalous , and there is no reason to suspect that software for seismic calculations is any worse than for lots of other areas .</tokentext>
<sentencetext>From reading the actual paper, the analysis of source code is based on automatic static analysis, NOT on humans actually reading the code.
Static analysis software can generate a high amount of false positives, so knowing that lots of software triggers the static analysis criteria for a fault doesn't necessarily mean anything at all about number of bugs or quality of the software.
It does mildly suggest that there might be a problem, though.
The second part of the paper is about comparing different commercial software for doing calculations on seismic data.
The results of this is that even though the operations that these software systems are supposed to carry out are completely mathematically stringently defined algorithms, the answers you get in the end differ wildly, and in some cases the different packages agree on only 1 figure!
There is no one package that seems to generate better output than the others.
As the paper states, this could result in drilling a 20 million dollar oil well in the wrong place, since up to three significant figures can be needed for that purpose.
To sum up, this is absolutely scandalous, and there is no reason to suspect that software for seismic calculations is any worse than for lots of other areas.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073166</id>
	<title>Re:all</title>
	<author>John Hasler</author>
	<datestamp>1265735760000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>&gt; So if scientists use MS Excel for part of their data analysis...</p><p>Then their results are suspect since Excel is known to be unreliable.</p></htmltext>
<tokenext>&gt; So if scientists use MS Excel for part of their data analysis...Then their results are suspect since Excel is known to be unreliable .</tokentext>
<sentencetext>&gt; So if scientists use MS Excel for part of their data analysis...Then their results are suspect since Excel is known to be unreliable.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072296</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072120</id>
	<title>Peer Review vs. Funding</title>
	<author>stokessd</author>
	<datestamp>1265731440000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>2</modscore>
	<htmltext><p>I got my PhD in fluid mechanics funded by NASA, and as such my findings are easily publishable and shared with others.  My analysis code (such as it was) was and is available for those would would like to use it.  More importantly my experimental data is available as well.</p><p>This represents the classical pure research side of research where we all get together and talk about our findings and there really aren't any secrets.  But even with this open example, there are still secrets when it comes to ideas for future funding.  You only tip your cards when it comes to things you've already done, not future plans.</p><p>But more importantly, there are whole areas of research that are very closed off.  Pharma is a good example.  Sure there are lots of peer reviewed articles published and methods discussed, but you'll never really get into their shorts like this guy wants.  There's a lot that goes on behind that curtain.  And even if you are a grad student with high ideals and a desire to share all your findings, you may find that the rules of your funding prevent you from sharing.</p><p>Sheldon</p></htmltext>
<tokenext>I got my PhD in fluid mechanics funded by NASA , and as such my findings are easily publishable and shared with others .
My analysis code ( such as it was ) was and is available for those would would like to use it .
More importantly my experimental data is available as well.This represents the classical pure research side of research where we all get together and talk about our findings and there really are n't any secrets .
But even with this open example , there are still secrets when it comes to ideas for future funding .
You only tip your cards when it comes to things you 've already done , not future plans.But more importantly , there are whole areas of research that are very closed off .
Pharma is a good example .
Sure there are lots of peer reviewed articles published and methods discussed , but you 'll never really get into their shorts like this guy wants .
There 's a lot that goes on behind that curtain .
And even if you are a grad student with high ideals and a desire to share all your findings , you may find that the rules of your funding prevent you from sharing.Sheldon</tokentext>
<sentencetext>I got my PhD in fluid mechanics funded by NASA, and as such my findings are easily publishable and shared with others.
My analysis code (such as it was) was and is available for those would would like to use it.
More importantly my experimental data is available as well.This represents the classical pure research side of research where we all get together and talk about our findings and there really aren't any secrets.
But even with this open example, there are still secrets when it comes to ideas for future funding.
You only tip your cards when it comes to things you've already done, not future plans.But more importantly, there are whole areas of research that are very closed off.
Pharma is a good example.
Sure there are lots of peer reviewed articles published and methods discussed, but you'll never really get into their shorts like this guy wants.
There's a lot that goes on behind that curtain.
And even if you are a grad student with high ideals and a desire to share all your findings, you may find that the rules of your funding prevent you from sharing.Sheldon</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072312</id>
	<title>social.... science.</title>
	<author>Anonymous</author>
	<datestamp>1265732400000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext>Sure it's nice for peers to review, but to make it a mandatory thing? I thought science was based on rules with the assumption there are no rules.
<br>
<br>
I wonder what Newton, Einstein, Kepler, or Goddard would have thought if they were demanded to follow this type of review. Really. Peer review has become the Java of the research world if you know what I mean (the solution for everything)--there should be multiple forums for informal discussion/verification, formal proposals/verification.</htmltext>
<tokenext>Sure it 's nice for peers to review , but to make it a mandatory thing ?
I thought science was based on rules with the assumption there are no rules .
I wonder what Newton , Einstein , Kepler , or Goddard would have thought if they were demanded to follow this type of review .
Really. Peer review has become the Java of the research world if you know what I mean ( the solution for everything ) --there should be multiple forums for informal discussion/verification , formal proposals/verification .</tokentext>
<sentencetext>Sure it's nice for peers to review, but to make it a mandatory thing?
I thought science was based on rules with the assumption there are no rules.
I wonder what Newton, Einstein, Kepler, or Goddard would have thought if they were demanded to follow this type of review.
Really. Peer review has become the Java of the research world if you know what I mean (the solution for everything)--there should be multiple forums for informal discussion/verification, formal proposals/verification.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31077638</id>
	<title>Keep the lid on the trash closed</title>
	<author>namgge</author>
	<datestamp>1265708880000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>I believe that scientists should publish their algorithms and methods, but publishing code may be counterproductive for several reasons. Firstly, another group trying to replicate and/or verify the method should start from scratch to ensure their work doesn't simply import flaws from the original. Secondy, I don't believe it is possible to debug science code to the point where it is defect free - people keep debugging only until the results agree with their intuition. Thirdly, scientists should not waste their lives sifting through thousands of line of Fortran written by long-gone grad students hoping to find errors, they should be creating and investigating new stuff.

Namgge</htmltext>
<tokenext>I believe that scientists should publish their algorithms and methods , but publishing code may be counterproductive for several reasons .
Firstly , another group trying to replicate and/or verify the method should start from scratch to ensure their work does n't simply import flaws from the original .
Secondy , I do n't believe it is possible to debug science code to the point where it is defect free - people keep debugging only until the results agree with their intuition .
Thirdly , scientists should not waste their lives sifting through thousands of line of Fortran written by long-gone grad students hoping to find errors , they should be creating and investigating new stuff .
Namgge</tokentext>
<sentencetext>I believe that scientists should publish their algorithms and methods, but publishing code may be counterproductive for several reasons.
Firstly, another group trying to replicate and/or verify the method should start from scratch to ensure their work doesn't simply import flaws from the original.
Secondy, I don't believe it is possible to debug science code to the point where it is defect free - people keep debugging only until the results agree with their intuition.
Thirdly, scientists should not waste their lives sifting through thousands of line of Fortran written by long-gone grad students hoping to find errors, they should be creating and investigating new stuff.
Namgge</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071878</id>
	<title>Seems reasonable</title>
	<author>NathanE</author>
	<datestamp>1265730240000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>4</modscore>
	<htmltext><p>Particularly if the research is publicly funded.</p></htmltext>
<tokenext>Particularly if the research is publicly funded .</tokentext>
<sentencetext>Particularly if the research is publicly funded.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073742</id>
	<title>Scientific research as a real open source project</title>
	<author>\_\_roo</author>
	<datestamp>1265737800000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>I would go further than just publishing the code used in scientific research. I would build the code by running it a real open source project. In fact, I've done exactly that, and it worked out incredibly well. I believe our open source approach lead to better science, and also better software.</p><p>I worked with researchers from <a href="http://pazoulay.scripts.mit.edu/" title="mit.edu">MIT</a> [mit.edu] and <a href="http://www.columbia.edu/~jz126/" title="columbia.edu">Columbia</a> [columbia.edu] on a research project that involved gathering and analyzing a large amount of publication data. The results of the study are about to be published (you can read the working paper at the <a href="http://pazoulay.scripts.mit.edu/Publications.html" title="mit.edu">lead researcher's website</a> [mit.edu]).</p><p>We intended the code for this project to be released from the beginning, so we ran it as an open source project. I followed the basic formula from Karl Fogel's excellent (and free to download) book, <a href="http://producingoss.com/" title="producingoss.com">Producing Open Source Software</a> [producingoss.com]: set up a <a href="http://www.stellman-greene.com/PublicationHarvester" title="stellman-greene.com">website for the project</a> [stellman-greene.com], created lots of documentation, tried to make it as easy as possible for someone to get up and running, made the source available via Subversion, and made it easy to contact us.</p><p>Quality was really important for us, so we put a lot of effort into testing. I definitely believe that the fact that we intended the project to be open source from the beginning helped with that. We weren't treating the code as some piece of throwaway or replaceable lab equipment. I'm convinced that treating it as a real product of the research caused us to take the development and the quality much more seriously than a lot of researchers. I've since heard from other researchers who are starting to use the software as well, and everyone who sees it feels that it came out really well.</p><p>There was another scientific benefit that should definitely appeal to anyone who lives in the publish-or-perish world of science research. We published a paper specifically on the project (Azoulay P, Stellman A, Zivin JG. <em>PublicationHarvester. An open-source software tool for science policy research.</em> Research Policy 35 (2006) 970-974. -- there's a link to the PDF on the lead researcher's website.)</p><p>It's funny -- I wrote an article a few years ago with Jennifer Greene for O'Reilly ONLamp called <a href="http://onlamp.com/pub/a/onlamp/2006/02/27/what-corp-projects-learn-from-open-source.html" title="onlamp.com">What Corporate Projects Should Learn from Open Source</a> [onlamp.com]. I'm now convinced that science research projects can also learn a great deal from open source as well.</p></htmltext>
<tokenext>I would go further than just publishing the code used in scientific research .
I would build the code by running it a real open source project .
In fact , I 've done exactly that , and it worked out incredibly well .
I believe our open source approach lead to better science , and also better software.I worked with researchers from MIT [ mit.edu ] and Columbia [ columbia.edu ] on a research project that involved gathering and analyzing a large amount of publication data .
The results of the study are about to be published ( you can read the working paper at the lead researcher 's website [ mit.edu ] ) .We intended the code for this project to be released from the beginning , so we ran it as an open source project .
I followed the basic formula from Karl Fogel 's excellent ( and free to download ) book , Producing Open Source Software [ producingoss.com ] : set up a website for the project [ stellman-greene.com ] , created lots of documentation , tried to make it as easy as possible for someone to get up and running , made the source available via Subversion , and made it easy to contact us.Quality was really important for us , so we put a lot of effort into testing .
I definitely believe that the fact that we intended the project to be open source from the beginning helped with that .
We were n't treating the code as some piece of throwaway or replaceable lab equipment .
I 'm convinced that treating it as a real product of the research caused us to take the development and the quality much more seriously than a lot of researchers .
I 've since heard from other researchers who are starting to use the software as well , and everyone who sees it feels that it came out really well.There was another scientific benefit that should definitely appeal to anyone who lives in the publish-or-perish world of science research .
We published a paper specifically on the project ( Azoulay P , Stellman A , Zivin JG .
PublicationHarvester. An open-source software tool for science policy research .
Research Policy 35 ( 2006 ) 970-974 .
-- there 's a link to the PDF on the lead researcher 's website .
) It 's funny -- I wrote an article a few years ago with Jennifer Greene for O'Reilly ONLamp called What Corporate Projects Should Learn from Open Source [ onlamp.com ] .
I 'm now convinced that science research projects can also learn a great deal from open source as well .</tokentext>
<sentencetext>I would go further than just publishing the code used in scientific research.
I would build the code by running it a real open source project.
In fact, I've done exactly that, and it worked out incredibly well.
I believe our open source approach lead to better science, and also better software.I worked with researchers from MIT [mit.edu] and Columbia [columbia.edu] on a research project that involved gathering and analyzing a large amount of publication data.
The results of the study are about to be published (you can read the working paper at the lead researcher's website [mit.edu]).We intended the code for this project to be released from the beginning, so we ran it as an open source project.
I followed the basic formula from Karl Fogel's excellent (and free to download) book, Producing Open Source Software [producingoss.com]: set up a website for the project [stellman-greene.com], created lots of documentation, tried to make it as easy as possible for someone to get up and running, made the source available via Subversion, and made it easy to contact us.Quality was really important for us, so we put a lot of effort into testing.
I definitely believe that the fact that we intended the project to be open source from the beginning helped with that.
We weren't treating the code as some piece of throwaway or replaceable lab equipment.
I'm convinced that treating it as a real product of the research caused us to take the development and the quality much more seriously than a lot of researchers.
I've since heard from other researchers who are starting to use the software as well, and everyone who sees it feels that it came out really well.There was another scientific benefit that should definitely appeal to anyone who lives in the publish-or-perish world of science research.
We published a paper specifically on the project (Azoulay P, Stellman A, Zivin JG.
PublicationHarvester. An open-source software tool for science policy research.
Research Policy 35 (2006) 970-974.
-- there's a link to the PDF on the lead researcher's website.
)It's funny -- I wrote an article a few years ago with Jennifer Greene for O'Reilly ONLamp called What Corporate Projects Should Learn from Open Source [onlamp.com].
I'm now convinced that science research projects can also learn a great deal from open source as well.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072594</id>
	<title>Re:Slashdot Egocentrism.</title>
	<author>AlXtreme</author>
	<datestamp>1265733660000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>3</modscore>
	<htmltext><blockquote><div><p>that scientists outside of computer science are too busy in their respective fields to know anything about code, or even care.</p></div></blockquote><p>If their code results in predictions that affect millions of lives and trillions of dollars, perhaps they should learn to care.</p><p>What I've personally seen of scientists is a frantic determination to publish papers anywhere and everywhere, no matter how well-founded the results in those papers are. The IPCC-gate is merely a symptom of a deeper problem within scientific research.</p><p>If scientists are too busy because of publication quota's and funding issues to focus on delivering proper scientific research, maybe we should question our current means of supporting scientific research. Currently we've got quantity, but very little quality.</p></div>
	</htmltext>
<tokenext>that scientists outside of computer science are too busy in their respective fields to know anything about code , or even care.If their code results in predictions that affect millions of lives and trillions of dollars , perhaps they should learn to care.What I 've personally seen of scientists is a frantic determination to publish papers anywhere and everywhere , no matter how well-founded the results in those papers are .
The IPCC-gate is merely a symptom of a deeper problem within scientific research.If scientists are too busy because of publication quota 's and funding issues to focus on delivering proper scientific research , maybe we should question our current means of supporting scientific research .
Currently we 've got quantity , but very little quality .</tokentext>
<sentencetext>that scientists outside of computer science are too busy in their respective fields to know anything about code, or even care.If their code results in predictions that affect millions of lives and trillions of dollars, perhaps they should learn to care.What I've personally seen of scientists is a frantic determination to publish papers anywhere and everywhere, no matter how well-founded the results in those papers are.
The IPCC-gate is merely a symptom of a deeper problem within scientific research.If scientists are too busy because of publication quota's and funding issues to focus on delivering proper scientific research, maybe we should question our current means of supporting scientific research.
Currently we've got quantity, but very little quality.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072056</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31082620</id>
	<title>Re:Not that simple</title>
	<author>Anonymous</author>
	<datestamp>1265744640000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>In the part of NASA I'm familiar with, data is publicly  released along with software tools.</p><p>I searched for GRACE and found that they make data available:  http://www.csr.utexas.edu/grace/asdp.html.</p></htmltext>
<tokenext>In the part of NASA I 'm familiar with , data is publicly released along with software tools.I searched for GRACE and found that they make data available : http : //www.csr.utexas.edu/grace/asdp.html .</tokentext>
<sentencetext>In the part of NASA I'm familiar with, data is publicly  released along with software tools.I searched for GRACE and found that they make data available:  http://www.csr.utexas.edu/grace/asdp.html.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072694</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072346</id>
	<title>fear over fact</title>
	<author>xzvf</author>
	<datestamp>1265732520000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>Humans are hardwired for fear and have to learn to think factually.  Like most scientific issues that become political, fear and misinformation dominate over political fact.  There will always be a certain segment of the population that believes vaccines cause autism and global warming is a trick to tax us with cap and trade.  With vaccines you wait for the kids of autism avoiders to die of measles and polio.  With global warming change the message from tax to disincentive to tax credit to incentive.  Energy independence (make it a defense issue), tax credits for solar and wind that make the payback for a home owner less than a decade (I suspect a five year payback will get homeowners and home builders forking over for energy improvements).</htmltext>
<tokenext>Humans are hardwired for fear and have to learn to think factually .
Like most scientific issues that become political , fear and misinformation dominate over political fact .
There will always be a certain segment of the population that believes vaccines cause autism and global warming is a trick to tax us with cap and trade .
With vaccines you wait for the kids of autism avoiders to die of measles and polio .
With global warming change the message from tax to disincentive to tax credit to incentive .
Energy independence ( make it a defense issue ) , tax credits for solar and wind that make the payback for a home owner less than a decade ( I suspect a five year payback will get homeowners and home builders forking over for energy improvements ) .</tokentext>
<sentencetext>Humans are hardwired for fear and have to learn to think factually.
Like most scientific issues that become political, fear and misinformation dominate over political fact.
There will always be a certain segment of the population that believes vaccines cause autism and global warming is a trick to tax us with cap and trade.
With vaccines you wait for the kids of autism avoiders to die of measles and polio.
With global warming change the message from tax to disincentive to tax credit to incentive.
Energy independence (make it a defense issue), tax credits for solar and wind that make the payback for a home owner less than a decade (I suspect a five year payback will get homeowners and home builders forking over for energy improvements).</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071884</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31076418</id>
	<title>Re:This is not science.</title>
	<author>bunratty</author>
	<datestamp>1265747280000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>What about physics? <a href="http://en.wikipedia.org/wiki/Jan\_Hendrik\_Sch\%C3\%B6n" title="wikipedia.org">Sch&#246;n</a> [wikipedia.org] was a physicist who was discovered to have published papers based on outright fraudulent research. Do you not "go along" with physics because they're "shady people"?</htmltext>
<tokenext>What about physics ?
Sch   n [ wikipedia.org ] was a physicist who was discovered to have published papers based on outright fraudulent research .
Do you not " go along " with physics because they 're " shady people " ?</tokentext>
<sentencetext>What about physics?
Schön [wikipedia.org] was a physicist who was discovered to have published papers based on outright fraudulent research.
Do you not "go along" with physics because they're "shady people"?</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072742</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072638</id>
	<title>Re:Stuff like Sweave</title>
	<author>shabtai87</author>
	<datestamp>1265733780000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>There's a lot of nice extensions using the listings package in LaTeX. I use a lot of MATLAB so I usually end up using the mcode.sty available on mathworks (http://www.mathworks.com/matlabcentral/fileexchange/8015). Its got the color coded parts right too, which is nice for readability. More importantly I'll save the current code at the time of that report with the report itself, just in case I get really drunk and decide try to "fix" any base code.</htmltext>
<tokenext>There 's a lot of nice extensions using the listings package in LaTeX .
I use a lot of MATLAB so I usually end up using the mcode.sty available on mathworks ( http : //www.mathworks.com/matlabcentral/fileexchange/8015 ) .
Its got the color coded parts right too , which is nice for readability .
More importantly I 'll save the current code at the time of that report with the report itself , just in case I get really drunk and decide try to " fix " any base code .</tokentext>
<sentencetext>There's a lot of nice extensions using the listings package in LaTeX.
I use a lot of MATLAB so I usually end up using the mcode.sty available on mathworks (http://www.mathworks.com/matlabcentral/fileexchange/8015).
Its got the color coded parts right too, which is nice for readability.
More importantly I'll save the current code at the time of that report with the report itself, just in case I get really drunk and decide try to "fix" any base code.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071944</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072446</id>
	<title>engineering or science</title>
	<author>Anonymous</author>
	<datestamp>1265733000000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><i>For example, interface inconsistencies between software modules which pass data from one part of a program to another occurred at the rate of one in every seven interfaces on average in the programming language Fortran, and one in every 37 interfaces in the language C. </i>
<br>
<br>
Ah, classic example of the difference between s/w engineering and s/w development. Problem is it's hard to tell and engineer to thinking like a
scientist and vice versa.</htmltext>
<tokenext>For example , interface inconsistencies between software modules which pass data from one part of a program to another occurred at the rate of one in every seven interfaces on average in the programming language Fortran , and one in every 37 interfaces in the language C . Ah , classic example of the difference between s/w engineering and s/w development .
Problem is it 's hard to tell and engineer to thinking like a scientist and vice versa .</tokentext>
<sentencetext>For example, interface inconsistencies between software modules which pass data from one part of a program to another occurred at the rate of one in every seven interfaces on average in the programming language Fortran, and one in every 37 interfaces in the language C. 


Ah, classic example of the difference between s/w engineering and s/w development.
Problem is it's hard to tell and engineer to thinking like a
scientist and vice versa.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31076396</id>
	<title>Re:This is not science.</title>
	<author>IICV</author>
	<datestamp>1265747160000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>If you're not qualified to review someone's scientific data, how do you know that he's shady? Is it because your shady-detector goes ping when you wave it over him? Then how do you quantify the accuracy of your shady-detector? How do you insulate it against the interference of the media, who love to paint things in an exaggerated light? How do you isolate it from the effect of your own emotions - after all, if global warming is happening, then you should probably behave in a different way and you might not want to.</p></htmltext>
<tokenext>If you 're not qualified to review someone 's scientific data , how do you know that he 's shady ?
Is it because your shady-detector goes ping when you wave it over him ?
Then how do you quantify the accuracy of your shady-detector ?
How do you insulate it against the interference of the media , who love to paint things in an exaggerated light ?
How do you isolate it from the effect of your own emotions - after all , if global warming is happening , then you should probably behave in a different way and you might not want to .</tokentext>
<sentencetext>If you're not qualified to review someone's scientific data, how do you know that he's shady?
Is it because your shady-detector goes ping when you wave it over him?
Then how do you quantify the accuracy of your shady-detector?
How do you insulate it against the interference of the media, who love to paint things in an exaggerated light?
How do you isolate it from the effect of your own emotions - after all, if global warming is happening, then you should probably behave in a different way and you might not want to.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072742</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071884</id>
	<title>Why release it?</title>
	<author>Anonymous</author>
	<datestamp>1265730240000</datestamp>
	<modclass>Flamebait</modclass>
	<modscore>-1</modscore>
	<htmltext><p>I mean, it is just easier to keep lying to people to get them to believe what you want them to believe.  It works for politicians.</p></htmltext>
<tokenext>I mean , it is just easier to keep lying to people to get them to believe what you want them to believe .
It works for politicians .</tokentext>
<sentencetext>I mean, it is just easier to keep lying to people to get them to believe what you want them to believe.
It works for politicians.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072826</id>
	<title>Peer Review / publication process</title>
	<author>Wardish</author>
	<datestamp>1265734500000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext><p>As part of publication and peer review all data and providence of the data as well as any additional formula's, algorithms, and the exact code that was used to process the data should be placed online in a neutral holding area.</p><p>Neutral area needs to be independent and needs to show any updates and changes, preserving the original content in the process.</p><p>If your data and code (readable and compilable by other researchers) isn't available then peer review and reproduction of results is foolish.  If you can't look in the black box then you can't trust it.</p></htmltext>
<tokenext>As part of publication and peer review all data and providence of the data as well as any additional formula 's , algorithms , and the exact code that was used to process the data should be placed online in a neutral holding area.Neutral area needs to be independent and needs to show any updates and changes , preserving the original content in the process.If your data and code ( readable and compilable by other researchers ) is n't available then peer review and reproduction of results is foolish .
If you ca n't look in the black box then you ca n't trust it .</tokentext>
<sentencetext>As part of publication and peer review all data and providence of the data as well as any additional formula's, algorithms, and the exact code that was used to process the data should be placed online in a neutral holding area.Neutral area needs to be independent and needs to show any updates and changes, preserving the original content in the process.If your data and code (readable and compilable by other researchers) isn't available then peer review and reproduction of results is foolish.
If you can't look in the black box then you can't trust it.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31076742</id>
	<title>Re:I concur</title>
	<author>jafac</author>
	<datestamp>1265748600000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Oh - lets not even get started discussing the difference in coding style between software industry professional developers, and computer scientists.</p></htmltext>
<tokenext>Oh - lets not even get started discussing the difference in coding style between software industry professional developers , and computer scientists .</tokentext>
<sentencetext>Oh - lets not even get started discussing the difference in coding style between software industry professional developers, and computer scientists.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072260</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071998</id>
	<title>MaDnEsS !</title>
	<author>Anonymous</author>
	<datestamp>1265730780000</datestamp>
	<modclass>Funny</modclass>
	<modscore>4</modscore>
	<htmltext>What? Scientists showing their work for peer-review?

It's MADNESS I tell you. MADNESS !</htmltext>
<tokenext>What ?
Scientists showing their work for peer-review ?
It 's MADNESS I tell you .
MADNESS !</tokentext>
<sentencetext>What?
Scientists showing their work for peer-review?
It's MADNESS I tell you.
MADNESS !</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072056</id>
	<title>Slashdot Egocentrism.</title>
	<author>stewbacca</author>
	<datestamp>1265731200000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext><p>My bet is there is a simple explanation...namely that scientists outside of computer science are too busy in their respective fields to know anything about code, or even care.  The egocentric Slashdot-worldview strikes at the heart of logic yet again.</p></htmltext>
<tokenext>My bet is there is a simple explanation...namely that scientists outside of computer science are too busy in their respective fields to know anything about code , or even care .
The egocentric Slashdot-worldview strikes at the heart of logic yet again .</tokentext>
<sentencetext>My bet is there is a simple explanation...namely that scientists outside of computer science are too busy in their respective fields to know anything about code, or even care.
The egocentric Slashdot-worldview strikes at the heart of logic yet again.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073302</id>
	<title>Re:MaDnEsS !</title>
	<author>c\_sd\_m</author>
	<datestamp>1265736360000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>The madness would ensue when we try to find people to review it. I've seen some pretty loony reviewers comments and I can only imagine what they would come up with if we gave them code.</htmltext>
<tokenext>The madness would ensue when we try to find people to review it .
I 've seen some pretty loony reviewers comments and I can only imagine what they would come up with if we gave them code .</tokentext>
<sentencetext>The madness would ensue when we try to find people to review it.
I've seen some pretty loony reviewers comments and I can only imagine what they would come up with if we gave them code.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071998</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074074</id>
	<title>Re:Observations...</title>
	<author>quadelirus</author>
	<datestamp>1265738880000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>I think conferences and journals should require complete code submission alongside paper submissions. Then the code won't be published unless the paper is published, but we will create a more open and honest system and stimulate more advancement (since other groups can then build on top of a good sturdy platform instead of always having to start from scratch to build up their own code base).</htmltext>
<tokenext>I think conferences and journals should require complete code submission alongside paper submissions .
Then the code wo n't be published unless the paper is published , but we will create a more open and honest system and stimulate more advancement ( since other groups can then build on top of a good sturdy platform instead of always having to start from scratch to build up their own code base ) .</tokentext>
<sentencetext>I think conferences and journals should require complete code submission alongside paper submissions.
Then the code won't be published unless the paper is published, but we will create a more open and honest system and stimulate more advancement (since other groups can then build on top of a good sturdy platform instead of always having to start from scratch to build up their own code base).</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072268</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31075444</id>
	<title>Reproducible Research with sweave</title>
	<author>akakaak</author>
	<datestamp>1265743920000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>If you do your data analysis in R and write your paper in latex, then you can use <a href="http://www.statistik.lmu.de/~leisch/Sweave/" title="statistik.lmu.de" rel="nofollow">sweave</a> [statistik.lmu.de] to create a single file with the R code embedded in the latex. When you process the latex file, the R code is run, generating your stats and figures on the fly for the resulting document. If this file (plus any data files it reads, and any non-standard code it calls) is posted as "supplementary material" along with the PDF journal article, then there is no question about the software or analysis that led to the figures in the paper. Of course, the data itself is still open to question.</p></htmltext>
<tokenext>If you do your data analysis in R and write your paper in latex , then you can use sweave [ statistik.lmu.de ] to create a single file with the R code embedded in the latex .
When you process the latex file , the R code is run , generating your stats and figures on the fly for the resulting document .
If this file ( plus any data files it reads , and any non-standard code it calls ) is posted as " supplementary material " along with the PDF journal article , then there is no question about the software or analysis that led to the figures in the paper .
Of course , the data itself is still open to question .</tokentext>
<sentencetext>If you do your data analysis in R and write your paper in latex, then you can use sweave [statistik.lmu.de] to create a single file with the R code embedded in the latex.
When you process the latex file, the R code is run, generating your stats and figures on the fly for the resulting document.
If this file (plus any data files it reads, and any non-standard code it calls) is posted as "supplementary material" along with the PDF journal article, then there is no question about the software or analysis that led to the figures in the paper.
Of course, the data itself is still open to question.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31076086</id>
	<title>reproducible research = code to generate figures</title>
	<author>peter303</author>
	<datestamp>1265745960000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>My thesis advisor rewrote his textbooks every five years or so. But bemoaned losing the original copies of figures and being able to regenerate them in ever-improving computer/print media.  So he started the requirement of <a href="http://sepwww.stanford.edu/doku.php?id=sep:research:reproducible" title="stanford.edu"> reproducible documents </a> [stanford.edu]: the computer programs, both scientific &amp; graphic along with raw data much me assembled together for every figure in your thesis and scientific paper. These would be assembled into makefile-like system to create whatever portion one needed. Then they were archived for posterity. The ultimate test was to "burn" your figures, i.e. erase them from the upcoming document. Then the programs would be run to regenerate them. In practice there are "degrees" of regeneration. Sometimes the figure data is the output of a multi-month supercomputer run. So just the document formating programs would actually be run on the raw output data.
<br>
This system was just mentioned in Science magazine Jan 22 2010 p 415. (no free link)</htmltext>
<tokenext>My thesis advisor rewrote his textbooks every five years or so .
But bemoaned losing the original copies of figures and being able to regenerate them in ever-improving computer/print media .
So he started the requirement of reproducible documents [ stanford.edu ] : the computer programs , both scientific &amp; graphic along with raw data much me assembled together for every figure in your thesis and scientific paper .
These would be assembled into makefile-like system to create whatever portion one needed .
Then they were archived for posterity .
The ultimate test was to " burn " your figures , i.e .
erase them from the upcoming document .
Then the programs would be run to regenerate them .
In practice there are " degrees " of regeneration .
Sometimes the figure data is the output of a multi-month supercomputer run .
So just the document formating programs would actually be run on the raw output data .
This system was just mentioned in Science magazine Jan 22 2010 p 415 .
( no free link )</tokentext>
<sentencetext>My thesis advisor rewrote his textbooks every five years or so.
But bemoaned losing the original copies of figures and being able to regenerate them in ever-improving computer/print media.
So he started the requirement of  reproducible documents  [stanford.edu]: the computer programs, both scientific &amp; graphic along with raw data much me assembled together for every figure in your thesis and scientific paper.
These would be assembled into makefile-like system to create whatever portion one needed.
Then they were archived for posterity.
The ultimate test was to "burn" your figures, i.e.
erase them from the upcoming document.
Then the programs would be run to regenerate them.
In practice there are "degrees" of regeneration.
Sometimes the figure data is the output of a multi-month supercomputer run.
So just the document formating programs would actually be run on the raw output data.
This system was just mentioned in Science magazine Jan 22 2010 p 415.
(no free link)</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072450</id>
	<title>Re:That's all wrong</title>
	<author>insufflate10mg</author>
	<datestamp>1265733000000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>The scientists aren't being asked to release every piece of code in their repository, just the code they used to reach the conclusions they published.</htmltext>
<tokenext>The scientists are n't being asked to release every piece of code in their repository , just the code they used to reach the conclusions they published .</tokentext>
<sentencetext>The scientists aren't being asked to release every piece of code in their repository, just the code they used to reach the conclusions they published.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072140</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073044</id>
	<title>Re:Engineering Course Grade = F</title>
	<author>khallow</author>
	<datestamp>1265735400000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>There are interesting things that can be done with a merely single significant digit, namely, order of magnitude calculations. It's a useful to be able to determine the useful weighting of contributions to greenhouse gasses, for example. A classic case from climatology is figuring out the relative contribution to carbon dioxide emissions of human activity and volcanism (the former is much greater).</htmltext>
<tokenext>There are interesting things that can be done with a merely single significant digit , namely , order of magnitude calculations .
It 's a useful to be able to determine the useful weighting of contributions to greenhouse gasses , for example .
A classic case from climatology is figuring out the relative contribution to carbon dioxide emissions of human activity and volcanism ( the former is much greater ) .</tokentext>
<sentencetext>There are interesting things that can be done with a merely single significant digit, namely, order of magnitude calculations.
It's a useful to be able to determine the useful weighting of contributions to greenhouse gasses, for example.
A classic case from climatology is figuring out the relative contribution to carbon dioxide emissions of human activity and volcanism (the former is much greater).</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071980</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072290</id>
	<title>Code isn't good enough.</title>
	<author>FlyingBishop</author>
	<datestamp>1265732340000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>2</modscore>
	<htmltext><p>Back in college, I did some computer vision research. Most people provided open source code for anyone to use. However, aside from the code being of questionable quality, it was mostly written in Matlab with C handlers for optimization.</p><p>In order to properly test all of the software out there you would need:</p><p>1. A license for every version of Matlab.<br>2. Windows<br>3. Linux<br>4. Octave</p><p>I had our school's Matlab,  but none of the code we found was written on that version. Some was Linux, some Windows, (the machine I had was a Windows box with Matlab) consequently we had to play with Cygwin...</p><p>I mean, basically, you need to distribute a straight-up VM if you want your results to be reproducible. (which naturally rules out Windows or Matlab or anything else proprietary being at the core.)</p></htmltext>
<tokenext>Back in college , I did some computer vision research .
Most people provided open source code for anyone to use .
However , aside from the code being of questionable quality , it was mostly written in Matlab with C handlers for optimization.In order to properly test all of the software out there you would need : 1 .
A license for every version of Matlab.2 .
Windows3. Linux4 .
OctaveI had our school 's Matlab , but none of the code we found was written on that version .
Some was Linux , some Windows , ( the machine I had was a Windows box with Matlab ) consequently we had to play with Cygwin...I mean , basically , you need to distribute a straight-up VM if you want your results to be reproducible .
( which naturally rules out Windows or Matlab or anything else proprietary being at the core .
)</tokentext>
<sentencetext>Back in college, I did some computer vision research.
Most people provided open source code for anyone to use.
However, aside from the code being of questionable quality, it was mostly written in Matlab with C handlers for optimization.In order to properly test all of the software out there you would need:1.
A license for every version of Matlab.2.
Windows3. Linux4.
OctaveI had our school's Matlab,  but none of the code we found was written on that version.
Some was Linux, some Windows, (the machine I had was a Windows box with Matlab) consequently we had to play with Cygwin...I mean, basically, you need to distribute a straight-up VM if you want your results to be reproducible.
(which naturally rules out Windows or Matlab or anything else proprietary being at the core.
)</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072392</id>
	<title>Re:Why release it?</title>
	<author>Foolicious</author>
	<datestamp>1265732760000</datestamp>
	<modclass>Offtopic</modclass>
	<modscore>0</modscore>
	<htmltext>Since you brought up the socially inept idea, I might also suggest taking a look at <a href="http://en.wikipedia.org/wiki/Soci\%C3\%A9t\%C3\%A9\_Bic" title="wikipedia.org">Bic's razor</a> [wikipedia.org] or <a href="http://en.wikipedia.org/wiki/Gillette\_(brand)" title="wikipedia.org">Gillette's razor</a> [wikipedia.org].</htmltext>
<tokenext>Since you brought up the socially inept idea , I might also suggest taking a look at Bic 's razor [ wikipedia.org ] or Gillette 's razor [ wikipedia.org ] .</tokentext>
<sentencetext>Since you brought up the socially inept idea, I might also suggest taking a look at Bic's razor [wikipedia.org] or Gillette's razor [wikipedia.org].</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071954</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074630</id>
	<title>Re: tools</title>
	<author>jrvz</author>
	<datestamp>1265741160000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>I recommend the "reproducible research" methodology described at <a href="http://reproducibleresearch.net/index.php/Main\_Page" title="reproducibleresearch.net" rel="nofollow">http://reproducibleresearch.net/index.php/Main\_Page</a> [reproducibleresearch.net] .  The idea is that for each paper you publish, you make available an archive with the software, data, scripts, etc., so the user need only type "make" to reproduce every figure in the paper.</htmltext>
<tokenext>I recommend the " reproducible research " methodology described at http : //reproducibleresearch.net/index.php/Main \ _Page [ reproducibleresearch.net ] .
The idea is that for each paper you publish , you make available an archive with the software , data , scripts , etc. , so the user need only type " make " to reproduce every figure in the paper .</tokentext>
<sentencetext>I recommend the "reproducible research" methodology described at http://reproducibleresearch.net/index.php/Main\_Page [reproducibleresearch.net] .
The idea is that for each paper you publish, you make available an archive with the software, data, scripts, etc., so the user need only type "make" to reproduce every figure in the paper.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071944</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073436</id>
	<title>Re:Slashdot Egocentrism.</title>
	<author>Daniel Dvorkin</author>
	<datestamp>1265736780000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><i>scientists outside of computer science are too busy in their respective fields to know anything about code, or even care</i></p><p>This is true, but it's not an excuse.  If your interpretation of the data, or even the data itself, depends on your code, then if you say "I don't care about the code" then you're really saying "I don't care about the science."  Scientists tend to be very picky about the quality of their lab equipment, as well they should be, but all too often are willing to let sloppy, untested code make that quality pretty much meaningless.</p><p>As a bioinformaticist who used to work in industry as a programmer and DBA, I've spent an enormous amount of time going through other people's code just to get it to the point where it even starts to make sense, so I can be sure it does what it's claimed to do.  And very often, it doesn't, which means I have to spend more time fixing it.  I'm always happy to do this, and my collaborators are usually happy for my fixes<nobr> <wbr></nobr>... but it really has to mean that there are an awful lot of published papers out there which depend on code that's never been through this kind of review.</p><p>Scientists who want to teach themselves good software engineering should do so.  They're certainly capable of it; if you can get a PhD in any scientific subject, you can damn well learn to program at the level of a competent industry developer.  Those who don't (and I don't blame them, since they are, after all busy doing other things) need to hire assistants who have, or are willing to gain, the necessary level of knowledge.  It makes absolutely no sense to buy a half-million dollars worth of lab equipment and then run the output through code written for the equivalent of a hundred dollars worth of work.</p></htmltext>
<tokenext>scientists outside of computer science are too busy in their respective fields to know anything about code , or even careThis is true , but it 's not an excuse .
If your interpretation of the data , or even the data itself , depends on your code , then if you say " I do n't care about the code " then you 're really saying " I do n't care about the science .
" Scientists tend to be very picky about the quality of their lab equipment , as well they should be , but all too often are willing to let sloppy , untested code make that quality pretty much meaningless.As a bioinformaticist who used to work in industry as a programmer and DBA , I 've spent an enormous amount of time going through other people 's code just to get it to the point where it even starts to make sense , so I can be sure it does what it 's claimed to do .
And very often , it does n't , which means I have to spend more time fixing it .
I 'm always happy to do this , and my collaborators are usually happy for my fixes ... but it really has to mean that there are an awful lot of published papers out there which depend on code that 's never been through this kind of review.Scientists who want to teach themselves good software engineering should do so .
They 're certainly capable of it ; if you can get a PhD in any scientific subject , you can damn well learn to program at the level of a competent industry developer .
Those who do n't ( and I do n't blame them , since they are , after all busy doing other things ) need to hire assistants who have , or are willing to gain , the necessary level of knowledge .
It makes absolutely no sense to buy a half-million dollars worth of lab equipment and then run the output through code written for the equivalent of a hundred dollars worth of work .</tokentext>
<sentencetext>scientists outside of computer science are too busy in their respective fields to know anything about code, or even careThis is true, but it's not an excuse.
If your interpretation of the data, or even the data itself, depends on your code, then if you say "I don't care about the code" then you're really saying "I don't care about the science.
"  Scientists tend to be very picky about the quality of their lab equipment, as well they should be, but all too often are willing to let sloppy, untested code make that quality pretty much meaningless.As a bioinformaticist who used to work in industry as a programmer and DBA, I've spent an enormous amount of time going through other people's code just to get it to the point where it even starts to make sense, so I can be sure it does what it's claimed to do.
And very often, it doesn't, which means I have to spend more time fixing it.
I'm always happy to do this, and my collaborators are usually happy for my fixes ... but it really has to mean that there are an awful lot of published papers out there which depend on code that's never been through this kind of review.Scientists who want to teach themselves good software engineering should do so.
They're certainly capable of it; if you can get a PhD in any scientific subject, you can damn well learn to program at the level of a competent industry developer.
Those who don't (and I don't blame them, since they are, after all busy doing other things) need to hire assistants who have, or are willing to gain, the necessary level of knowledge.
It makes absolutely no sense to buy a half-million dollars worth of lab equipment and then run the output through code written for the equivalent of a hundred dollars worth of work.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072056</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31076228</id>
	<title>Re:Slashdot Egocentrism.</title>
	<author>stewbacca</author>
	<datestamp>1265746440000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Like I said, I know plenty of scientists that can't even run a spreadsheet formula like,  =SUM(cell:range), let alone write lines of code.</p><p>My car analogy is a race car driver doesn't need to know how to build a race car, only how to drive one.  I imagine scientists are the same way. They use technology to crunch numbers, but don't know how the numbers are crunched (nor should they, as long as it is a peer-reviewed/industry accepted method).</p></htmltext>
<tokenext>Like I said , I know plenty of scientists that ca n't even run a spreadsheet formula like , = SUM ( cell : range ) , let alone write lines of code.My car analogy is a race car driver does n't need to know how to build a race car , only how to drive one .
I imagine scientists are the same way .
They use technology to crunch numbers , but do n't know how the numbers are crunched ( nor should they , as long as it is a peer-reviewed/industry accepted method ) .</tokentext>
<sentencetext>Like I said, I know plenty of scientists that can't even run a spreadsheet formula like,  =SUM(cell:range), let alone write lines of code.My car analogy is a race car driver doesn't need to know how to build a race car, only how to drive one.
I imagine scientists are the same way.
They use technology to crunch numbers, but don't know how the numbers are crunched (nor should they, as long as it is a peer-reviewed/industry accepted method).</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072396</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071946</id>
	<title>It should be released and under a free licence!</title>
	<author>bramp</author>
	<datestamp>1265730600000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>3</modscore>
	<htmltext>I've always been a big fan of releasing my academic work under a BSD licence. My work is funded by the taxpayers, so I think the taxpayers should be able to do what they like with my software.

So I fully agree that all software should be released. It is not always enough to just publish a paper, but you should release your code so others can fully review the accuracy of your work.</htmltext>
<tokenext>I 've always been a big fan of releasing my academic work under a BSD licence .
My work is funded by the taxpayers , so I think the taxpayers should be able to do what they like with my software .
So I fully agree that all software should be released .
It is not always enough to just publish a paper , but you should release your code so others can fully review the accuracy of your work .</tokentext>
<sentencetext>I've always been a big fan of releasing my academic work under a BSD licence.
My work is funded by the taxpayers, so I think the taxpayers should be able to do what they like with my software.
So I fully agree that all software should be released.
It is not always enough to just publish a paper, but you should release your code so others can fully review the accuracy of your work.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072570</id>
	<title>Nothing to do with CS</title>
	<author>nten</author>
	<datestamp>1265733540000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext><p>I am suspect of the interface reference.  Are they counting things where an enumeration got used as an int, or there was an implicit cast from a 32bit float to a 64bit one?  From a recent TV show "A difference that makes no difference is no difference."  Stepping back a bit there will be howls from OO/Functional/FSM zealots that look at a program and declare its inferior architecture, lack of maintainability etc. indicate its results are wrong.  These are programs written to be run once to turn one set of data into a more understandable and concise one.  A truth test set run through it is good enough, they don't need iso compliant, triply refactored, perfectly architectured code to get the right answer.  I don't think any of my CS proffs would have cared about such inane drivel they barely paid attention to what language we each picked to solve the assignment in.  My software engineering proff would have yelled about comment density and coding standards compliance, but I consider that a different discipline primarily applicable to widely used and/or safety critical code.</p><p>*However*<br>Keeping track of digit precision through a calculation isn't CS, its fundamental grade school science.  That is only one step from forgetting to do unit analysis for a sanity check.  If they are forgetting that, they are probably also not looking at numerical conditioning, or trying to get by with doubles when they need bignums.  None of this is CS egocentrism, its stuff we learn in math and science courses.</p></htmltext>
<tokenext>I am suspect of the interface reference .
Are they counting things where an enumeration got used as an int , or there was an implicit cast from a 32bit float to a 64bit one ?
From a recent TV show " A difference that makes no difference is no difference .
" Stepping back a bit there will be howls from OO/Functional/FSM zealots that look at a program and declare its inferior architecture , lack of maintainability etc .
indicate its results are wrong .
These are programs written to be run once to turn one set of data into a more understandable and concise one .
A truth test set run through it is good enough , they do n't need iso compliant , triply refactored , perfectly architectured code to get the right answer .
I do n't think any of my CS proffs would have cared about such inane drivel they barely paid attention to what language we each picked to solve the assignment in .
My software engineering proff would have yelled about comment density and coding standards compliance , but I consider that a different discipline primarily applicable to widely used and/or safety critical code .
* However * Keeping track of digit precision through a calculation is n't CS , its fundamental grade school science .
That is only one step from forgetting to do unit analysis for a sanity check .
If they are forgetting that , they are probably also not looking at numerical conditioning , or trying to get by with doubles when they need bignums .
None of this is CS egocentrism , its stuff we learn in math and science courses .</tokentext>
<sentencetext>I am suspect of the interface reference.
Are they counting things where an enumeration got used as an int, or there was an implicit cast from a 32bit float to a 64bit one?
From a recent TV show "A difference that makes no difference is no difference.
"  Stepping back a bit there will be howls from OO/Functional/FSM zealots that look at a program and declare its inferior architecture, lack of maintainability etc.
indicate its results are wrong.
These are programs written to be run once to turn one set of data into a more understandable and concise one.
A truth test set run through it is good enough, they don't need iso compliant, triply refactored, perfectly architectured code to get the right answer.
I don't think any of my CS proffs would have cared about such inane drivel they barely paid attention to what language we each picked to solve the assignment in.
My software engineering proff would have yelled about comment density and coding standards compliance, but I consider that a different discipline primarily applicable to widely used and/or safety critical code.
*However*Keeping track of digit precision through a calculation isn't CS, its fundamental grade school science.
That is only one step from forgetting to do unit analysis for a sanity check.
If they are forgetting that, they are probably also not looking at numerical conditioning, or trying to get by with doubles when they need bignums.
None of this is CS egocentrism, its stuff we learn in math and science courses.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072056</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072500</id>
	<title>Well known problem...</title>
	<author>Wdi</author>
	<datestamp>1265733180000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>The code quality of many well-known scientific software packages is abysmal.</p><p>In chemistry, you should at least expect that the outcome of descriptor computations on a set of molecules is independent of the order of atoms and bonds in a molecule, and the order of file records.</p><p>Well, this is disturbingly often not the case, as we discovered in a recent study.</p><p>In an attempt to raise awareness of this problem, we have launched a public Web-accessible computational result verification service (http://www.xemistry.com/cv). A poster explaining this app and some background, including sample test results, can be found at http://www.xemistry.com/Presentations/verifier\_panel\_2009.pdf.</p><p>Unfortunately, the worst application we have encountered so far appears to be a standard tool for adding Wikipedia data for chemicals, systematically poisoning it with incorrect data.</p></htmltext>
<tokenext>The code quality of many well-known scientific software packages is abysmal.In chemistry , you should at least expect that the outcome of descriptor computations on a set of molecules is independent of the order of atoms and bonds in a molecule , and the order of file records.Well , this is disturbingly often not the case , as we discovered in a recent study.In an attempt to raise awareness of this problem , we have launched a public Web-accessible computational result verification service ( http : //www.xemistry.com/cv ) .
A poster explaining this app and some background , including sample test results , can be found at http : //www.xemistry.com/Presentations/verifier \ _panel \ _2009.pdf.Unfortunately , the worst application we have encountered so far appears to be a standard tool for adding Wikipedia data for chemicals , systematically poisoning it with incorrect data .</tokentext>
<sentencetext>The code quality of many well-known scientific software packages is abysmal.In chemistry, you should at least expect that the outcome of descriptor computations on a set of molecules is independent of the order of atoms and bonds in a molecule, and the order of file records.Well, this is disturbingly often not the case, as we discovered in a recent study.In an attempt to raise awareness of this problem, we have launched a public Web-accessible computational result verification service (http://www.xemistry.com/cv).
A poster explaining this app and some background, including sample test results, can be found at http://www.xemistry.com/Presentations/verifier\_panel\_2009.pdf.Unfortunately, the worst application we have encountered so far appears to be a standard tool for adding Wikipedia data for chemicals, systematically poisoning it with incorrect data.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073330</id>
	<title>Re:This is not science.</title>
	<author>acoustix</author>
	<datestamp>1265736420000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>5</modscore>
	<htmltext><p><i>"Why should I make the data available to you, when your aim is to find something wrong with it?"</i></p><p>That used to be what Science was. Of course, that was when truth was the goal.</p></htmltext>
<tokenext>" Why should I make the data available to you , when your aim is to find something wrong with it ?
" That used to be what Science was .
Of course , that was when truth was the goal .</tokentext>
<sentencetext>"Why should I make the data available to you, when your aim is to find something wrong with it?
"That used to be what Science was.
Of course, that was when truth was the goal.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072052</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072174</id>
	<title>Not possible.</title>
	<author>MindlessAutomata</author>
	<datestamp>1265731740000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Many scientists get their code from companies or individuals that license it to them, much like most other software.  They're not in the position to release the code for many experiments...!</p></htmltext>
<tokenext>Many scientists get their code from companies or individuals that license it to them , much like most other software .
They 're not in the position to release the code for many experiments... !</tokentext>
<sentencetext>Many scientists get their code from companies or individuals that license it to them, much like most other software.
They're not in the position to release the code for many experiments...!</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072694</id>
	<title>Not that simple</title>
	<author>Anonymous</author>
	<datestamp>1265734020000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>3</modscore>
	<htmltext><p>I'm finishing a program that inverts GRACE data to reveal fluctuations in gravity such as those caused by melting glaciers. This program will eventually be released as open source software under the GPLv3. It's largely built on open source libraries like the GNU Scientific Library, but snippets of proprietary code from JPL found their way into the program years ago, and I'm currently trying to untangle them. The program can't be made open source until I succeed because of an NDA that I had to sign in order to work at JPL.</p><p>It's impossible to say how long it will take to banish the proprietary code. While working on this project, my research is at a standstill. There's <em>very</em> little academic incentive to waste time on this idealistic goal when I could be increasing my publication count.</p><p>Annoyingly, the data itself doesn't belong to me. Again, I had to sign an NDA to receive it. So I <em>can't</em> release the data. This situation is common to scientists in many different fields.</p><p>Incidentally, Harry's README file is typical of my experiences with scientific software. Fragile, unportable, uncommented spaghetti code is common because scientists aren't professional programmers. Of course, this doesn't invalidate the results of that code because it's tested primarily through independent verification, not unit tests. Scientists describe their algorithms in peer-reviewed papers, which are then re-implemented (often from scratch) by other scientists. Open source code practices would certainly improve science, but he's wrong to imply that a single bug could have a significant impact on our understanding of the greenhouse effect.</p></htmltext>
<tokenext>I 'm finishing a program that inverts GRACE data to reveal fluctuations in gravity such as those caused by melting glaciers .
This program will eventually be released as open source software under the GPLv3 .
It 's largely built on open source libraries like the GNU Scientific Library , but snippets of proprietary code from JPL found their way into the program years ago , and I 'm currently trying to untangle them .
The program ca n't be made open source until I succeed because of an NDA that I had to sign in order to work at JPL.It 's impossible to say how long it will take to banish the proprietary code .
While working on this project , my research is at a standstill .
There 's very little academic incentive to waste time on this idealistic goal when I could be increasing my publication count.Annoyingly , the data itself does n't belong to me .
Again , I had to sign an NDA to receive it .
So I ca n't release the data .
This situation is common to scientists in many different fields.Incidentally , Harry 's README file is typical of my experiences with scientific software .
Fragile , unportable , uncommented spaghetti code is common because scientists are n't professional programmers .
Of course , this does n't invalidate the results of that code because it 's tested primarily through independent verification , not unit tests .
Scientists describe their algorithms in peer-reviewed papers , which are then re-implemented ( often from scratch ) by other scientists .
Open source code practices would certainly improve science , but he 's wrong to imply that a single bug could have a significant impact on our understanding of the greenhouse effect .</tokentext>
<sentencetext>I'm finishing a program that inverts GRACE data to reveal fluctuations in gravity such as those caused by melting glaciers.
This program will eventually be released as open source software under the GPLv3.
It's largely built on open source libraries like the GNU Scientific Library, but snippets of proprietary code from JPL found their way into the program years ago, and I'm currently trying to untangle them.
The program can't be made open source until I succeed because of an NDA that I had to sign in order to work at JPL.It's impossible to say how long it will take to banish the proprietary code.
While working on this project, my research is at a standstill.
There's very little academic incentive to waste time on this idealistic goal when I could be increasing my publication count.Annoyingly, the data itself doesn't belong to me.
Again, I had to sign an NDA to receive it.
So I can't release the data.
This situation is common to scientists in many different fields.Incidentally, Harry's README file is typical of my experiences with scientific software.
Fragile, unportable, uncommented spaghetti code is common because scientists aren't professional programmers.
Of course, this doesn't invalidate the results of that code because it's tested primarily through independent verification, not unit tests.
Scientists describe their algorithms in peer-reviewed papers, which are then re-implemented (often from scratch) by other scientists.
Open source code practices would certainly improve science, but he's wrong to imply that a single bug could have a significant impact on our understanding of the greenhouse effect.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073006</id>
	<title>They should write their code in Type Theory...</title>
	<author>Anonymous</author>
	<datestamp>1265735220000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>...so they can also release the proofs.</p></htmltext>
<tokenext>...so they can also release the proofs .</tokentext>
<sentencetext>...so they can also release the proofs.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074502</id>
	<title>Qualification is what matters!</title>
	<author>laxsu19</author>
	<datestamp>1265740680000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>So what if there are bugs, isn't what matters that the answer is correct?  This is done, at least in my organization, as follows:

1) with a test problem.  you can run a calculation that is easily solved analyitically and then compare results.  You can also challenge yourself a little more by running a problem with ready experimental results for, and then again, comparing results.  Only after this first step is done (many, many, many times)does confidence in the code build up and it can begin to be used in new areas.  This is called qualification, verification, or validation.

2) When attacking problems not previously solved (which, after all, is the reason for writing the code), the scientist/engineer/end-user must have an expectation of what the results will be like.  They may not know values, but they should expect what has changed since the last model they ran (i.e., "if I increase temperature by 10 degrees in my model, then this should happen...").

3) While this may not be possible in all fields, either an experiment, or manufactured product should be tested to ensure that you got out what you predicted with your code.  Engineering organizations can do this.  Climatologists probably can't, I'd imagine.


While I don't care about the debate of opening up the source code, I take issue with the fact that a comp sci guy looked at some scientist/engineer's code and said 'omg bugs!'  Sure, it may not be how the comp sci expert would program, but it doesn't matter in the end (provided qualification is done adequately).

Personally, I don't want to open up my code beyond who is necessary to see it - the code is not the end, its just a means.  Its like a Doctor allowing everyone to see his personal diary on patients - its only work to support the diagnosis, and not the diagnosis itself.</htmltext>
<tokenext>So what if there are bugs , is n't what matters that the answer is correct ?
This is done , at least in my organization , as follows : 1 ) with a test problem .
you can run a calculation that is easily solved analyitically and then compare results .
You can also challenge yourself a little more by running a problem with ready experimental results for , and then again , comparing results .
Only after this first step is done ( many , many , many times ) does confidence in the code build up and it can begin to be used in new areas .
This is called qualification , verification , or validation .
2 ) When attacking problems not previously solved ( which , after all , is the reason for writing the code ) , the scientist/engineer/end-user must have an expectation of what the results will be like .
They may not know values , but they should expect what has changed since the last model they ran ( i.e. , " if I increase temperature by 10 degrees in my model , then this should happen... " ) .
3 ) While this may not be possible in all fields , either an experiment , or manufactured product should be tested to ensure that you got out what you predicted with your code .
Engineering organizations can do this .
Climatologists probably ca n't , I 'd imagine .
While I do n't care about the debate of opening up the source code , I take issue with the fact that a comp sci guy looked at some scientist/engineer 's code and said 'omg bugs !
' Sure , it may not be how the comp sci expert would program , but it does n't matter in the end ( provided qualification is done adequately ) .
Personally , I do n't want to open up my code beyond who is necessary to see it - the code is not the end , its just a means .
Its like a Doctor allowing everyone to see his personal diary on patients - its only work to support the diagnosis , and not the diagnosis itself .</tokentext>
<sentencetext>So what if there are bugs, isn't what matters that the answer is correct?
This is done, at least in my organization, as follows:

1) with a test problem.
you can run a calculation that is easily solved analyitically and then compare results.
You can also challenge yourself a little more by running a problem with ready experimental results for, and then again, comparing results.
Only after this first step is done (many, many, many times)does confidence in the code build up and it can begin to be used in new areas.
This is called qualification, verification, or validation.
2) When attacking problems not previously solved (which, after all, is the reason for writing the code), the scientist/engineer/end-user must have an expectation of what the results will be like.
They may not know values, but they should expect what has changed since the last model they ran (i.e., "if I increase temperature by 10 degrees in my model, then this should happen...").
3) While this may not be possible in all fields, either an experiment, or manufactured product should be tested to ensure that you got out what you predicted with your code.
Engineering organizations can do this.
Climatologists probably can't, I'd imagine.
While I don't care about the debate of opening up the source code, I take issue with the fact that a comp sci guy looked at some scientist/engineer's code and said 'omg bugs!
'  Sure, it may not be how the comp sci expert would program, but it doesn't matter in the end (provided qualification is done adequately).
Personally, I don't want to open up my code beyond who is necessary to see it - the code is not the end, its just a means.
Its like a Doctor allowing everyone to see his personal diary on patients - its only work to support the diagnosis, and not the diagnosis itself.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31094512</id>
	<title>Simply look for the value of Pi</title>
	<author>niftymitch</author>
	<datestamp>1265036880000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>Having looked at some of these "research" codes I was astounded to see "PI=3.14" in one.   I got access to this bit code because a parallel version would differ in the 19th digit of an IEEE float as the number of processors changed and I was supposed to fix the machine.</htmltext>
<tokenext>Having looked at some of these " research " codes I was astounded to see " PI = 3.14 " in one .
I got access to this bit code because a parallel version would differ in the 19th digit of an IEEE float as the number of processors changed and I was supposed to fix the machine .</tokentext>
<sentencetext>Having looked at some of these "research" codes I was astounded to see "PI=3.14" in one.
I got access to this bit code because a parallel version would differ in the 19th digit of an IEEE float as the number of processors changed and I was supposed to fix the machine.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31077166</id>
	<title>Re:Why release it?</title>
	<author>WhiplashII</author>
	<datestamp>1265706900000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Please read up on the history of behind <a href="http://en.wikipedia.org/wiki/Oil-drop\_experiment" title="wikipedia.org">measuring the charge of an electron</a> [wikipedia.org].  You are wrong in essence, the conspiracy theorists are wrong about motivation.</p><p>But either way, you cannot trust scientists data as truth.  Especially early science, when the experiment has not been copied by millions.</p><p>Scientists are human, just like anyone else.  To misquote, "the scientific method is the least terrible method of finding truth that we have yet discovered."</p></htmltext>
<tokenext>Please read up on the history of behind measuring the charge of an electron [ wikipedia.org ] .
You are wrong in essence , the conspiracy theorists are wrong about motivation.But either way , you can not trust scientists data as truth .
Especially early science , when the experiment has not been copied by millions.Scientists are human , just like anyone else .
To misquote , " the scientific method is the least terrible method of finding truth that we have yet discovered .
"</tokentext>
<sentencetext>Please read up on the history of behind measuring the charge of an electron [wikipedia.org].
You are wrong in essence, the conspiracy theorists are wrong about motivation.But either way, you cannot trust scientists data as truth.
Especially early science, when the experiment has not been copied by millions.Scientists are human, just like anyone else.
To misquote, "the scientific method is the least terrible method of finding truth that we have yet discovered.
"</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071954</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073594</id>
	<title>Wolfram Alpha, IDL, MATLAB, etc.?</title>
	<author>Anonymous</author>
	<datestamp>1265737260000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>This brings up an interesting point: what about all the different closed source packages which are used in the hard sciences? On a regular basis I am required to use code written using closed source framework al la IDL or MATLAB. These frameworks are invaluable in the sense that we do not have to write the interface between the detectors and a standard PC, but they are often essentially black boxes. Do people really want to require scientists to write (inevitably bad code) to interface their scope to a PC just so they can release that code to the public?
<br> <br>
Finally, I waste enough time fixing bugs in code that will likely never be used by anyone else that I would loath to have to clean it all up for others to use and understand. Scientists are writing tools to get things done, if they had the resources most would love to hire a programmer to write and document the program from a requirements document but very few if any do have such resources. There should be a balance between the publics desire to look over the shoulder of scientists are scientists desire to do science and not waste their time getting 60k emails regarding a bug which has no effect on their result.</htmltext>
<tokenext>This brings up an interesting point : what about all the different closed source packages which are used in the hard sciences ?
On a regular basis I am required to use code written using closed source framework al la IDL or MATLAB .
These frameworks are invaluable in the sense that we do not have to write the interface between the detectors and a standard PC , but they are often essentially black boxes .
Do people really want to require scientists to write ( inevitably bad code ) to interface their scope to a PC just so they can release that code to the public ?
Finally , I waste enough time fixing bugs in code that will likely never be used by anyone else that I would loath to have to clean it all up for others to use and understand .
Scientists are writing tools to get things done , if they had the resources most would love to hire a programmer to write and document the program from a requirements document but very few if any do have such resources .
There should be a balance between the publics desire to look over the shoulder of scientists are scientists desire to do science and not waste their time getting 60k emails regarding a bug which has no effect on their result .</tokentext>
<sentencetext>This brings up an interesting point: what about all the different closed source packages which are used in the hard sciences?
On a regular basis I am required to use code written using closed source framework al la IDL or MATLAB.
These frameworks are invaluable in the sense that we do not have to write the interface between the detectors and a standard PC, but they are often essentially black boxes.
Do people really want to require scientists to write (inevitably bad code) to interface their scope to a PC just so they can release that code to the public?
Finally, I waste enough time fixing bugs in code that will likely never be used by anyone else that I would loath to have to clean it all up for others to use and understand.
Scientists are writing tools to get things done, if they had the resources most would love to hire a programmer to write and document the program from a requirements document but very few if any do have such resources.
There should be a balance between the publics desire to look over the shoulder of scientists are scientists desire to do science and not waste their time getting 60k emails regarding a bug which has no effect on their result.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073350</id>
	<title>Re:Not a good idea</title>
	<author>Anonymous</author>
	<datestamp>1265736540000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>I think you are missing the point of putting the code out there. The point is not, as you suggest, so that others can run your software and see the same results. This is more akin to writing up your experimental methodology so the reader can judge if the experiment was performed correctly, and can make their own assessments if the methodology introduced any potential experimental errors or confounds. In the case of software, it would involve assessing the quality of the code and looking for places where the software itself may have introduced errors, not running the code and seeing if the same results come out (though if it doesn't that is even more damning).</p><p>Of course, the secondary reason to share the source code is that it is frequently part of the product of the research, and could be used by others to take the research further, etc... However, that is not the main thrust of this article.</p></htmltext>
<tokenext>I think you are missing the point of putting the code out there .
The point is not , as you suggest , so that others can run your software and see the same results .
This is more akin to writing up your experimental methodology so the reader can judge if the experiment was performed correctly , and can make their own assessments if the methodology introduced any potential experimental errors or confounds .
In the case of software , it would involve assessing the quality of the code and looking for places where the software itself may have introduced errors , not running the code and seeing if the same results come out ( though if it does n't that is even more damning ) .Of course , the secondary reason to share the source code is that it is frequently part of the product of the research , and could be used by others to take the research further , etc... However , that is not the main thrust of this article .</tokentext>
<sentencetext>I think you are missing the point of putting the code out there.
The point is not, as you suggest, so that others can run your software and see the same results.
This is more akin to writing up your experimental methodology so the reader can judge if the experiment was performed correctly, and can make their own assessments if the methodology introduced any potential experimental errors or confounds.
In the case of software, it would involve assessing the quality of the code and looking for places where the software itself may have introduced errors, not running the code and seeing if the same results come out (though if it doesn't that is even more damning).Of course, the secondary reason to share the source code is that it is frequently part of the product of the research, and could be used by others to take the research further, etc... However, that is not the main thrust of this article.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072364</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073638</id>
	<title>Re:one error will invalidate a computer program?!?</title>
	<author>mjwalshe</author>
	<datestamp>1265737320000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>yes but its the Guardian and their grasp of technology is a little weak at the best of times.</htmltext>
<tokenext>yes but its the Guardian and their grasp of technology is a little weak at the best of times .</tokentext>
<sentencetext>yes but its the Guardian and their grasp of technology is a little weak at the best of times.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072196</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072816</id>
	<title>Maybe it's my Berkeley roots: we release source</title>
	<author>PeterM from Berkeley</author>
	<datestamp>1265734500000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>All the software I and my team write is version controlled (CVS and SVN) and releasable (some of it with export restriction.)  I do admit that our software engineering is not the best, but we also have a rule that code cannot be committed before an extensive suite of tests is run on the code (for our main scientific application--'helper' tools are not so tightly controlled.)</p><p>Our scientific colleagues, provided they can satisfy the export control restrictions, can get source code and poke around all they want.  Some have even contributed back valuable changes, and most have contributed back valuable feedback.</p><p>In fact, we look down upon colleagues who do not release source code.  Are you really doing serious science if others cannot delve into your methods?</p><p>--PeterM</p></htmltext>
<tokenext>All the software I and my team write is version controlled ( CVS and SVN ) and releasable ( some of it with export restriction .
) I do admit that our software engineering is not the best , but we also have a rule that code can not be committed before an extensive suite of tests is run on the code ( for our main scientific application--'helper ' tools are not so tightly controlled .
) Our scientific colleagues , provided they can satisfy the export control restrictions , can get source code and poke around all they want .
Some have even contributed back valuable changes , and most have contributed back valuable feedback.In fact , we look down upon colleagues who do not release source code .
Are you really doing serious science if others can not delve into your methods ? --PeterM</tokentext>
<sentencetext>All the software I and my team write is version controlled (CVS and SVN) and releasable (some of it with export restriction.
)  I do admit that our software engineering is not the best, but we also have a rule that code cannot be committed before an extensive suite of tests is run on the code (for our main scientific application--'helper' tools are not so tightly controlled.
)Our scientific colleagues, provided they can satisfy the export control restrictions, can get source code and poke around all they want.
Some have even contributed back valuable changes, and most have contributed back valuable feedback.In fact, we look down upon colleagues who do not release source code.
Are you really doing serious science if others cannot delve into your methods?--PeterM</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074062</id>
	<title>outrageous</title>
	<author>Anonymous</author>
	<datestamp>1265738820000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Not all code needs to be released; sometimes, the code isn't needed for reproducing a result or the formulas in the paper are sufficient.</p><p>However, climate modeling is such a complex process, and its implications so serious, that it is outrageous if climate modeling code isn't fully and completely available.  Climate modeling code needs to be extensively peer reviewed and until people can reproduce the results and show that the models behave reasonably under different conditions, the results cannot be trusted.</p></htmltext>
<tokenext>Not all code needs to be released ; sometimes , the code is n't needed for reproducing a result or the formulas in the paper are sufficient.However , climate modeling is such a complex process , and its implications so serious , that it is outrageous if climate modeling code is n't fully and completely available .
Climate modeling code needs to be extensively peer reviewed and until people can reproduce the results and show that the models behave reasonably under different conditions , the results can not be trusted .</tokentext>
<sentencetext>Not all code needs to be released; sometimes, the code isn't needed for reproducing a result or the formulas in the paper are sufficient.However, climate modeling is such a complex process, and its implications so serious, that it is outrageous if climate modeling code isn't fully and completely available.
Climate modeling code needs to be extensively peer reviewed and until people can reproduce the results and show that the models behave reasonably under different conditions, the results cannot be trusted.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31075852</id>
	<title>Re:Not a good idea</title>
	<author>dj\_tla</author>
	<datestamp>1265745240000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>By your logic, no one should have access to a programming language because <i>what if that language is wrong</i>. A ton of scientific research is done in Matlab, yet you don't hear anyone complaining that code produced in Matlab may not be correct because you aren't looking at each individual bit of information as it is processed.</p><p>The idea of providing your code, in fact, solves the exact problem that you're describing. The point of research is not to reproduce results -- certainly, that's a first step in many lines of research, but it by itself is not a result. However, if you find that the code used to produce some results is incorrect, then you do have a result, and this furthers that field of research immensely, because no longer are a string of papers going to build on an incorrect result. Everyone can be confident in a result and move on from that point.</p><p>Your line of reasoning may make sense when you talk about "equipment" in terms of sensors and proprietary hardware, but when we're talking about software that runs the same on whatever hardware you're using, being able to reproduce a result is only a first step. Shortening that step and allowing everyone to scrutinize how you did it only catalyzes further research.</p></htmltext>
<tokenext>By your logic , no one should have access to a programming language because what if that language is wrong .
A ton of scientific research is done in Matlab , yet you do n't hear anyone complaining that code produced in Matlab may not be correct because you are n't looking at each individual bit of information as it is processed.The idea of providing your code , in fact , solves the exact problem that you 're describing .
The point of research is not to reproduce results -- certainly , that 's a first step in many lines of research , but it by itself is not a result .
However , if you find that the code used to produce some results is incorrect , then you do have a result , and this furthers that field of research immensely , because no longer are a string of papers going to build on an incorrect result .
Everyone can be confident in a result and move on from that point.Your line of reasoning may make sense when you talk about " equipment " in terms of sensors and proprietary hardware , but when we 're talking about software that runs the same on whatever hardware you 're using , being able to reproduce a result is only a first step .
Shortening that step and allowing everyone to scrutinize how you did it only catalyzes further research .</tokentext>
<sentencetext>By your logic, no one should have access to a programming language because what if that language is wrong.
A ton of scientific research is done in Matlab, yet you don't hear anyone complaining that code produced in Matlab may not be correct because you aren't looking at each individual bit of information as it is processed.The idea of providing your code, in fact, solves the exact problem that you're describing.
The point of research is not to reproduce results -- certainly, that's a first step in many lines of research, but it by itself is not a result.
However, if you find that the code used to produce some results is incorrect, then you do have a result, and this furthers that field of research immensely, because no longer are a string of papers going to build on an incorrect result.
Everyone can be confident in a result and move on from that point.Your line of reasoning may make sense when you talk about "equipment" in terms of sensors and proprietary hardware, but when we're talking about software that runs the same on whatever hardware you're using, being able to reproduce a result is only a first step.
Shortening that step and allowing everyone to scrutinize how you did it only catalyzes further research.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072364</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31078286</id>
	<title>Yeah right</title>
	<author>SoftwareArtist</author>
	<datestamp>1265711460000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><div class="quote"><p>This is hugely worrying when you realise that just one error -- just one -- will usually invalidate a computer program.</p></div><p>If you believe that, you are forced to concluded that most likely no valid program has ever been written in the history of the human race.  <i>All</i> programs have bugs in them (yes, I truly mean all), and in most cases those bugs do not invalidate all their results.
<br> <br>
Don't misunderstand me.  I definitely support releasing the source code for scientific programs, and I believe that finding bugs in them will ultimately lead to better science.  But nothing useful is achieved by absurd hyperbole like the quote above.</p></div>
	</htmltext>
<tokenext>This is hugely worrying when you realise that just one error -- just one -- will usually invalidate a computer program.If you believe that , you are forced to concluded that most likely no valid program has ever been written in the history of the human race .
All programs have bugs in them ( yes , I truly mean all ) , and in most cases those bugs do not invalidate all their results .
Do n't misunderstand me .
I definitely support releasing the source code for scientific programs , and I believe that finding bugs in them will ultimately lead to better science .
But nothing useful is achieved by absurd hyperbole like the quote above .</tokentext>
<sentencetext>This is hugely worrying when you realise that just one error -- just one -- will usually invalidate a computer program.If you believe that, you are forced to concluded that most likely no valid program has ever been written in the history of the human race.
All programs have bugs in them (yes, I truly mean all), and in most cases those bugs do not invalidate all their results.
Don't misunderstand me.
I definitely support releasing the source code for scientific programs, and I believe that finding bugs in them will ultimately lead to better science.
But nothing useful is achieved by absurd hyperbole like the quote above.
	</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072822</id>
	<title>The problem is with government funding standards</title>
	<author>Anonymous</author>
	<datestamp>1265734500000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>1</modscore>
	<htmltext><p>NIH funding standards promote commercialization of publicly funded software. This appears to have been implemented before the modern internet, and the idea may have been that a commercial product would make the code more available, and perhaps fix some of the quality issues with code cobbled together by "non-programmers". The result is that companies like Accelrys own a huge amount of software developed under public funding. Now, the public has to pay to use software trhat they paid to develop, and it is impossible for other scientific research to extend that publicly funded effort.</p><p>I want to see an NIH version of SourceForge, and mandate all government funded software development to be stored there. Unlike SourceForge, there could be delayed release to the public so that researchers have time to publish their work.</p></htmltext>
<tokenext>NIH funding standards promote commercialization of publicly funded software .
This appears to have been implemented before the modern internet , and the idea may have been that a commercial product would make the code more available , and perhaps fix some of the quality issues with code cobbled together by " non-programmers " .
The result is that companies like Accelrys own a huge amount of software developed under public funding .
Now , the public has to pay to use software trhat they paid to develop , and it is impossible for other scientific research to extend that publicly funded effort.I want to see an NIH version of SourceForge , and mandate all government funded software development to be stored there .
Unlike SourceForge , there could be delayed release to the public so that researchers have time to publish their work .</tokentext>
<sentencetext>NIH funding standards promote commercialization of publicly funded software.
This appears to have been implemented before the modern internet, and the idea may have been that a commercial product would make the code more available, and perhaps fix some of the quality issues with code cobbled together by "non-programmers".
The result is that companies like Accelrys own a huge amount of software developed under public funding.
Now, the public has to pay to use software trhat they paid to develop, and it is impossible for other scientific research to extend that publicly funded effort.I want to see an NIH version of SourceForge, and mandate all government funded software development to be stored there.
Unlike SourceForge, there could be delayed release to the public so that researchers have time to publish their work.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072122</id>
	<title>Does this apply to climate deniers too?</title>
	<author>Anonymous</author>
	<datestamp>1265731440000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>Will ExxonMobil release all code that their scientists use?</p></htmltext>
<tokenext>Will ExxonMobil release all code that their scientists use ?</tokentext>
<sentencetext>Will ExxonMobil release all code that their scientists use?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071980</id>
	<title>Engineering Course Grade = F</title>
	<author>BoRegardless</author>
	<datestamp>1265730660000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>4</modscore>
	<htmltext><p>One significant figure?</p></htmltext>
<tokenext>One significant figure ?</tokentext>
<sentencetext>One significant figure?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072314</id>
	<title>Re:Why release it?</title>
	<author>Anonymous</author>
	<datestamp>1265732400000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>You're right, Occam's Razor. Conspiracy is generally too hard, even if you know what you're doing. Who needs conspiracy? Group-think, socio-political cliques, popular public funding streams, fashion, peer pressure, yearning for acceptance by an in-crowd. Know what really brought the US to its knees in Viet Nam? Hippy Chicks. Wanted to get laid? You were anti-war.</htmltext>
<tokenext>You 're right , Occam 's Razor .
Conspiracy is generally too hard , even if you know what you 're doing .
Who needs conspiracy ?
Group-think , socio-political cliques , popular public funding streams , fashion , peer pressure , yearning for acceptance by an in-crowd .
Know what really brought the US to its knees in Viet Nam ?
Hippy Chicks .
Wanted to get laid ?
You were anti-war .</tokentext>
<sentencetext>You're right, Occam's Razor.
Conspiracy is generally too hard, even if you know what you're doing.
Who needs conspiracy?
Group-think, socio-political cliques, popular public funding streams, fashion, peer pressure, yearning for acceptance by an in-crowd.
Know what really brought the US to its knees in Viet Nam?
Hippy Chicks.
Wanted to get laid?
You were anti-war.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071954</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31080662</id>
	<title>Feeding Climate Denialist Trolls?</title>
	<author>benjfowler</author>
	<datestamp>1265723460000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Who's gonna wager their hard-earned that this is a tactic by the climate denial industry to open up another avenue to discredit researchers?</p><p>And how long until idiots like Monckton miraculously become expert software engineers overnight, then start ripping climate researcher new assholes because their computer models contained logic errors?</p></htmltext>
<tokenext>Who 's gon na wager their hard-earned that this is a tactic by the climate denial industry to open up another avenue to discredit researchers ? And how long until idiots like Monckton miraculously become expert software engineers overnight , then start ripping climate researcher new assholes because their computer models contained logic errors ?</tokentext>
<sentencetext>Who's gonna wager their hard-earned that this is a tactic by the climate denial industry to open up another avenue to discredit researchers?And how long until idiots like Monckton miraculously become expert software engineers overnight, then start ripping climate researcher new assholes because their computer models contained logic errors?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074118</id>
	<title>Re:Not a good idea</title>
	<author>quadelirus</author>
	<datestamp>1265739060000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>The problem with what you are saying is that a code base for a single experiment may take years to write. No one will ever validate that result if they have to start coding from scratch. Somewhat faulty verification based on having an open code base is much better than no verification at all. The code should always be open.
<br> <br>
Credentials: A doctoral student and coder in a scientific field.</htmltext>
<tokenext>The problem with what you are saying is that a code base for a single experiment may take years to write .
No one will ever validate that result if they have to start coding from scratch .
Somewhat faulty verification based on having an open code base is much better than no verification at all .
The code should always be open .
Credentials : A doctoral student and coder in a scientific field .</tokentext>
<sentencetext>The problem with what you are saying is that a code base for a single experiment may take years to write.
No one will ever validate that result if they have to start coding from scratch.
Somewhat faulty verification based on having an open code base is much better than no verification at all.
The code should always be open.
Credentials: A doctoral student and coder in a scientific field.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072364</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071920</id>
	<title>great!</title>
	<author>StripedCow</author>
	<datestamp>1265730420000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>3</modscore>
	<htmltext><p>Great!</p><p>I'm getting somewhat tired from reading articles, where there is little or no information regarding program accuracy, total running time, memory used, etc.<br>And in some cases, i'm actually questioning whether the proposed algorithms actually work in practical situations...</p></htmltext>
<tokenext>Great ! I 'm getting somewhat tired from reading articles , where there is little or no information regarding program accuracy , total running time , memory used , etc.And in some cases , i 'm actually questioning whether the proposed algorithms actually work in practical situations.. .</tokentext>
<sentencetext>Great!I'm getting somewhat tired from reading articles, where there is little or no information regarding program accuracy, total running time, memory used, etc.And in some cases, i'm actually questioning whether the proposed algorithms actually work in practical situations...</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31077058</id>
	<title>Re:Not that simple</title>
	<author>mrxak</author>
	<datestamp>1265706480000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Hopefully your experiences will cause you to use OSS to begin with instead of using proprietary code in the future. It may be a pain now, and I hope you keep at it. In the long run, it'll be worth it.</p></htmltext>
<tokenext>Hopefully your experiences will cause you to use OSS to begin with instead of using proprietary code in the future .
It may be a pain now , and I hope you keep at it .
In the long run , it 'll be worth it .</tokentext>
<sentencetext>Hopefully your experiences will cause you to use OSS to begin with instead of using proprietary code in the future.
It may be a pain now, and I hope you keep at it.
In the long run, it'll be worth it.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072694</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074094</id>
	<title>Re:Why release it?</title>
	<author>mcgrew</author>
	<datestamp>1265738940000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>I don't subscribe to Hanlon's razor; I have my own. Mine says "never ascribe to incompetence or stupidity that which can be explained by greedy self-interest".</p><p>Although in this case, Occam rules. The "mcgrew's razor" almost never applies to scientists and almost always applies to corporate types.</p></htmltext>
<tokenext>I do n't subscribe to Hanlon 's razor ; I have my own .
Mine says " never ascribe to incompetence or stupidity that which can be explained by greedy self-interest " .Although in this case , Occam rules .
The " mcgrew 's razor " almost never applies to scientists and almost always applies to corporate types .</tokentext>
<sentencetext>I don't subscribe to Hanlon's razor; I have my own.
Mine says "never ascribe to incompetence or stupidity that which can be explained by greedy self-interest".Although in this case, Occam rules.
The "mcgrew's razor" almost never applies to scientists and almost always applies to corporate types.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071954</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073160</id>
	<title>They have a solution to the inaccuracies ...</title>
	<author>tomhudson</author>
	<datestamp>1265735760000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><blockquote><div><p>This is hugely worrying when you realise that just one error -- just one -- will usually invalidate a computer program.</p></div>
</blockquote><p>
They hire statisticians to argue that the errors average out<nobr> <wbr></nobr>...
</p><p><nobr> <wbr></nobr>... because after all, when neither lies nor damn lies will do the job<nobr> <wbr></nobr>...</p></div>
	</htmltext>
<tokenext>This is hugely worrying when you realise that just one error -- just one -- will usually invalidate a computer program .
They hire statisticians to argue that the errors average out .. . ... because after all , when neither lies nor damn lies will do the job .. .</tokentext>
<sentencetext>This is hugely worrying when you realise that just one error -- just one -- will usually invalidate a computer program.
They hire statisticians to argue that the errors average out ...
 ... because after all, when neither lies nor damn lies will do the job ...
	</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31135350</id>
	<title>Re:Slashdot Egocentrism.</title>
	<author>PastaLover</author>
	<datestamp>1266172080000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><div class="quote"><p>My bet is there is a simple explanation...namely that scientists outside of computer science are too busy in their respective fields to know anything about code, or even care.  The egocentric Slashdot-worldview strikes at the heart of logic yet again.</p></div><p>I think it's worse than that. With some of the focus these days being on doing science in public-private partnerships (because the public money simply isn't there anymore) and generating spinoffs from ongoing research, the actual software often gets labeled "Intellectual Property". You can see where I'm going with this. Suddenly software is an asset, not to be shared openly with the rest of the world. Luckily this is a mindset the actual researchers almost never share and as a result plenty of software is out there in an open source form. In my field (bioinformatics) having freely available software out there is the norm rather than the exception, but that certainly doesn't apply to all research areas everywhere. In any field however I don't think you could get away with publishing results that nobody can verify (by rolling their own) because the basic algorithm is secret. "Trust me" doesn't quite cut it, unless you're publishing in Cranks R Us.</p><p>You do come across the occasional result in a paper that is just not well documented enough to reproduce, even if you were to write all the software yourself. Any scientist would agree that this is just plain bad science (though you shouldn't assume it was done intentionally, often isn't). In a decent journal, the review process should catch that, which I think will increasingly be implemented in the future as people are more aware of the issue.</p></div>
	</htmltext>
<tokenext>My bet is there is a simple explanation...namely that scientists outside of computer science are too busy in their respective fields to know anything about code , or even care .
The egocentric Slashdot-worldview strikes at the heart of logic yet again.I think it 's worse than that .
With some of the focus these days being on doing science in public-private partnerships ( because the public money simply is n't there anymore ) and generating spinoffs from ongoing research , the actual software often gets labeled " Intellectual Property " .
You can see where I 'm going with this .
Suddenly software is an asset , not to be shared openly with the rest of the world .
Luckily this is a mindset the actual researchers almost never share and as a result plenty of software is out there in an open source form .
In my field ( bioinformatics ) having freely available software out there is the norm rather than the exception , but that certainly does n't apply to all research areas everywhere .
In any field however I do n't think you could get away with publishing results that nobody can verify ( by rolling their own ) because the basic algorithm is secret .
" Trust me " does n't quite cut it , unless you 're publishing in Cranks R Us.You do come across the occasional result in a paper that is just not well documented enough to reproduce , even if you were to write all the software yourself .
Any scientist would agree that this is just plain bad science ( though you should n't assume it was done intentionally , often is n't ) .
In a decent journal , the review process should catch that , which I think will increasingly be implemented in the future as people are more aware of the issue .</tokentext>
<sentencetext>My bet is there is a simple explanation...namely that scientists outside of computer science are too busy in their respective fields to know anything about code, or even care.
The egocentric Slashdot-worldview strikes at the heart of logic yet again.I think it's worse than that.
With some of the focus these days being on doing science in public-private partnerships (because the public money simply isn't there anymore) and generating spinoffs from ongoing research, the actual software often gets labeled "Intellectual Property".
You can see where I'm going with this.
Suddenly software is an asset, not to be shared openly with the rest of the world.
Luckily this is a mindset the actual researchers almost never share and as a result plenty of software is out there in an open source form.
In my field (bioinformatics) having freely available software out there is the norm rather than the exception, but that certainly doesn't apply to all research areas everywhere.
In any field however I don't think you could get away with publishing results that nobody can verify (by rolling their own) because the basic algorithm is secret.
"Trust me" doesn't quite cut it, unless you're publishing in Cranks R Us.You do come across the occasional result in a paper that is just not well documented enough to reproduce, even if you were to write all the software yourself.
Any scientist would agree that this is just plain bad science (though you shouldn't assume it was done intentionally, often isn't).
In a decent journal, the review process should catch that, which I think will increasingly be implemented in the future as people are more aware of the issue.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072056</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31077146</id>
	<title>Impediments to releasing scientific code.</title>
	<author>Anonymous</author>
	<datestamp>1265706840000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>
There are benefits and drawbacks to releasing code.  First, let me say I am a scientist, and I do release my code, primarily under the GPL unless I am contractually obligated by license agreements to do otherwise.  The exception would be trivial single use code or limited use code.  Despite that, I don't get a lot of eyes looking at my code.
</p><p>
Some people here have claimed that journal policies are a part of the problem.  Not as far as code releases go.  Journals don't publish code. I think there are real impediments to code release, even when most scientists would claim that the release is a good idea.
</p><ul>
<li>A large amount of code is written by students with limited programming experience.  Therefore it is difficult to read, poorly commented, and poorly optimized.  That's a strong argument that it should be released. But a lot of people would be embarrassed if that code was released.  So there will be some push back.  Especially by established, famous, and respected professors who really don't want their crappy code to be a source of ridicule.</li>
<li>A lot of large bodies of code are controlled by scientific consortia.  A library for simulating particle accelerator collision products might have several hundred authors.  In many of the files the authors will have placed a copyright statement naming themselves as the copyright holder, in others they may have named the institution they work for as the copyright holder.  Since the code was donated to the consortium, the consortium can claim its members have the implied right to used the code.  But the consortium probably can't release the code to the public, since it would need the permission of all authors (many of them deceased) and the institutions they were working for when they developed the code in question.</li>
<li>A lot of scientific programmers use code that they don't have a license to release.  For example, we've all pulled a routine out of Numerical Recipes, because it was easy, did the job we wanted, and was fast enough.  Oops, sorry, can't distribute that code.  We've all used a GPL library in an application linked to closed source or limited distribution libraries. Oops, sorry, it's illegal to distribute that code.  (Don't tell my University about this, because they'll make me consult with a lawyer before releasing any code.)</li>
<li>Scientists may, in general, be intelligent and well informed, but when it comes to the intricacies of licensing agreements and copyright law most don't have more than a very limited understanding.</li>
<li>A lot of scientists don't want to be scooped by competitors.</li>
<li>There are some people who think releasing code or making it available to colleagues works against the scientific method by discouraging reimplementation of an application for the purpose of replicating earlier results.</li>
</ul><p>
In the case of climate modeling code, I'm guessing that #2 is probably the biggest hurdle.  In my code, #3 is probably the biggest hurdle, and it does take significant effort to work around it.</p></htmltext>
<tokenext>There are benefits and drawbacks to releasing code .
First , let me say I am a scientist , and I do release my code , primarily under the GPL unless I am contractually obligated by license agreements to do otherwise .
The exception would be trivial single use code or limited use code .
Despite that , I do n't get a lot of eyes looking at my code .
Some people here have claimed that journal policies are a part of the problem .
Not as far as code releases go .
Journals do n't publish code .
I think there are real impediments to code release , even when most scientists would claim that the release is a good idea .
A large amount of code is written by students with limited programming experience .
Therefore it is difficult to read , poorly commented , and poorly optimized .
That 's a strong argument that it should be released .
But a lot of people would be embarrassed if that code was released .
So there will be some push back .
Especially by established , famous , and respected professors who really do n't want their crappy code to be a source of ridicule .
A lot of large bodies of code are controlled by scientific consortia .
A library for simulating particle accelerator collision products might have several hundred authors .
In many of the files the authors will have placed a copyright statement naming themselves as the copyright holder , in others they may have named the institution they work for as the copyright holder .
Since the code was donated to the consortium , the consortium can claim its members have the implied right to used the code .
But the consortium probably ca n't release the code to the public , since it would need the permission of all authors ( many of them deceased ) and the institutions they were working for when they developed the code in question .
A lot of scientific programmers use code that they do n't have a license to release .
For example , we 've all pulled a routine out of Numerical Recipes , because it was easy , did the job we wanted , and was fast enough .
Oops , sorry , ca n't distribute that code .
We 've all used a GPL library in an application linked to closed source or limited distribution libraries .
Oops , sorry , it 's illegal to distribute that code .
( Do n't tell my University about this , because they 'll make me consult with a lawyer before releasing any code .
) Scientists may , in general , be intelligent and well informed , but when it comes to the intricacies of licensing agreements and copyright law most do n't have more than a very limited understanding .
A lot of scientists do n't want to be scooped by competitors .
There are some people who think releasing code or making it available to colleagues works against the scientific method by discouraging reimplementation of an application for the purpose of replicating earlier results .
In the case of climate modeling code , I 'm guessing that # 2 is probably the biggest hurdle .
In my code , # 3 is probably the biggest hurdle , and it does take significant effort to work around it .</tokentext>
<sentencetext>
There are benefits and drawbacks to releasing code.
First, let me say I am a scientist, and I do release my code, primarily under the GPL unless I am contractually obligated by license agreements to do otherwise.
The exception would be trivial single use code or limited use code.
Despite that, I don't get a lot of eyes looking at my code.
Some people here have claimed that journal policies are a part of the problem.
Not as far as code releases go.
Journals don't publish code.
I think there are real impediments to code release, even when most scientists would claim that the release is a good idea.
A large amount of code is written by students with limited programming experience.
Therefore it is difficult to read, poorly commented, and poorly optimized.
That's a strong argument that it should be released.
But a lot of people would be embarrassed if that code was released.
So there will be some push back.
Especially by established, famous, and respected professors who really don't want their crappy code to be a source of ridicule.
A lot of large bodies of code are controlled by scientific consortia.
A library for simulating particle accelerator collision products might have several hundred authors.
In many of the files the authors will have placed a copyright statement naming themselves as the copyright holder, in others they may have named the institution they work for as the copyright holder.
Since the code was donated to the consortium, the consortium can claim its members have the implied right to used the code.
But the consortium probably can't release the code to the public, since it would need the permission of all authors (many of them deceased) and the institutions they were working for when they developed the code in question.
A lot of scientific programmers use code that they don't have a license to release.
For example, we've all pulled a routine out of Numerical Recipes, because it was easy, did the job we wanted, and was fast enough.
Oops, sorry, can't distribute that code.
We've all used a GPL library in an application linked to closed source or limited distribution libraries.
Oops, sorry, it's illegal to distribute that code.
(Don't tell my University about this, because they'll make me consult with a lawyer before releasing any code.
)
Scientists may, in general, be intelligent and well informed, but when it comes to the intricacies of licensing agreements and copyright law most don't have more than a very limited understanding.
A lot of scientists don't want to be scooped by competitors.
There are some people who think releasing code or making it available to colleagues works against the scientific method by discouraging reimplementation of an application for the purpose of replicating earlier results.
In the case of climate modeling code, I'm guessing that #2 is probably the biggest hurdle.
In my code, #3 is probably the biggest hurdle, and it does take significant effort to work around it.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074216</id>
	<title>For climatology, this is a non-issue</title>
	<author>azgard</author>
	<datestamp>1265739420000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>2</modscore>
	<htmltext><p>While I am fan of open source and this idea in general, for climatology, this is a non-issue. Look there: <a href="http://www.realclimate.org/index.php/data-sources/" title="realclimate.org">http://www.realclimate.org/index.php/data-sources/</a> [realclimate.org]</p><p>It's more code out there than one amateur can eat for life. And you know what? From the experience of people who wrote these programs, there isn't actually much people looking at it. I doubt that any scientific code will get many eyeballs. This is more a PR exercise.</p></htmltext>
<tokenext>While I am fan of open source and this idea in general , for climatology , this is a non-issue .
Look there : http : //www.realclimate.org/index.php/data-sources/ [ realclimate.org ] It 's more code out there than one amateur can eat for life .
And you know what ?
From the experience of people who wrote these programs , there is n't actually much people looking at it .
I doubt that any scientific code will get many eyeballs .
This is more a PR exercise .</tokentext>
<sentencetext>While I am fan of open source and this idea in general, for climatology, this is a non-issue.
Look there: http://www.realclimate.org/index.php/data-sources/ [realclimate.org]It's more code out there than one amateur can eat for life.
And you know what?
From the experience of people who wrote these programs, there isn't actually much people looking at it.
I doubt that any scientific code will get many eyeballs.
This is more a PR exercise.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072358</id>
	<title>Re:Conspiracy?</title>
	<author>bunratty</author>
	<datestamp>1265732580000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext>Let's think through what would really happen if scientists released their code. The code has bugs, as all code does. People with an ulterior motive would point to the bugs and say "Look here! A bug! The science cannot be trusted!" And millions of sheeple would repeat "Yes! The code has bugs! And therefore I refuse to believe it!" It won't matter whether the bugs are relevant to the science; the fact that there are any bugs at all will cause people who want to disagree to say there's doubt about the results. Meanwhile, they will go about their business using computer systems that are riddled with bugs, but function well enough the vast majority of the time they're not even aware of the bugs.</htmltext>
<tokenext>Let 's think through what would really happen if scientists released their code .
The code has bugs , as all code does .
People with an ulterior motive would point to the bugs and say " Look here !
A bug !
The science can not be trusted !
" And millions of sheeple would repeat " Yes !
The code has bugs !
And therefore I refuse to believe it !
" It wo n't matter whether the bugs are relevant to the science ; the fact that there are any bugs at all will cause people who want to disagree to say there 's doubt about the results .
Meanwhile , they will go about their business using computer systems that are riddled with bugs , but function well enough the vast majority of the time they 're not even aware of the bugs .</tokentext>
<sentencetext>Let's think through what would really happen if scientists released their code.
The code has bugs, as all code does.
People with an ulterior motive would point to the bugs and say "Look here!
A bug!
The science cannot be trusted!
" And millions of sheeple would repeat "Yes!
The code has bugs!
And therefore I refuse to believe it!
" It won't matter whether the bugs are relevant to the science; the fact that there are any bugs at all will cause people who want to disagree to say there's doubt about the results.
Meanwhile, they will go about their business using computer systems that are riddled with bugs, but function well enough the vast majority of the time they're not even aware of the bugs.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072148</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074318</id>
	<title>Re:Not a good idea</title>
	<author>Goalie\_Ca</author>
	<datestamp>1265739780000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>I find that scientists dont often bother replicating results because their funding is to do new stuff.. not old stuff. It can be very costly and time consuming to thoroughly review.</htmltext>
<tokenext>I find that scientists dont often bother replicating results because their funding is to do new stuff.. not old stuff .
It can be very costly and time consuming to thoroughly review .</tokentext>
<sentencetext>I find that scientists dont often bother replicating results because their funding is to do new stuff.. not old stuff.
It can be very costly and time consuming to thoroughly review.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072364</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31083240</id>
	<title>Some practical steps</title>
	<author>mhwombat</author>
	<datestamp>1265017740000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>I work in "IT for research". I see a lot of researchers from different disciplines who write code, or in some cases hire developers. In my experience there are a few things that can make a big difference:
<ul>
<li>Appropriate Methods journals - scientists are MUCH more likely to go to the effort of releasing their code if they will get cited by scientists who re-use it, and cited in a journal with some respectability. In fields with these kinds of respected journals there is much more code publication. And if they're going to release it, they will look harder at the quality.</li>
<li>Pressure on instrument manufacturers to release standards - proprietary standards can be a major barrier in developing open code, not to mention a huge waste of time. These instruments are very expensive and bought with public money. Funding bodies which fund hardware purchases could apply a LOT of pressure here.</li>
<li>Research IT support from universities (not just IT support for the educational branch of the university). The quality of this can be wildly variable.</li>
</ul></htmltext>
<tokenext>I work in " IT for research " .
I see a lot of researchers from different disciplines who write code , or in some cases hire developers .
In my experience there are a few things that can make a big difference : Appropriate Methods journals - scientists are MUCH more likely to go to the effort of releasing their code if they will get cited by scientists who re-use it , and cited in a journal with some respectability .
In fields with these kinds of respected journals there is much more code publication .
And if they 're going to release it , they will look harder at the quality .
Pressure on instrument manufacturers to release standards - proprietary standards can be a major barrier in developing open code , not to mention a huge waste of time .
These instruments are very expensive and bought with public money .
Funding bodies which fund hardware purchases could apply a LOT of pressure here .
Research IT support from universities ( not just IT support for the educational branch of the university ) .
The quality of this can be wildly variable .</tokentext>
<sentencetext>I work in "IT for research".
I see a lot of researchers from different disciplines who write code, or in some cases hire developers.
In my experience there are a few things that can make a big difference:

Appropriate Methods journals - scientists are MUCH more likely to go to the effort of releasing their code if they will get cited by scientists who re-use it, and cited in a journal with some respectability.
In fields with these kinds of respected journals there is much more code publication.
And if they're going to release it, they will look harder at the quality.
Pressure on instrument manufacturers to release standards - proprietary standards can be a major barrier in developing open code, not to mention a huge waste of time.
These instruments are very expensive and bought with public money.
Funding bodies which fund hardware purchases could apply a LOT of pressure here.
Research IT support from universities (not just IT support for the educational branch of the university).
The quality of this can be wildly variable.
</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31078792</id>
	<title>Re:Slashdot Egocentrism.</title>
	<author>Anonymous</author>
	<datestamp>1265713440000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>AGREED!</p></htmltext>
<tokenext>AGREED !</tokentext>
<sentencetext>AGREED!</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072594</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31076054</id>
	<title>We need a good central repository</title>
	<author>dj\_tla</author>
	<datestamp>1265745900000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>If a proposal like this is to succeed -- and I hope so hard that it does -- we need a central repository to store code and meaningfully link it to the papers that use it.</p><p>This repository should have the same amount of peer review and, therefore, authority that scientific journals have now. Maybe that can happen by existing journals adding the ability to link code to a paper (and enforce that any code used to generate results is included), maybe a new organization has to rise up to the challenge (I would love to see a code.arxiv.org).</p><p>Already I can hear the outcry of scientists claiming that their code is "sloppy" and "not ready to be released," but those concerns are simply irrelevant: all that matters is that the code produces the output cited in the paper given the input cited in the paper. That's it. If another researcher finds your result interesting, then let it be up to them to parse out your code -- it's probably still way better than trying to reproduce your result based on the prose that describes your algorithm.</p></htmltext>
<tokenext>If a proposal like this is to succeed -- and I hope so hard that it does -- we need a central repository to store code and meaningfully link it to the papers that use it.This repository should have the same amount of peer review and , therefore , authority that scientific journals have now .
Maybe that can happen by existing journals adding the ability to link code to a paper ( and enforce that any code used to generate results is included ) , maybe a new organization has to rise up to the challenge ( I would love to see a code.arxiv.org ) .Already I can hear the outcry of scientists claiming that their code is " sloppy " and " not ready to be released , " but those concerns are simply irrelevant : all that matters is that the code produces the output cited in the paper given the input cited in the paper .
That 's it .
If another researcher finds your result interesting , then let it be up to them to parse out your code -- it 's probably still way better than trying to reproduce your result based on the prose that describes your algorithm .</tokentext>
<sentencetext>If a proposal like this is to succeed -- and I hope so hard that it does -- we need a central repository to store code and meaningfully link it to the papers that use it.This repository should have the same amount of peer review and, therefore, authority that scientific journals have now.
Maybe that can happen by existing journals adding the ability to link code to a paper (and enforce that any code used to generate results is included), maybe a new organization has to rise up to the challenge (I would love to see a code.arxiv.org).Already I can hear the outcry of scientists claiming that their code is "sloppy" and "not ready to be released," but those concerns are simply irrelevant: all that matters is that the code produces the output cited in the paper given the input cited in the paper.
That's it.
If another researcher finds your result interesting, then let it be up to them to parse out your code -- it's probably still way better than trying to reproduce your result based on the prose that describes your algorithm.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072260</id>
	<title>I concur</title>
	<author>Anonymous</author>
	<datestamp>1265732160000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>4</modscore>
	<htmltext>As a software engineer who has spent 20 years coding in research labs, I can say with certainty that the code written by many, if not most, scientists is utter garbage. As an example, a colleague of mine was approached recently to debug a piece of code: "<i>Oh, it's going to be easy, it was written by one of our postdocs on his last day here...</i>". 600 lines of code in the main, no functions, no comments. He's been at it for 2 months.
<p>
I'm perfectly OK with the fact that their job is science and not coding, but would they go to the satellite assembly guys and start gluing parts at random ?</p></htmltext>
<tokenext>As a software engineer who has spent 20 years coding in research labs , I can say with certainty that the code written by many , if not most , scientists is utter garbage .
As an example , a colleague of mine was approached recently to debug a piece of code : " Oh , it 's going to be easy , it was written by one of our postdocs on his last day here... " .
600 lines of code in the main , no functions , no comments .
He 's been at it for 2 months .
I 'm perfectly OK with the fact that their job is science and not coding , but would they go to the satellite assembly guys and start gluing parts at random ?</tokentext>
<sentencetext>As a software engineer who has spent 20 years coding in research labs, I can say with certainty that the code written by many, if not most, scientists is utter garbage.
As an example, a colleague of mine was approached recently to debug a piece of code: "Oh, it's going to be easy, it was written by one of our postdocs on his last day here...".
600 lines of code in the main, no functions, no comments.
He's been at it for 2 months.
I'm perfectly OK with the fact that their job is science and not coding, but would they go to the satellite assembly guys and start gluing parts at random ?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072058</id>
	<title>This is news?</title>
	<author>andyh-rayleigh</author>
	<datestamp>1265731200000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Nothing seems to change<nobr> <wbr></nobr>...<br>30 years ago it was a standard joke that most "fundamental particles" were bugs in the Fortran programs of the day.</p><p>I wouldn't be surprised to discover that some of the programs inestigated are just the result of 30 years of further modification of the ones we knew<nobr> <wbr></nobr>... and that nobody understands them now!</p></htmltext>
<tokenext>Nothing seems to change ...30 years ago it was a standard joke that most " fundamental particles " were bugs in the Fortran programs of the day.I would n't be surprised to discover that some of the programs inestigated are just the result of 30 years of further modification of the ones we knew ... and that nobody understands them now !</tokentext>
<sentencetext>Nothing seems to change ...30 years ago it was a standard joke that most "fundamental particles" were bugs in the Fortran programs of the day.I wouldn't be surprised to discover that some of the programs inestigated are just the result of 30 years of further modification of the ones we knew ... and that nobody understands them now!</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072884</id>
	<title>mechanically verifyable proofs too please</title>
	<author>StripedCow</author>
	<datestamp>1265734740000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Besides code, it would be nice to have mechanically verifyable proofs too!</p><p>But code would be a nice first bit of progression.</p></htmltext>
<tokenext>Besides code , it would be nice to have mechanically verifyable proofs too ! But code would be a nice first bit of progression .</tokentext>
<sentencetext>Besides code, it would be nice to have mechanically verifyable proofs too!But code would be a nice first bit of progression.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073398</id>
	<title>OO.org seems more suited to science anyway</title>
	<author>maccallr</author>
	<datestamp>1265736660000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>I switched from MS Excel to OOcalc for some analysis I'm doing at the moment.  Excel was slow, made huge files and the bar charts were hideously shaded by default.</p></htmltext>
<tokenext>I switched from MS Excel to OOcalc for some analysis I 'm doing at the moment .
Excel was slow , made huge files and the bar charts were hideously shaded by default .</tokentext>
<sentencetext>I switched from MS Excel to OOcalc for some analysis I'm doing at the moment.
Excel was slow, made huge files and the bar charts were hideously shaded by default.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072296</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31076970</id>
	<title>Re:Not a good idea</title>
	<author>mrxak</author>
	<datestamp>1265706180000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Other scientists shouldn't be using the same software to reproduce the results. That's pretty obvious.</p><p>What we're talking about here is an added layer of assurance that the initial results are as good as they can be. Having an independent auditing of code means that the methodology described in a paper is the one actually used in the software. It fixes simple errors, and ensures that there's no fraud. The programmers who would do this are not being taken away from creating new scientific research, because they're not scientists, nor are they competing for the same research grants. What's more, it's free QA that keeps the science more scientific.</p><p>You have a whole lot of coders looking at the code and making sure it's a perfect implementation of the model or algorithms described by the scientists, and it won't matter if somebody uses the same code to reproduce the results, because you'll know the software is working perfectly. All that's left then is for other scientists to criticize the methodology and assumptions of the research as part of the normal peer review process. It turns the code into just another tool at a scientist's disposal.</p><p>We're talking about science here. The whole point of science is challenging something repeatedly and thoroughly, and if it stands up, you know it's true. Adding more challenges is the most scientific thing you can do.</p></htmltext>
<tokenext>Other scientists should n't be using the same software to reproduce the results .
That 's pretty obvious.What we 're talking about here is an added layer of assurance that the initial results are as good as they can be .
Having an independent auditing of code means that the methodology described in a paper is the one actually used in the software .
It fixes simple errors , and ensures that there 's no fraud .
The programmers who would do this are not being taken away from creating new scientific research , because they 're not scientists , nor are they competing for the same research grants .
What 's more , it 's free QA that keeps the science more scientific.You have a whole lot of coders looking at the code and making sure it 's a perfect implementation of the model or algorithms described by the scientists , and it wo n't matter if somebody uses the same code to reproduce the results , because you 'll know the software is working perfectly .
All that 's left then is for other scientists to criticize the methodology and assumptions of the research as part of the normal peer review process .
It turns the code into just another tool at a scientist 's disposal.We 're talking about science here .
The whole point of science is challenging something repeatedly and thoroughly , and if it stands up , you know it 's true .
Adding more challenges is the most scientific thing you can do .</tokentext>
<sentencetext>Other scientists shouldn't be using the same software to reproduce the results.
That's pretty obvious.What we're talking about here is an added layer of assurance that the initial results are as good as they can be.
Having an independent auditing of code means that the methodology described in a paper is the one actually used in the software.
It fixes simple errors, and ensures that there's no fraud.
The programmers who would do this are not being taken away from creating new scientific research, because they're not scientists, nor are they competing for the same research grants.
What's more, it's free QA that keeps the science more scientific.You have a whole lot of coders looking at the code and making sure it's a perfect implementation of the model or algorithms described by the scientists, and it won't matter if somebody uses the same code to reproduce the results, because you'll know the software is working perfectly.
All that's left then is for other scientists to criticize the methodology and assumptions of the research as part of the normal peer review process.
It turns the code into just another tool at a scientist's disposal.We're talking about science here.
The whole point of science is challenging something repeatedly and thoroughly, and if it stands up, you know it's true.
Adding more challenges is the most scientific thing you can do.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072364</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073558</id>
	<title>Film at 11</title>
	<author>Hognoxious</author>
	<datestamp>1265737080000</datestamp>
	<modclass>Flamebait</modclass>
	<modscore>0</modscore>
	<htmltext><p>OMG there is bugzorz in teh codezor'z?  Oh Noooooesonehundredandeleventyoneoneone!!!!!</p></htmltext>
<tokenext>OMG there is bugzorz in teh codezor'z ?
Oh Noooooesonehundredandeleventyoneoneone ! ! ! !
!</tokentext>
<sentencetext>OMG there is bugzorz in teh codezor'z?
Oh Noooooesonehundredandeleventyoneoneone!!!!
!</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31075614</id>
	<title>Re:Peer Review vs. Funding</title>
	<author>Anonymous</author>
	<datestamp>1265744520000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>Actually, this is one reason why many people are, rightly or wrongly, so skeptical nowadays of scientific studies funded by pharmaceutical companies.</p></htmltext>
<tokenext>Actually , this is one reason why many people are , rightly or wrongly , so skeptical nowadays of scientific studies funded by pharmaceutical companies .</tokentext>
<sentencetext>Actually, this is one reason why many people are, rightly or wrongly, so skeptical nowadays of scientific studies funded by pharmaceutical companies.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072120</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072078</id>
	<title>Re:Why release it?</title>
	<author>Anonymusing</author>
	<datestamp>1265731260000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>And it's situations like this which make the general public distrust scientists, or even science in general.
</p><p>The media plays a major role, as well -- it oversimplifies and dramatizes scientific research as if it comes to conclusions that it usually doesn't -- but when it comes to light that a scientist has made a mistake, or that a research paper has had false premises or inaccurate results, then the average Joe Public thinks to himself, "Can't trust those scientists. Shoulda known."</p></htmltext>
<tokenext>And it 's situations like this which make the general public distrust scientists , or even science in general .
The media plays a major role , as well -- it oversimplifies and dramatizes scientific research as if it comes to conclusions that it usually does n't -- but when it comes to light that a scientist has made a mistake , or that a research paper has had false premises or inaccurate results , then the average Joe Public thinks to himself , " Ca n't trust those scientists .
Shoulda known .
"</tokentext>
<sentencetext>And it's situations like this which make the general public distrust scientists, or even science in general.
The media plays a major role, as well -- it oversimplifies and dramatizes scientific research as if it comes to conclusions that it usually doesn't -- but when it comes to light that a scientist has made a mistake, or that a research paper has had false premises or inaccurate results, then the average Joe Public thinks to himself, "Can't trust those scientists.
Shoulda known.
"</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071884</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072452</id>
	<title>Re:Engineering Course Grade = F</title>
	<author>natoochtoniket</author>
	<datestamp>1265733000000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>2</modscore>
	<htmltext><p>That actually surprised me, too.   Loss of precision is nothing new.  When you use floats to do the arithmetic, you lose precision in each operation, and particularly when you multiply two numbers with different scales (exponents).  The thing that surprised me was not that a calculation could lose precision.  It was the assertion that any precision would remain, at all.</p><p>Numeric code can be written using algorithms that minimize loss of precision, or that are able to quantify the amount of precision that is lost (and that remains) in the final answers.  But, if you don't use those algorithms, or don't use them correctly and carefully, you really cannot assert \_any\_ precision in the result.</p><p>If you know your confidence interval, you can state your result with confidence.  But, if you don't bother to calculate the confidence interval, or if you don't know what a CI is, or if you are not careful, it usually ends up being plus-or-minus 100 percent of the scale.</p></htmltext>
<tokenext>That actually surprised me , too .
Loss of precision is nothing new .
When you use floats to do the arithmetic , you lose precision in each operation , and particularly when you multiply two numbers with different scales ( exponents ) .
The thing that surprised me was not that a calculation could lose precision .
It was the assertion that any precision would remain , at all.Numeric code can be written using algorithms that minimize loss of precision , or that are able to quantify the amount of precision that is lost ( and that remains ) in the final answers .
But , if you do n't use those algorithms , or do n't use them correctly and carefully , you really can not assert \ _any \ _ precision in the result.If you know your confidence interval , you can state your result with confidence .
But , if you do n't bother to calculate the confidence interval , or if you do n't know what a CI is , or if you are not careful , it usually ends up being plus-or-minus 100 percent of the scale .</tokentext>
<sentencetext>That actually surprised me, too.
Loss of precision is nothing new.
When you use floats to do the arithmetic, you lose precision in each operation, and particularly when you multiply two numbers with different scales (exponents).
The thing that surprised me was not that a calculation could lose precision.
It was the assertion that any precision would remain, at all.Numeric code can be written using algorithms that minimize loss of precision, or that are able to quantify the amount of precision that is lost (and that remains) in the final answers.
But, if you don't use those algorithms, or don't use them correctly and carefully, you really cannot assert \_any\_ precision in the result.If you know your confidence interval, you can state your result with confidence.
But, if you don't bother to calculate the confidence interval, or if you don't know what a CI is, or if you are not careful, it usually ends up being plus-or-minus 100 percent of the scale.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071980</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072052</id>
	<title>This is not science.</title>
	<author>Coolhand2120</author>
	<datestamp>1265731140000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>4</modscore>
	<htmltext><a href="http://www.google.com/search?hl=en&amp;q=\%22Why+should+I+make+the+data+available+to+you\%2C+when+your+aim+is+to+try+and+find+something+wrong+with+it\%22" title="google.com">"Why should I make the data available to you, when your aim is to try and find something wrong with it"</a> [google.com]
<br>
-Prof. Jones CRU</htmltext>
<tokenext>" Why should I make the data available to you , when your aim is to try and find something wrong with it " [ google.com ] -Prof. Jones CRU</tokentext>
<sentencetext>"Why should I make the data available to you, when your aim is to try and find something wrong with it" [google.com]

-Prof. Jones CRU</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31075456</id>
	<title>Re:Slashdot Egocentrism.</title>
	<author>david\_thornley</author>
	<datestamp>1265743980000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>
If their code results in predictions that affect millions of lives and trillions of dollars, perhaps the people giving out the grants should budget for some real programming types rather than expect the scientists to get necessary software done somehow or another.
</p><p>
Just because people throw around large numbers of dollars in discussions doesn't mean any of that gets to the actual scientists trying to get their work done.</p></htmltext>
<tokenext>If their code results in predictions that affect millions of lives and trillions of dollars , perhaps the people giving out the grants should budget for some real programming types rather than expect the scientists to get necessary software done somehow or another .
Just because people throw around large numbers of dollars in discussions does n't mean any of that gets to the actual scientists trying to get their work done .</tokentext>
<sentencetext>
If their code results in predictions that affect millions of lives and trillions of dollars, perhaps the people giving out the grants should budget for some real programming types rather than expect the scientists to get necessary software done somehow or another.
Just because people throw around large numbers of dollars in discussions doesn't mean any of that gets to the actual scientists trying to get their work done.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072594</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31077000</id>
	<title>I've seen it</title>
	<author>Anonymous</author>
	<datestamp>1265706300000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>Its been 15 years since I worked in university labs, but I clearly recall that the code written by most Physics professors was horrid.</p><p>It was only the people like myself who had studied Computer Science who knew now bad most of that software was. Nightmares to debug and maintain.</p><p>But it doesn't stop there. Consider the data handling techniques used in the social sciences. I've seen first hand how the data from survey's were manipulated over and over, replacing the original data sets on each step. The original data was completely lost and the steps to get from the original to the published data were completely untraceable.</p><p>My conclusion is that (in general) academic scientists are no better than the general public at data handling and data verification techniques.</p></htmltext>
<tokenext>Its been 15 years since I worked in university labs , but I clearly recall that the code written by most Physics professors was horrid.It was only the people like myself who had studied Computer Science who knew now bad most of that software was .
Nightmares to debug and maintain.But it does n't stop there .
Consider the data handling techniques used in the social sciences .
I 've seen first hand how the data from survey 's were manipulated over and over , replacing the original data sets on each step .
The original data was completely lost and the steps to get from the original to the published data were completely untraceable.My conclusion is that ( in general ) academic scientists are no better than the general public at data handling and data verification techniques .</tokentext>
<sentencetext>Its been 15 years since I worked in university labs, but I clearly recall that the code written by most Physics professors was horrid.It was only the people like myself who had studied Computer Science who knew now bad most of that software was.
Nightmares to debug and maintain.But it doesn't stop there.
Consider the data handling techniques used in the social sciences.
I've seen first hand how the data from survey's were manipulated over and over, replacing the original data sets on each step.
The original data was completely lost and the steps to get from the original to the published data were completely untraceable.My conclusion is that (in general) academic scientists are no better than the general public at data handling and data verification techniques.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074714</id>
	<title>Duh?</title>
	<author>b4upoo</author>
	<datestamp>1265741460000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>       I'm old school but we were drilled to death on knowing the degree of accuracy of any mathematical results. I can't imagine scientists who do not know the degree of inaccuracy in any work product.</p></htmltext>
<tokenext>I 'm old school but we were drilled to death on knowing the degree of accuracy of any mathematical results .
I ca n't imagine scientists who do not know the degree of inaccuracy in any work product .</tokentext>
<sentencetext>       I'm old school but we were drilled to death on knowing the degree of accuracy of any mathematical results.
I can't imagine scientists who do not know the degree of inaccuracy in any work product.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31104186</id>
	<title>Re:MaDnEsS !</title>
	<author>DarthVain</author>
	<datestamp>1265879880000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>I know it is a joke... but the argument being made by most scientists is that everyone  peer.</p><p>Personally I think everything should be open, but I am a dirty hippy.</p></htmltext>
<tokenext>I know it is a joke... but the argument being made by most scientists is that everyone peer.Personally I think everything should be open , but I am a dirty hippy .</tokentext>
<sentencetext>I know it is a joke... but the argument being made by most scientists is that everyone  peer.Personally I think everything should be open, but I am a dirty hippy.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071998</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073062</id>
	<title>Re:great!</title>
	<author>Anonymous</author>
	<datestamp>1265735460000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>1</modscore>
	<htmltext><p>Yet more stupidity by people who know nothing. By the logic  of the posters  above since the government paid EDS under a contract to perform some work for the government ANY software developed by EDS should suddenly become freely available. Since Boeing was paid to develop tF-15 ANY software written to design or build the f-15 should now be freely available. I suggest you idiots try that with any company that does business with the government. I'll know when you do because the gales of laughter from the corporate offices will be heard around the world. Yet you think that software developed to perform a work under contract to the government by a researcher mysteriously should freely available. The funny part is if the software written by researchers under contract to government wasn't freely available how is it possible that the idiot writing for the Guardian was able to perform the analysis? Wups! I suggest he try the same analysis on the regenerative breaking software that Toyota has on its Prius or maybe the Airbus 330 fly-by-wire software (think AirFrance) Wups!</p><p>Yes I am very aware of the legal requirements and their consequences. For the third I've have  large chunks of my code copied verbatim within commercial products after my institution was forced release it to companies repeating the same "the research is publicly funded." line of bullshit. The companies actually had the brass balls to actually try to sell me my own software. Yes it's a long protracted process to get the companies to either remove the offending code or pay the university for it.</p></htmltext>
<tokenext>Yet more stupidity by people who know nothing .
By the logic of the posters above since the government paid EDS under a contract to perform some work for the government ANY software developed by EDS should suddenly become freely available .
Since Boeing was paid to develop tF-15 ANY software written to design or build the f-15 should now be freely available .
I suggest you idiots try that with any company that does business with the government .
I 'll know when you do because the gales of laughter from the corporate offices will be heard around the world .
Yet you think that software developed to perform a work under contract to the government by a researcher mysteriously should freely available .
The funny part is if the software written by researchers under contract to government was n't freely available how is it possible that the idiot writing for the Guardian was able to perform the analysis ?
Wups ! I suggest he try the same analysis on the regenerative breaking software that Toyota has on its Prius or maybe the Airbus 330 fly-by-wire software ( think AirFrance ) Wups ! Yes I am very aware of the legal requirements and their consequences .
For the third I 've have large chunks of my code copied verbatim within commercial products after my institution was forced release it to companies repeating the same " the research is publicly funded .
" line of bullshit .
The companies actually had the brass balls to actually try to sell me my own software .
Yes it 's a long protracted process to get the companies to either remove the offending code or pay the university for it .</tokentext>
<sentencetext>Yet more stupidity by people who know nothing.
By the logic  of the posters  above since the government paid EDS under a contract to perform some work for the government ANY software developed by EDS should suddenly become freely available.
Since Boeing was paid to develop tF-15 ANY software written to design or build the f-15 should now be freely available.
I suggest you idiots try that with any company that does business with the government.
I'll know when you do because the gales of laughter from the corporate offices will be heard around the world.
Yet you think that software developed to perform a work under contract to the government by a researcher mysteriously should freely available.
The funny part is if the software written by researchers under contract to government wasn't freely available how is it possible that the idiot writing for the Guardian was able to perform the analysis?
Wups! I suggest he try the same analysis on the regenerative breaking software that Toyota has on its Prius or maybe the Airbus 330 fly-by-wire software (think AirFrance) Wups!Yes I am very aware of the legal requirements and their consequences.
For the third I've have  large chunks of my code copied verbatim within commercial products after my institution was forced release it to companies repeating the same "the research is publicly funded.
" line of bullshit.
The companies actually had the brass balls to actually try to sell me my own software.
Yes it's a long protracted process to get the companies to either remove the offending code or pay the university for it.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071920</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074346</id>
	<title>Example of Disastrous Programming Error</title>
	<author>structural\_biologist</author>
	<datestamp>1265739900000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>A good example of how disastrous one error in data analysis code can be comes from the field of biochemistry, specifically analyzing the x-ray diffraction patterns from crystallized proteins to determine the three dimensional structure of the proteins.  Geoff Chang, faculty at the prestigious Scripps Research Institute in San Diego, had published a series of landmark papers describing the structures of various important membrane proteins, whose structures had never been solved before.  Although these results did not mesh other researchers' models for how these proteins worked, many researchers used Chang's structures as starting points to develop and test new models for how these proteins might work.  However, in 2006, things came crashing down:</p><p><div class="quote"><p>In September, Swiss researchers published a paper in <i>Nature</i> that cast serious doubt on a protein structure Chang's group had described in a 2001 <i>Science</i> paper. When he investigated, Chang was horrified to discover that a homemade data-analysis program had flipped two columns of data, inverting the electron-density map from which his team had derived the final protein structure. Unfortunately, his group had used the program to analyze data for other proteins. As a result, on page 1875, Chang and his colleagues retract three <i>Science</i> papers and report that two papers in other journals also contain erroneous structures.</p></div><p>(from a <a href="http://www.sciencemag.org/cgi/content/summary/314/5807/1856" title="sciencemag.org" rel="nofollow"> <i>Science</i> </a> [sciencemag.org] news article (subscription required to view full article):</p><p>Of course, there were other factors that caused this situation (because the proteins are notoriously difficult to work with, the data were fairly poor quality.  Had the data quality been better, Chang would have likely realized the mistakes prior to publishing the papers).  However, it is sobering to note the resources wasted on research following up on these incorrect structures produced by a simple coding error (I know a few people whose entire theses were invalidated by these retractions).</p><p>It is, however, unclear whether releasing the data analysis code would have fixed this situation.  The software for analyzing x-ray diffraction data is fairly standard (I don't know why Chang was using his own homemade software) and various open-source software are available.  Furthermore, in his field, it is common to release the raw diffraction data (I'm not sure if it was released in the case of these five structures), so it may have been possible for others to double check his work with their own analysis software.  Perhaps the greater error here is in Chang, the peer reviewers of his publications, and the scientific community for believing Chang's conclusions (based on relatively poor quality diffraction data) over the conclusions of many other researches whose techniques may not have been as sophisticated, but who had generated data of much higher quality.</p></div>
	</htmltext>
<tokenext>A good example of how disastrous one error in data analysis code can be comes from the field of biochemistry , specifically analyzing the x-ray diffraction patterns from crystallized proteins to determine the three dimensional structure of the proteins .
Geoff Chang , faculty at the prestigious Scripps Research Institute in San Diego , had published a series of landmark papers describing the structures of various important membrane proteins , whose structures had never been solved before .
Although these results did not mesh other researchers ' models for how these proteins worked , many researchers used Chang 's structures as starting points to develop and test new models for how these proteins might work .
However , in 2006 , things came crashing down : In September , Swiss researchers published a paper in Nature that cast serious doubt on a protein structure Chang 's group had described in a 2001 Science paper .
When he investigated , Chang was horrified to discover that a homemade data-analysis program had flipped two columns of data , inverting the electron-density map from which his team had derived the final protein structure .
Unfortunately , his group had used the program to analyze data for other proteins .
As a result , on page 1875 , Chang and his colleagues retract three Science papers and report that two papers in other journals also contain erroneous structures .
( from a Science [ sciencemag.org ] news article ( subscription required to view full article ) : Of course , there were other factors that caused this situation ( because the proteins are notoriously difficult to work with , the data were fairly poor quality .
Had the data quality been better , Chang would have likely realized the mistakes prior to publishing the papers ) .
However , it is sobering to note the resources wasted on research following up on these incorrect structures produced by a simple coding error ( I know a few people whose entire theses were invalidated by these retractions ) .It is , however , unclear whether releasing the data analysis code would have fixed this situation .
The software for analyzing x-ray diffraction data is fairly standard ( I do n't know why Chang was using his own homemade software ) and various open-source software are available .
Furthermore , in his field , it is common to release the raw diffraction data ( I 'm not sure if it was released in the case of these five structures ) , so it may have been possible for others to double check his work with their own analysis software .
Perhaps the greater error here is in Chang , the peer reviewers of his publications , and the scientific community for believing Chang 's conclusions ( based on relatively poor quality diffraction data ) over the conclusions of many other researches whose techniques may not have been as sophisticated , but who had generated data of much higher quality .</tokentext>
<sentencetext>A good example of how disastrous one error in data analysis code can be comes from the field of biochemistry, specifically analyzing the x-ray diffraction patterns from crystallized proteins to determine the three dimensional structure of the proteins.
Geoff Chang, faculty at the prestigious Scripps Research Institute in San Diego, had published a series of landmark papers describing the structures of various important membrane proteins, whose structures had never been solved before.
Although these results did not mesh other researchers' models for how these proteins worked, many researchers used Chang's structures as starting points to develop and test new models for how these proteins might work.
However, in 2006, things came crashing down:In September, Swiss researchers published a paper in Nature that cast serious doubt on a protein structure Chang's group had described in a 2001 Science paper.
When he investigated, Chang was horrified to discover that a homemade data-analysis program had flipped two columns of data, inverting the electron-density map from which his team had derived the final protein structure.
Unfortunately, his group had used the program to analyze data for other proteins.
As a result, on page 1875, Chang and his colleagues retract three Science papers and report that two papers in other journals also contain erroneous structures.
(from a  Science  [sciencemag.org] news article (subscription required to view full article):Of course, there were other factors that caused this situation (because the proteins are notoriously difficult to work with, the data were fairly poor quality.
Had the data quality been better, Chang would have likely realized the mistakes prior to publishing the papers).
However, it is sobering to note the resources wasted on research following up on these incorrect structures produced by a simple coding error (I know a few people whose entire theses were invalidated by these retractions).It is, however, unclear whether releasing the data analysis code would have fixed this situation.
The software for analyzing x-ray diffraction data is fairly standard (I don't know why Chang was using his own homemade software) and various open-source software are available.
Furthermore, in his field, it is common to release the raw diffraction data (I'm not sure if it was released in the case of these five structures), so it may have been possible for others to double check his work with their own analysis software.
Perhaps the greater error here is in Chang, the peer reviewers of his publications, and the scientific community for believing Chang's conclusions (based on relatively poor quality diffraction data) over the conclusions of many other researches whose techniques may not have been as sophisticated, but who had generated data of much higher quality.
	</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073244</id>
	<title>Undeclared function prototypes a source of error??</title>
	<author>Anonymous</author>
	<datestamp>1265736120000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>People are taking the article the wrong way if you actually read it you will see that most of the errors are "Undeclared function prototypes". I hardly see how that can scientifically effect the outcome of any result. Next, the article is awful in that it hardly defines what it is saying at any moment, it doesn't mention actual programs except Motif and X11??? Are you serious? Since when is X11 a scientific program?</p></htmltext>
<tokenext>People are taking the article the wrong way if you actually read it you will see that most of the errors are " Undeclared function prototypes " .
I hardly see how that can scientifically effect the outcome of any result .
Next , the article is awful in that it hardly defines what it is saying at any moment , it does n't mention actual programs except Motif and X11 ? ? ?
Are you serious ?
Since when is X11 a scientific program ?</tokentext>
<sentencetext>People are taking the article the wrong way if you actually read it you will see that most of the errors are "Undeclared function prototypes".
I hardly see how that can scientifically effect the outcome of any result.
Next, the article is awful in that it hardly defines what it is saying at any moment, it doesn't mention actual programs except Motif and X11???
Are you serious?
Since when is X11 a scientific program?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072396</id>
	<title>Re:Slashdot Egocentrism.</title>
	<author>FlyingBishop</author>
	<datestamp>1265732760000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext><p>What's your point? If a Biologist has no understanding of code, they have no business running a simulation of an ecological system. If a physicist has no understanding of code, they have no business writing software to simulate atomic processes. If a Geneticist has no understanding of code, they have no business writing software that does pattern matching across genes.</p><p>Those who don't want to write software to aid in their research may continue not to do so (and continue to lose relevance.) But if they're going to use software, they have to use best practices. To do otherwise likewise makes their work quickly fading in relevance.</p></htmltext>
<tokenext>What 's your point ?
If a Biologist has no understanding of code , they have no business running a simulation of an ecological system .
If a physicist has no understanding of code , they have no business writing software to simulate atomic processes .
If a Geneticist has no understanding of code , they have no business writing software that does pattern matching across genes.Those who do n't want to write software to aid in their research may continue not to do so ( and continue to lose relevance .
) But if they 're going to use software , they have to use best practices .
To do otherwise likewise makes their work quickly fading in relevance .</tokentext>
<sentencetext>What's your point?
If a Biologist has no understanding of code, they have no business running a simulation of an ecological system.
If a physicist has no understanding of code, they have no business writing software to simulate atomic processes.
If a Geneticist has no understanding of code, they have no business writing software that does pattern matching across genes.Those who don't want to write software to aid in their research may continue not to do so (and continue to lose relevance.
) But if they're going to use software, they have to use best practices.
To do otherwise likewise makes their work quickly fading in relevance.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072056</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072586</id>
	<title>This should probably be tagged RANDU</title>
	<author>Anonymous</author>
	<datestamp>1265733600000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>After the flawed pseudorandom number algorithm whose use may have invalidated quite a few statistical simulations.</p></htmltext>
<tokenext>After the flawed pseudorandom number algorithm whose use may have invalidated quite a few statistical simulations .</tokentext>
<sentencetext>After the flawed pseudorandom number algorithm whose use may have invalidated quite a few statistical simulations.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071948</id>
	<title>About time!</title>
	<author>Anonymous</author>
	<datestamp>1265730600000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>5</modscore>
	<htmltext><p>The scientific community needs to get as far as we can from the policies of companies like Gaussian Inc., who will <a href="http://www.bannedbygaussian.org/" title="bannedbygaussian.org" rel="nofollow">ban</a> [bannedbygaussian.org] you and your institution for simply publishing any sort of comparative statistics on calculation time, accuracy, etc. from their computational chemistry software.</p><p>  I can't imagine what they'd do to you if you started sorting through their code...</p></htmltext>
<tokenext>The scientific community needs to get as far as we can from the policies of companies like Gaussian Inc. , who will ban [ bannedbygaussian.org ] you and your institution for simply publishing any sort of comparative statistics on calculation time , accuracy , etc .
from their computational chemistry software .
I ca n't imagine what they 'd do to you if you started sorting through their code.. .</tokentext>
<sentencetext>The scientific community needs to get as far as we can from the policies of companies like Gaussian Inc., who will ban [bannedbygaussian.org] you and your institution for simply publishing any sort of comparative statistics on calculation time, accuracy, etc.
from their computational chemistry software.
I can't imagine what they'd do to you if you started sorting through their code...</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31077940</id>
	<title>Re:Code isn't good enough.</title>
	<author>wfolta</author>
	<datestamp>1265710260000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Yes, that's one of the things I dislike in Machine Learning and Computer Vision: the lingua franca seems to be Matlab. Ugh. An ugly, primitive language with a culture that seems to value Perlesque code obfuscation and the proprietary lock-in you get with Matlab. Octave is helpful, and at least if the Matlab code is published you stand a chance of reproducing the experiment in a reasonable alternative. I'm the odd man out, though, as I've used R throughout graduate school, even for ML and Biometrics classes.</p></htmltext>
<tokenext>Yes , that 's one of the things I dislike in Machine Learning and Computer Vision : the lingua franca seems to be Matlab .
Ugh. An ugly , primitive language with a culture that seems to value Perlesque code obfuscation and the proprietary lock-in you get with Matlab .
Octave is helpful , and at least if the Matlab code is published you stand a chance of reproducing the experiment in a reasonable alternative .
I 'm the odd man out , though , as I 've used R throughout graduate school , even for ML and Biometrics classes .</tokentext>
<sentencetext>Yes, that's one of the things I dislike in Machine Learning and Computer Vision: the lingua franca seems to be Matlab.
Ugh. An ugly, primitive language with a culture that seems to value Perlesque code obfuscation and the proprietary lock-in you get with Matlab.
Octave is helpful, and at least if the Matlab code is published you stand a chance of reproducing the experiment in a reasonable alternative.
I'm the odd man out, though, as I've used R throughout graduate school, even for ML and Biometrics classes.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072290</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074286</id>
	<title>Not necessary</title>
	<author>Sycraft-fu</author>
	<datestamp>1265739660000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>The problem isn't so much one of not releasing source code, but not releasing any code at all, not releasing the methods used. If someone uses an excel sheet to do calculations and releases that sheet, that's good enough. You can then test it and see how it works. You don't need to audit the excel code, you only need to verify that the results you are getting are valid.</p><p>What is important is full disclosure of methods. Someone else should be able to replicate your findings independently. That means you need to disclose all your data (and how you obtained it) as well as all your methods. Well, of your wrote custom code, that code would be part of your methods. If you used an off the shelf program, say which one.</p><p>In the case of the Excel situation so long as they released the excel sheet everything would be fine. You could of course load it up in excel yourself and see what happened. You could also test excel if you though there was a bug with your own data. You could take the calculations they used in excel and put them in to OO or SPSS or whatever other calculations package you liked and see if the result was the same. You could even do it by hand, if you had the time.</p><p>The problem starts when methods and/or data are kept hidden away. When there is a "We analyzed this data using our special program and got this result but no you can't see it," situation. The experiment can't be replicated at that point, and there's all sorts of room for error. On point with the climate thing would be the "hockey stick" program. When it was analyzed, by running it not by looking at the source, it turned out the thing just liked to generate graphs that curved up like a hockey stick, regardless of the data input. Ok well clearly there was a problem with the method, the code. Doesn't really matter what that is, you don't need to audit the code and find it, just to find out that the method was flawed, so the conclusion doesn't follow the data.</p></htmltext>
<tokenext>The problem is n't so much one of not releasing source code , but not releasing any code at all , not releasing the methods used .
If someone uses an excel sheet to do calculations and releases that sheet , that 's good enough .
You can then test it and see how it works .
You do n't need to audit the excel code , you only need to verify that the results you are getting are valid.What is important is full disclosure of methods .
Someone else should be able to replicate your findings independently .
That means you need to disclose all your data ( and how you obtained it ) as well as all your methods .
Well , of your wrote custom code , that code would be part of your methods .
If you used an off the shelf program , say which one.In the case of the Excel situation so long as they released the excel sheet everything would be fine .
You could of course load it up in excel yourself and see what happened .
You could also test excel if you though there was a bug with your own data .
You could take the calculations they used in excel and put them in to OO or SPSS or whatever other calculations package you liked and see if the result was the same .
You could even do it by hand , if you had the time.The problem starts when methods and/or data are kept hidden away .
When there is a " We analyzed this data using our special program and got this result but no you ca n't see it , " situation .
The experiment ca n't be replicated at that point , and there 's all sorts of room for error .
On point with the climate thing would be the " hockey stick " program .
When it was analyzed , by running it not by looking at the source , it turned out the thing just liked to generate graphs that curved up like a hockey stick , regardless of the data input .
Ok well clearly there was a problem with the method , the code .
Does n't really matter what that is , you do n't need to audit the code and find it , just to find out that the method was flawed , so the conclusion does n't follow the data .</tokentext>
<sentencetext>The problem isn't so much one of not releasing source code, but not releasing any code at all, not releasing the methods used.
If someone uses an excel sheet to do calculations and releases that sheet, that's good enough.
You can then test it and see how it works.
You don't need to audit the excel code, you only need to verify that the results you are getting are valid.What is important is full disclosure of methods.
Someone else should be able to replicate your findings independently.
That means you need to disclose all your data (and how you obtained it) as well as all your methods.
Well, of your wrote custom code, that code would be part of your methods.
If you used an off the shelf program, say which one.In the case of the Excel situation so long as they released the excel sheet everything would be fine.
You could of course load it up in excel yourself and see what happened.
You could also test excel if you though there was a bug with your own data.
You could take the calculations they used in excel and put them in to OO or SPSS or whatever other calculations package you liked and see if the result was the same.
You could even do it by hand, if you had the time.The problem starts when methods and/or data are kept hidden away.
When there is a "We analyzed this data using our special program and got this result but no you can't see it," situation.
The experiment can't be replicated at that point, and there's all sorts of room for error.
On point with the climate thing would be the "hockey stick" program.
When it was analyzed, by running it not by looking at the source, it turned out the thing just liked to generate graphs that curved up like a hockey stick, regardless of the data input.
Ok well clearly there was a problem with the method, the code.
Doesn't really matter what that is, you don't need to audit the code and find it, just to find out that the method was flawed, so the conclusion doesn't follow the data.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072296</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31080788</id>
	<title>Re:Not a good idea</title>
	<author>ralphbecket</author>
	<datestamp>1265724360000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Hmm, you should contact the econometrics journals which require all code and data to be submitted alongside articles.</p><p>As I understand it, even Nature requires something similar, although for some reason climate scientists seem to be given a free pass.</p></htmltext>
<tokenext>Hmm , you should contact the econometrics journals which require all code and data to be submitted alongside articles.As I understand it , even Nature requires something similar , although for some reason climate scientists seem to be given a free pass .</tokentext>
<sentencetext>Hmm, you should contact the econometrics journals which require all code and data to be submitted alongside articles.As I understand it, even Nature requires something similar, although for some reason climate scientists seem to be given a free pass.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072364</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071944</id>
	<title>Stuff like Sweave</title>
	<author>langelgjm</author>
	<datestamp>1265730540000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>3</modscore>
	<htmltext><p>Much quantitative academic and scientific work could benefit from the use of tools like <a href="http://en.wikipedia.org/wiki/Sweave" title="wikipedia.org">Sweave,</a> [wikipedia.org] which allows you to embed the code used to produce statistical analyses within your LaTeX document. This makes your research easier to reproduce, both for yourself (when you've forgotten what you've done six months from now) and others.</p><p>What other kinds of tools like this are<nobr> <wbr></nobr>/.ers familiar with?</p></htmltext>
<tokenext>Much quantitative academic and scientific work could benefit from the use of tools like Sweave , [ wikipedia.org ] which allows you to embed the code used to produce statistical analyses within your LaTeX document .
This makes your research easier to reproduce , both for yourself ( when you 've forgotten what you 've done six months from now ) and others.What other kinds of tools like this are /.ers familiar with ?</tokentext>
<sentencetext>Much quantitative academic and scientific work could benefit from the use of tools like Sweave, [wikipedia.org] which allows you to embed the code used to produce statistical analyses within your LaTeX document.
This makes your research easier to reproduce, both for yourself (when you've forgotten what you've done six months from now) and others.What other kinds of tools like this are /.ers familiar with?</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31076462</id>
	<title>In the word of Feynman</title>
	<author>BlueParrot</author>
	<datestamp>1265747460000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>"Philosophy of science is about as important to scientists as ornithology is to birds." - Richard Feynman</p><p>You know how you guys usually cringe when some clueless Economist or Law professor wants to introduce some new law for how the internet should work? Like demanding that all TCP connections be logged and the data kept for 10 years ( or something even more stupid ).</p><p>Well a fair share of you should now know exactly why they do this, because you keep doing the exact same thing every time a Slashdot article about science is published.  To put it simply, if you're one of the idiots who thinks its a good idea to demand that every science paper to be published should document everything right down to what color of toilet paper the researchers used to blow their noses, then you never again get to complain when management wants all decisions to be accompanied with a cost-benefit analysis.</p></htmltext>
<tokenext>" Philosophy of science is about as important to scientists as ornithology is to birds .
" - Richard FeynmanYou know how you guys usually cringe when some clueless Economist or Law professor wants to introduce some new law for how the internet should work ?
Like demanding that all TCP connections be logged and the data kept for 10 years ( or something even more stupid ) .Well a fair share of you should now know exactly why they do this , because you keep doing the exact same thing every time a Slashdot article about science is published .
To put it simply , if you 're one of the idiots who thinks its a good idea to demand that every science paper to be published should document everything right down to what color of toilet paper the researchers used to blow their noses , then you never again get to complain when management wants all decisions to be accompanied with a cost-benefit analysis .</tokentext>
<sentencetext>"Philosophy of science is about as important to scientists as ornithology is to birds.
" - Richard FeynmanYou know how you guys usually cringe when some clueless Economist or Law professor wants to introduce some new law for how the internet should work?
Like demanding that all TCP connections be logged and the data kept for 10 years ( or something even more stupid ).Well a fair share of you should now know exactly why they do this, because you keep doing the exact same thing every time a Slashdot article about science is published.
To put it simply, if you're one of the idiots who thinks its a good idea to demand that every science paper to be published should document everything right down to what color of toilet paper the researchers used to blow their noses, then you never again get to complain when management wants all decisions to be accompanied with a cost-benefit analysis.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074192</id>
	<title>Losing significant digits? Then RTFM.</title>
	<author>rnturn</author>
	<datestamp>1265739300000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><blockquote><div><p> <i>"For example, interface inconsistencies between software modules which pass data from one part of a program to another occurred at the rate of one in every seven interfaces on average in the programming language Fortran, and one in every 37 interfaces in the language C. This is hugely worrying when you realise that just one error -- just one -- will usually invalidate a computer program. What he also discovered, even more worryingly, is that the accuracy of results declined from six significant figures to one significant figure during the running of programs.'"</i></p></div> </blockquote><p>The best way to keep this from happening is to avoid passing formatted, human-readable data between programs. That's what FORTRAN's unformatted I/O was meant for. Same thing for C. Don't convert to a convenient human-readable form until the very end.</p></div>
	</htmltext>
<tokenext>" For example , interface inconsistencies between software modules which pass data from one part of a program to another occurred at the rate of one in every seven interfaces on average in the programming language Fortran , and one in every 37 interfaces in the language C. This is hugely worrying when you realise that just one error -- just one -- will usually invalidate a computer program .
What he also discovered , even more worryingly , is that the accuracy of results declined from six significant figures to one significant figure during the running of programs .
' " The best way to keep this from happening is to avoid passing formatted , human-readable data between programs .
That 's what FORTRAN 's unformatted I/O was meant for .
Same thing for C. Do n't convert to a convenient human-readable form until the very end .</tokentext>
<sentencetext> "For example, interface inconsistencies between software modules which pass data from one part of a program to another occurred at the rate of one in every seven interfaces on average in the programming language Fortran, and one in every 37 interfaces in the language C. This is hugely worrying when you realise that just one error -- just one -- will usually invalidate a computer program.
What he also discovered, even more worryingly, is that the accuracy of results declined from six significant figures to one significant figure during the running of programs.
'" The best way to keep this from happening is to avoid passing formatted, human-readable data between programs.
That's what FORTRAN's unformatted I/O was meant for.
Same thing for C. Don't convert to a convenient human-readable form until the very end.
	</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072704</id>
	<title>Re:MaDnEsS !</title>
	<author>Anonymous</author>
	<datestamp>1265734080000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p><div class="quote"><p>What? Scientists showing their work for peer-review?</p><p>It's MADNESS I tell you. MADNESS !</p></div><p>Madness?  THIS IS SCIENCE!</p></div>
	</htmltext>
<tokenext>What ?
Scientists showing their work for peer-review ? It 's MADNESS I tell you .
MADNESS ! Madness ?
THIS IS SCIENCE !</tokentext>
<sentencetext>What?
Scientists showing their work for peer-review?It's MADNESS I tell you.
MADNESS !Madness?
THIS IS SCIENCE!
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071998</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073764</id>
	<title>Re:That's all wrong</title>
	<author>aflag</author>
	<datestamp>1265737860000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>If not even you can reproduce your own research, what does it tell you about your metodology?</htmltext>
<tokenext>If not even you can reproduce your own research , what does it tell you about your metodology ?</tokentext>
<sentencetext>If not even you can reproduce your own research, what does it tell you about your metodology?</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072140</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073218</id>
	<title>Re:Not a good idea</title>
	<author>John Hasler</author>
	<datestamp>1265736000000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>&gt; What you end up with is no-one having any confidence in the results - as<br>&gt; they have only ever been produced in one way...</p><p>Software does not produce results.  Experiments produce results.  Software assists with the math required to analyze those results.  We are asking that you publish all the steps in your analysis.  That means publishing the software.</p></htmltext>
<tokenext>&gt; What you end up with is no-one having any confidence in the results - as &gt; they have only ever been produced in one way...Software does not produce results .
Experiments produce results .
Software assists with the math required to analyze those results .
We are asking that you publish all the steps in your analysis .
That means publishing the software .</tokentext>
<sentencetext>&gt; What you end up with is no-one having any confidence in the results - as&gt; they have only ever been produced in one way...Software does not produce results.
Experiments produce results.
Software assists with the math required to analyze those results.
We are asking that you publish all the steps in your analysis.
That means publishing the software.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072364</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31076134</id>
	<title>Re:Observations...</title>
	<author>Anonymous</author>
	<datestamp>1265746140000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>&gt; (and explicitly avoided the GPL)</p><p>this is probably the most boneheaded decision you will make this year.</p><p>read the damn thing instead of relying on biases.</p><p>you still own the copyright to your code and can, in parallel, sell it without restriction to the highest bidder. but 3rd parties can not.</p><p>long live the GPL and the scientific method, they go hand in hand.<br>rah rah</p></htmltext>
<tokenext>&gt; ( and explicitly avoided the GPL ) this is probably the most boneheaded decision you will make this year.read the damn thing instead of relying on biases.you still own the copyright to your code and can , in parallel , sell it without restriction to the highest bidder .
but 3rd parties can not.long live the GPL and the scientific method , they go hand in hand.rah rah</tokentext>
<sentencetext>&gt; (and explicitly avoided the GPL)this is probably the most boneheaded decision you will make this year.read the damn thing instead of relying on biases.you still own the copyright to your code and can, in parallel, sell it without restriction to the highest bidder.
but 3rd parties can not.long live the GPL and the scientific method, they go hand in hand.rah rah</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072268</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31085724</id>
	<title>Re:Wolfram Alpha, IDL, MATLAB, etc.?</title>
	<author>quadelirus</author>
	<datestamp>1265039820000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>I feel somewhat the same way as you about cleaning up code. But forget about the public. It is too important that other researchers be able to evaluate and use the code. For instance, let's say I don't really want to verify that your work is correct, but I want to build on it. If your code is not available I have to duplicate effort and work through all the annoying engineering details that you, presumably, have already solved in order to get to the same place as you were when you published, just so I can test an addition to your ideas. If you released the code, however, this would not be the case. I could download your code and work from there. Not releasing the code hinders scientific advancement and the only benefit is that you (or me, I do it too) can hide your sloppy code, or worse, you can protect your sub-area of research by making the cost to enter to high for another research group. I say this because there are some interesting areas of research in my field that I would like to enter but I've been warned to stay away because to catch up would take 1-2 years of straight coding without any publishing. Why? Because in some areas you need extensive frameworks of code just to be able to do research (let's not even talk verification). This means that the one or two groups that started in these areas early are the only ones investigating. If there code were open, then anyone would have the ability to start adding to the body of knowledge on the subject and advancement would accelerate.</htmltext>
<tokenext>I feel somewhat the same way as you about cleaning up code .
But forget about the public .
It is too important that other researchers be able to evaluate and use the code .
For instance , let 's say I do n't really want to verify that your work is correct , but I want to build on it .
If your code is not available I have to duplicate effort and work through all the annoying engineering details that you , presumably , have already solved in order to get to the same place as you were when you published , just so I can test an addition to your ideas .
If you released the code , however , this would not be the case .
I could download your code and work from there .
Not releasing the code hinders scientific advancement and the only benefit is that you ( or me , I do it too ) can hide your sloppy code , or worse , you can protect your sub-area of research by making the cost to enter to high for another research group .
I say this because there are some interesting areas of research in my field that I would like to enter but I 've been warned to stay away because to catch up would take 1-2 years of straight coding without any publishing .
Why ? Because in some areas you need extensive frameworks of code just to be able to do research ( let 's not even talk verification ) .
This means that the one or two groups that started in these areas early are the only ones investigating .
If there code were open , then anyone would have the ability to start adding to the body of knowledge on the subject and advancement would accelerate .</tokentext>
<sentencetext>I feel somewhat the same way as you about cleaning up code.
But forget about the public.
It is too important that other researchers be able to evaluate and use the code.
For instance, let's say I don't really want to verify that your work is correct, but I want to build on it.
If your code is not available I have to duplicate effort and work through all the annoying engineering details that you, presumably, have already solved in order to get to the same place as you were when you published, just so I can test an addition to your ideas.
If you released the code, however, this would not be the case.
I could download your code and work from there.
Not releasing the code hinders scientific advancement and the only benefit is that you (or me, I do it too) can hide your sloppy code, or worse, you can protect your sub-area of research by making the cost to enter to high for another research group.
I say this because there are some interesting areas of research in my field that I would like to enter but I've been warned to stay away because to catch up would take 1-2 years of straight coding without any publishing.
Why? Because in some areas you need extensive frameworks of code just to be able to do research (let's not even talk verification).
This means that the one or two groups that started in these areas early are the only ones investigating.
If there code were open, then anyone would have the ability to start adding to the body of knowledge on the subject and advancement would accelerate.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073594</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072344</id>
	<title>Also true for CS research</title>
	<author>Anonymous</author>
	<datestamp>1265732520000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>2</modscore>
	<htmltext><p>I'm working on my dissertation proposal, and I'd like to be able to re-run the benchmarks that are shown in some of the papers I'm referencing.  But must of the source code for those papers has disappeared into the aether.  Without their code, it's impossible for me to rerun the old benchmark programs on modern computers so that I and others can determine whether or not my research has uncovered a better way of doing things.  This is very far from the idealized notion of the scientific method, and significantly calls into question many of the things that we think we know based on published research.</p></htmltext>
<tokenext>I 'm working on my dissertation proposal , and I 'd like to be able to re-run the benchmarks that are shown in some of the papers I 'm referencing .
But must of the source code for those papers has disappeared into the aether .
Without their code , it 's impossible for me to rerun the old benchmark programs on modern computers so that I and others can determine whether or not my research has uncovered a better way of doing things .
This is very far from the idealized notion of the scientific method , and significantly calls into question many of the things that we think we know based on published research .</tokentext>
<sentencetext>I'm working on my dissertation proposal, and I'd like to be able to re-run the benchmarks that are shown in some of the papers I'm referencing.
But must of the source code for those papers has disappeared into the aether.
Without their code, it's impossible for me to rerun the old benchmark programs on modern computers so that I and others can determine whether or not my research has uncovered a better way of doing things.
This is very far from the idealized notion of the scientific method, and significantly calls into question many of the things that we think we know based on published research.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073056</id>
	<title>Re:About time!</title>
	<author>je ne sais quoi</author>
	<datestamp>1265735460000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>2</modscore>
	<htmltext>One thing to point out is that there are now plenty of open source codes available for doing similar things as gaussian so it can be avoided now with relative ease.  Two that come to mind are the the Department of Energy funded codes: <a href="http://www.emsl.pnl.gov/capabilities/computing/nwchem/" title="pnl.gov">nwchem</a> [pnl.gov] for ab initio work and <a href="http://lammps.sandia.gov/" title="sandia.gov">lammps</a> [sandia.gov] for molecular dynamics.  I use the NIH funded code <a href="http://www.ks.uiuc.edu/Research/vmd/" title="uiuc.edu">vmd</a> [uiuc.edu] for visualization.  The best part about those codes is that they're designed to be compiled using gcc and run on linux so you can get off the non-open source software train all together if you wish.</htmltext>
<tokenext>One thing to point out is that there are now plenty of open source codes available for doing similar things as gaussian so it can be avoided now with relative ease .
Two that come to mind are the the Department of Energy funded codes : nwchem [ pnl.gov ] for ab initio work and lammps [ sandia.gov ] for molecular dynamics .
I use the NIH funded code vmd [ uiuc.edu ] for visualization .
The best part about those codes is that they 're designed to be compiled using gcc and run on linux so you can get off the non-open source software train all together if you wish .</tokentext>
<sentencetext>One thing to point out is that there are now plenty of open source codes available for doing similar things as gaussian so it can be avoided now with relative ease.
Two that come to mind are the the Department of Energy funded codes: nwchem [pnl.gov] for ab initio work and lammps [sandia.gov] for molecular dynamics.
I use the NIH funded code vmd [uiuc.edu] for visualization.
The best part about those codes is that they're designed to be compiled using gcc and run on linux so you can get off the non-open source software train all together if you wish.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071948</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31082022</id>
	<title>Re:Conspiracy?</title>
	<author>Anonymous</author>
	<datestamp>1265736540000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p><div class="quote"><p>Let's think through what would really happen if scientists released their code. The code has bugs, as all code does. People with an ulterior motive would point to the bugs and say "Look here! A bug! The science cannot be trusted!" And millions of sheeple would repeat "Yes! The code has bugs! And therefore I refuse to believe it!" It won't matter whether the bugs are relevant to the science; the fact that there are any bugs at all will cause people who want to disagree to say there's doubt about the results. Meanwhile, they will go about their business using computer systems that are riddled with bugs, but function well enough the vast majority of the time they're not even aware of the bugs.</p></div><p>By your logic, we shouldn't release the data you gathered either, based on the fear someone might not understand what a bad data point is and say "Look here! You're ignoring evidence!".</p><p>Every argument I've heard in this thread boils down to:</p><p>Do not look behind the curtain. Place your Faith and Trust in the established Order of Scientists.</p><p>If I wanted that line of bullshit I'd go to church. If you aren't providing the facts, you're asking me to believe you based on faith, and that's not science, it's religion.</p></div>
	</htmltext>
<tokenext>Let 's think through what would really happen if scientists released their code .
The code has bugs , as all code does .
People with an ulterior motive would point to the bugs and say " Look here !
A bug !
The science can not be trusted !
" And millions of sheeple would repeat " Yes !
The code has bugs !
And therefore I refuse to believe it !
" It wo n't matter whether the bugs are relevant to the science ; the fact that there are any bugs at all will cause people who want to disagree to say there 's doubt about the results .
Meanwhile , they will go about their business using computer systems that are riddled with bugs , but function well enough the vast majority of the time they 're not even aware of the bugs.By your logic , we should n't release the data you gathered either , based on the fear someone might not understand what a bad data point is and say " Look here !
You 're ignoring evidence !
" .Every argument I 've heard in this thread boils down to : Do not look behind the curtain .
Place your Faith and Trust in the established Order of Scientists.If I wanted that line of bullshit I 'd go to church .
If you are n't providing the facts , you 're asking me to believe you based on faith , and that 's not science , it 's religion .</tokentext>
<sentencetext>Let's think through what would really happen if scientists released their code.
The code has bugs, as all code does.
People with an ulterior motive would point to the bugs and say "Look here!
A bug!
The science cannot be trusted!
" And millions of sheeple would repeat "Yes!
The code has bugs!
And therefore I refuse to believe it!
" It won't matter whether the bugs are relevant to the science; the fact that there are any bugs at all will cause people who want to disagree to say there's doubt about the results.
Meanwhile, they will go about their business using computer systems that are riddled with bugs, but function well enough the vast majority of the time they're not even aware of the bugs.By your logic, we shouldn't release the data you gathered either, based on the fear someone might not understand what a bad data point is and say "Look here!
You're ignoring evidence!
".Every argument I've heard in this thread boils down to:Do not look behind the curtain.
Place your Faith and Trust in the established Order of Scientists.If I wanted that line of bullshit I'd go to church.
If you aren't providing the facts, you're asking me to believe you based on faith, and that's not science, it's religion.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072358</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31083356</id>
	<title>Anonymous Coward</title>
	<author>Anonymous</author>
	<datestamp>1265019060000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>Not so anonymous: I am Darrel Ince who wrote the article. It has generated a lot of reaction. It is a really tricky subject which 800 words in an article does no justice to. A major point is that there are a number of valid reasons why someone will refuse to divulge their code which seems fine by me: commercial agreements, the issue of intelelctual property rights (something which clouded the whole issue of the hockey stick code). Also there is the problem that developing computer code is tough and a scientist should be allowed time to develop publications from the work; Steve Scneider of MIT has suggested a two year moratorium.</p><p>There is also the problem of a vexatious demands. As far as I am concerned if you have released the code and it is complete then that is it. The recipient is on their own. The computer is chaning so much about science that one of the good things that has come out of the CRU incident is that it has highlighted it and the work that fourth paradigm people are doing.</p><p>Darrel Ince</p></htmltext>
<tokenext>Not so anonymous : I am Darrel Ince who wrote the article .
It has generated a lot of reaction .
It is a really tricky subject which 800 words in an article does no justice to .
A major point is that there are a number of valid reasons why someone will refuse to divulge their code which seems fine by me : commercial agreements , the issue of intelelctual property rights ( something which clouded the whole issue of the hockey stick code ) .
Also there is the problem that developing computer code is tough and a scientist should be allowed time to develop publications from the work ; Steve Scneider of MIT has suggested a two year moratorium.There is also the problem of a vexatious demands .
As far as I am concerned if you have released the code and it is complete then that is it .
The recipient is on their own .
The computer is chaning so much about science that one of the good things that has come out of the CRU incident is that it has highlighted it and the work that fourth paradigm people are doing.Darrel Ince</tokentext>
<sentencetext>Not so anonymous: I am Darrel Ince who wrote the article.
It has generated a lot of reaction.
It is a really tricky subject which 800 words in an article does no justice to.
A major point is that there are a number of valid reasons why someone will refuse to divulge their code which seems fine by me: commercial agreements, the issue of intelelctual property rights (something which clouded the whole issue of the hockey stick code).
Also there is the problem that developing computer code is tough and a scientist should be allowed time to develop publications from the work; Steve Scneider of MIT has suggested a two year moratorium.There is also the problem of a vexatious demands.
As far as I am concerned if you have released the code and it is complete then that is it.
The recipient is on their own.
The computer is chaning so much about science that one of the good things that has come out of the CRU incident is that it has highlighted it and the work that fourth paradigm people are doing.Darrel Ince</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31077588</id>
	<title>Never trust code</title>
	<author>drizzd</author>
	<datestamp>1265708700000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>It is already common knowledge among researches that simulated results can not be trusted. A program is only as good as it is tested. Only for scientific programs, testing is not usually as trivial as with application software. For example, you may have to analyze a system statistically and verify that the simulation results match the expected statistics. The scientific value is in that analysis and simulation results verified against such an analysis.

While I welcome the idea of making the code used in scientific work public, I believe a much better reason to do so is that other researchers can improve on it. Of course, research is not always meant to be for the common good...</htmltext>
<tokenext>It is already common knowledge among researches that simulated results can not be trusted .
A program is only as good as it is tested .
Only for scientific programs , testing is not usually as trivial as with application software .
For example , you may have to analyze a system statistically and verify that the simulation results match the expected statistics .
The scientific value is in that analysis and simulation results verified against such an analysis .
While I welcome the idea of making the code used in scientific work public , I believe a much better reason to do so is that other researchers can improve on it .
Of course , research is not always meant to be for the common good.. .</tokentext>
<sentencetext>It is already common knowledge among researches that simulated results can not be trusted.
A program is only as good as it is tested.
Only for scientific programs, testing is not usually as trivial as with application software.
For example, you may have to analyze a system statistically and verify that the simulation results match the expected statistics.
The scientific value is in that analysis and simulation results verified against such an analysis.
While I welcome the idea of making the code used in scientific work public, I believe a much better reason to do so is that other researchers can improve on it.
Of course, research is not always meant to be for the common good...</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072378</id>
	<title>Recent example Keith Baggerly vs Duke Clin. Trials</title>
	<author>bloosqr</author>
	<datestamp>1265732700000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>If you ever get a chance take a look at some of Baggerly's (MD Anderson / bioinformatics/stats) analysis of the number of rather embarrassing mistakes were used in developing genomic biomarkers used for a clinical trial at Duke. He has been giving talks around at stats conferences (and pharma's about this), its one of the best talks i've heard in recent years. But what it boils down to is the analysis (and input) programs used by Duke had a series of fundamental mistakes in it causes the results to be incorrect leading to an incorrect conclusions which unfortunately lead to a series of clinical trials which certainly should not have happened. After Baggerly attempted to respond negatively to the original series of articles being posted he reposted in a stats journal and basically got the clinical trial shut down. For slashdot readers, one of the rather many egregious mistakes here was the analysis program used has in its instructions the need for a header line, the input the Duke researchers used did not include a  header line causing a shift in the results with regards to their input. My understanding is nature medicine refused to publish baggerlies initial correspondence with full details as it was "too negative" so he published in a stats journal which then got the critical coverage to shut everything down..</p><p>Here are some random links</p><p>Here is the original Potti genomics article:<br><a href="http://www.nature.com/nm/journal/v12/n11/abs/nm1491.html" title="nature.com">http://www.nature.com/nm/journal/v12/n11/abs/nm1491.html</a> [nature.com]</p><p>Here is one of the baggerly nature medicine letters describing what is wrong in summarized form:</p><p><a href="http://www.nature.com/nm/journal/v13/n11/full/nm1107-1276b.html" title="nature.com">http://www.nature.com/nm/journal/v13/n11/full/nm1107-1276b.html</a> [nature.com]</p><p>here is the halt of the trials :</p><p><a href="http://cancerletter.com/tcl-blog/copy108\_of\_whats-going-on-with-nih" title="cancerletter.com">http://cancerletter.com/tcl-blog/copy108\_of\_whats-going-on-with-nih</a> [cancerletter.com]</p><p><a href="http://cancerletter.com/tcl-blog/copy111\_of\_whats-going-on-with-nih" title="cancerletter.com">http://cancerletter.com/tcl-blog/copy111\_of\_whats-going-on-with-nih</a> [cancerletter.com]</p></htmltext>
<tokenext>If you ever get a chance take a look at some of Baggerly 's ( MD Anderson / bioinformatics/stats ) analysis of the number of rather embarrassing mistakes were used in developing genomic biomarkers used for a clinical trial at Duke .
He has been giving talks around at stats conferences ( and pharma 's about this ) , its one of the best talks i 've heard in recent years .
But what it boils down to is the analysis ( and input ) programs used by Duke had a series of fundamental mistakes in it causes the results to be incorrect leading to an incorrect conclusions which unfortunately lead to a series of clinical trials which certainly should not have happened .
After Baggerly attempted to respond negatively to the original series of articles being posted he reposted in a stats journal and basically got the clinical trial shut down .
For slashdot readers , one of the rather many egregious mistakes here was the analysis program used has in its instructions the need for a header line , the input the Duke researchers used did not include a header line causing a shift in the results with regards to their input .
My understanding is nature medicine refused to publish baggerlies initial correspondence with full details as it was " too negative " so he published in a stats journal which then got the critical coverage to shut everything down..Here are some random linksHere is the original Potti genomics article : http : //www.nature.com/nm/journal/v12/n11/abs/nm1491.html [ nature.com ] Here is one of the baggerly nature medicine letters describing what is wrong in summarized form : http : //www.nature.com/nm/journal/v13/n11/full/nm1107-1276b.html [ nature.com ] here is the halt of the trials : http : //cancerletter.com/tcl-blog/copy108 \ _of \ _whats-going-on-with-nih [ cancerletter.com ] http : //cancerletter.com/tcl-blog/copy111 \ _of \ _whats-going-on-with-nih [ cancerletter.com ]</tokentext>
<sentencetext>If you ever get a chance take a look at some of Baggerly's (MD Anderson / bioinformatics/stats) analysis of the number of rather embarrassing mistakes were used in developing genomic biomarkers used for a clinical trial at Duke.
He has been giving talks around at stats conferences (and pharma's about this), its one of the best talks i've heard in recent years.
But what it boils down to is the analysis (and input) programs used by Duke had a series of fundamental mistakes in it causes the results to be incorrect leading to an incorrect conclusions which unfortunately lead to a series of clinical trials which certainly should not have happened.
After Baggerly attempted to respond negatively to the original series of articles being posted he reposted in a stats journal and basically got the clinical trial shut down.
For slashdot readers, one of the rather many egregious mistakes here was the analysis program used has in its instructions the need for a header line, the input the Duke researchers used did not include a  header line causing a shift in the results with regards to their input.
My understanding is nature medicine refused to publish baggerlies initial correspondence with full details as it was "too negative" so he published in a stats journal which then got the critical coverage to shut everything down..Here are some random linksHere is the original Potti genomics article:http://www.nature.com/nm/journal/v12/n11/abs/nm1491.html [nature.com]Here is one of the baggerly nature medicine letters describing what is wrong in summarized form:http://www.nature.com/nm/journal/v13/n11/full/nm1107-1276b.html [nature.com]here is the halt of the trials :http://cancerletter.com/tcl-blog/copy108\_of\_whats-going-on-with-nih [cancerletter.com]http://cancerletter.com/tcl-blog/copy111\_of\_whats-going-on-with-nih [cancerletter.com]</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072812</id>
	<title>Re:Stuff like Sweave</title>
	<author>xtracto</author>
	<datestamp>1265734440000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>The problem with "adding code to paper" is the length of the paper.</p><p>I find it is better to submit the actual code into a "publisher repository" which can make it available in a long term basis (as opposed to have it in the researcher's web page, which is closed when they leave the position, or which the researcher himself can remove after some time).</p><p>Of course it may be useful to reproduce some snippets of the used algorithm in the article's text, however I won't suggest showing the actual code because not all the audience will know such notation (very likely outside Comp.Sci and Soft Eng. circles).</p></htmltext>
<tokenext>The problem with " adding code to paper " is the length of the paper.I find it is better to submit the actual code into a " publisher repository " which can make it available in a long term basis ( as opposed to have it in the researcher 's web page , which is closed when they leave the position , or which the researcher himself can remove after some time ) .Of course it may be useful to reproduce some snippets of the used algorithm in the article 's text , however I wo n't suggest showing the actual code because not all the audience will know such notation ( very likely outside Comp.Sci and Soft Eng .
circles ) .</tokentext>
<sentencetext>The problem with "adding code to paper" is the length of the paper.I find it is better to submit the actual code into a "publisher repository" which can make it available in a long term basis (as opposed to have it in the researcher's web page, which is closed when they leave the position, or which the researcher himself can remove after some time).Of course it may be useful to reproduce some snippets of the used algorithm in the article's text, however I won't suggest showing the actual code because not all the audience will know such notation (very likely outside Comp.Sci and Soft Eng.
circles).</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071944</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074164</id>
	<title>It's an old story</title>
	<author>jc42</author>
	<datestamp>1265739240000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>4</modscore>
	<htmltext><p><i> This is hugely worrying when you realise that just one error -- just one -- will usually invalidate a computer program.</i></p><p>Back in the 1970s, a bunch of CompSci guys at the university where I was a grad student did a software study with interesting results.  Much of the research computing was done on the university's mainframe, and the dominant language of course was Fortran.  They instrumented the Fortran compiler so that for a couple of months, it collected data on numeric overflows, including which overflows were or weren't detected by the code.  They published the results:  slightly over half the Fortran jobs had undetected overflows that affected their output.</p><p>The response to this was interesting.  The CS folks, as you might expect, were appalled.  But among the scientific researchers, the general response was that enabling overflow checking slowed down the code measurably, so it shouldn't be done.  I personally knew a lot of researchers (as one of the managers of an inter-departmental microcomputer lab that was independent of the central mainframe computer center).  I asked a lot of them about this, and I was appalled to find that almost every one of them agreed that overflow checking should be turned off if it slowed down the code.  The mainframe's managers reported that almost all Fortran compiles had overflow checking turned off.  Pointing out that this meant that fully half of the computed results in their published papers were wrong (if they used the mainframe) didn't have any effect.</p><p>Our small cabal that ran the microprocessor lab reacted to this by silently enabling all error checking in our Fortran compiler.  We even checked with the vendor to make sure that we'd set it up so that a user couldn't disable the checking.  We didn't announce that we had done this; we just did it on our own authority.  It was also done in a couple of other similar department-level labs that had their own computers (which was rare at the time).  But the major research computer on campus was the central mainframe, and the folks running it weren't interested in dealing with the problem.</p><p>It taught us a lot about how such things are done.  And it gave us a healthy level of skepticism about published research data.  It was a good lesson on why we have an ongoing need to duplicate research results independently before believing them.</p><p>It might be interesting to read about studies similar to this done more recently.  I haven't seen any, but maybe they're out there.</p></htmltext>
<tokenext>This is hugely worrying when you realise that just one error -- just one -- will usually invalidate a computer program.Back in the 1970s , a bunch of CompSci guys at the university where I was a grad student did a software study with interesting results .
Much of the research computing was done on the university 's mainframe , and the dominant language of course was Fortran .
They instrumented the Fortran compiler so that for a couple of months , it collected data on numeric overflows , including which overflows were or were n't detected by the code .
They published the results : slightly over half the Fortran jobs had undetected overflows that affected their output.The response to this was interesting .
The CS folks , as you might expect , were appalled .
But among the scientific researchers , the general response was that enabling overflow checking slowed down the code measurably , so it should n't be done .
I personally knew a lot of researchers ( as one of the managers of an inter-departmental microcomputer lab that was independent of the central mainframe computer center ) .
I asked a lot of them about this , and I was appalled to find that almost every one of them agreed that overflow checking should be turned off if it slowed down the code .
The mainframe 's managers reported that almost all Fortran compiles had overflow checking turned off .
Pointing out that this meant that fully half of the computed results in their published papers were wrong ( if they used the mainframe ) did n't have any effect.Our small cabal that ran the microprocessor lab reacted to this by silently enabling all error checking in our Fortran compiler .
We even checked with the vendor to make sure that we 'd set it up so that a user could n't disable the checking .
We did n't announce that we had done this ; we just did it on our own authority .
It was also done in a couple of other similar department-level labs that had their own computers ( which was rare at the time ) .
But the major research computer on campus was the central mainframe , and the folks running it were n't interested in dealing with the problem.It taught us a lot about how such things are done .
And it gave us a healthy level of skepticism about published research data .
It was a good lesson on why we have an ongoing need to duplicate research results independently before believing them.It might be interesting to read about studies similar to this done more recently .
I have n't seen any , but maybe they 're out there .</tokentext>
<sentencetext> This is hugely worrying when you realise that just one error -- just one -- will usually invalidate a computer program.Back in the 1970s, a bunch of CompSci guys at the university where I was a grad student did a software study with interesting results.
Much of the research computing was done on the university's mainframe, and the dominant language of course was Fortran.
They instrumented the Fortran compiler so that for a couple of months, it collected data on numeric overflows, including which overflows were or weren't detected by the code.
They published the results:  slightly over half the Fortran jobs had undetected overflows that affected their output.The response to this was interesting.
The CS folks, as you might expect, were appalled.
But among the scientific researchers, the general response was that enabling overflow checking slowed down the code measurably, so it shouldn't be done.
I personally knew a lot of researchers (as one of the managers of an inter-departmental microcomputer lab that was independent of the central mainframe computer center).
I asked a lot of them about this, and I was appalled to find that almost every one of them agreed that overflow checking should be turned off if it slowed down the code.
The mainframe's managers reported that almost all Fortran compiles had overflow checking turned off.
Pointing out that this meant that fully half of the computed results in their published papers were wrong (if they used the mainframe) didn't have any effect.Our small cabal that ran the microprocessor lab reacted to this by silently enabling all error checking in our Fortran compiler.
We even checked with the vendor to make sure that we'd set it up so that a user couldn't disable the checking.
We didn't announce that we had done this; we just did it on our own authority.
It was also done in a couple of other similar department-level labs that had their own computers (which was rare at the time).
But the major research computer on campus was the central mainframe, and the folks running it weren't interested in dealing with the problem.It taught us a lot about how such things are done.
And it gave us a healthy level of skepticism about published research data.
It was a good lesson on why we have an ongoing need to duplicate research results independently before believing them.It might be interesting to read about studies similar to this done more recently.
I haven't seen any, but maybe they're out there.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072578</id>
	<title>Re:Slashdot Egocentrism.</title>
	<author>Anonymous</author>
	<datestamp>1265733600000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>In my department (applied mechanics), that probably holds true for alot of cases (which is also very troubling, as anyway who reads your work will almost certainly want to look at the code eventually), but there definitely is a large part of egoism behind this as well.</p><p>I honestly don't understand why, almost all the times, the code they have been tinkering with for a decade is not even remotely good enough to be sold anyway. And they already have a good job that pays well, so most of them probably wants a good reputation to go with it. The easiest way to do this is to open up the code. Would I ever have heard of X and Y if it wasn't for them releasing their meshing or computational code in some FLOSS license? No fucking way.</p></htmltext>
<tokenext>In my department ( applied mechanics ) , that probably holds true for alot of cases ( which is also very troubling , as anyway who reads your work will almost certainly want to look at the code eventually ) , but there definitely is a large part of egoism behind this as well.I honestly do n't understand why , almost all the times , the code they have been tinkering with for a decade is not even remotely good enough to be sold anyway .
And they already have a good job that pays well , so most of them probably wants a good reputation to go with it .
The easiest way to do this is to open up the code .
Would I ever have heard of X and Y if it was n't for them releasing their meshing or computational code in some FLOSS license ?
No fucking way .</tokentext>
<sentencetext>In my department (applied mechanics), that probably holds true for alot of cases (which is also very troubling, as anyway who reads your work will almost certainly want to look at the code eventually), but there definitely is a large part of egoism behind this as well.I honestly don't understand why, almost all the times, the code they have been tinkering with for a decade is not even remotely good enough to be sold anyway.
And they already have a good job that pays well, so most of them probably wants a good reputation to go with it.
The easiest way to do this is to open up the code.
Would I ever have heard of X and Y if it wasn't for them releasing their meshing or computational code in some FLOSS license?
No fucking way.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072056</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31074004</id>
	<title>Re:Conspiracy?</title>
	<author>Anonymous</author>
	<datestamp>1265738640000</datestamp>
	<modclass>None</modclass>
	<modscore>0</modscore>
	<htmltext><p>But thats a slippery slope. Put yourself in the place of the person that you claim has an ulterior motive. Would you particularly like it if someone told you that "no you can't see the particular's because you'll nit-pick it and I know I am right". They may very well nit-pick and run with completely stupid results based solely on preconceived notions. You can't shield them from facts just because they might do this.</p><p>The Best approach is to release it and in advance explain the bugs that you know are there. If they find something you didn't know about, great they helped you. You might have to explain how the data wasn't corrupted by this but that is better than hiding it completely.</p><p>The goal is truth or fact. Not you being right.</p></htmltext>
<tokenext>But thats a slippery slope .
Put yourself in the place of the person that you claim has an ulterior motive .
Would you particularly like it if someone told you that " no you ca n't see the particular 's because you 'll nit-pick it and I know I am right " .
They may very well nit-pick and run with completely stupid results based solely on preconceived notions .
You ca n't shield them from facts just because they might do this.The Best approach is to release it and in advance explain the bugs that you know are there .
If they find something you did n't know about , great they helped you .
You might have to explain how the data was n't corrupted by this but that is better than hiding it completely.The goal is truth or fact .
Not you being right .</tokentext>
<sentencetext>But thats a slippery slope.
Put yourself in the place of the person that you claim has an ulterior motive.
Would you particularly like it if someone told you that "no you can't see the particular's because you'll nit-pick it and I know I am right".
They may very well nit-pick and run with completely stupid results based solely on preconceived notions.
You can't shield them from facts just because they might do this.The Best approach is to release it and in advance explain the bugs that you know are there.
If they find something you didn't know about, great they helped you.
You might have to explain how the data wasn't corrupted by this but that is better than hiding it completely.The goal is truth or fact.
Not you being right.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072358</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31077698</id>
	<title>Re:Not that simple</title>
	<author>wfolta</author>
	<datestamp>1265709180000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><div class="quote"><p>Scientists describe their algorithms in peer-reviewed papers, which are then re-implemented (often from scratch) by other scientists.</p> </div><p>I recently went through this exercise for a graduate class in biometrics. In researching a particular fingerprint-evaluation algorithm, I found 6 papers that had an algorithmic description, and they all disagreed. Eventually, I could see that 5 out of the 6 were due to various kinds of typos. They simply would not work as written.</p></div>
	</htmltext>
<tokenext>Scientists describe their algorithms in peer-reviewed papers , which are then re-implemented ( often from scratch ) by other scientists .
I recently went through this exercise for a graduate class in biometrics .
In researching a particular fingerprint-evaluation algorithm , I found 6 papers that had an algorithmic description , and they all disagreed .
Eventually , I could see that 5 out of the 6 were due to various kinds of typos .
They simply would not work as written .</tokentext>
<sentencetext>Scientists describe their algorithms in peer-reviewed papers, which are then re-implemented (often from scratch) by other scientists.
I recently went through this exercise for a graduate class in biometrics.
In researching a particular fingerprint-evaluation algorithm, I found 6 papers that had an algorithmic description, and they all disagreed.
Eventually, I could see that 5 out of the 6 were due to various kinds of typos.
They simply would not work as written.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072694</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072148</id>
	<title>Conspiracy?</title>
	<author>Anonymous</author>
	<datestamp>1265731560000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext>Nobody said conspiracy, just plain crappy code.  You don't need a conspiracy if you are "trying to prove" something, your crappy code spits out what you want to see and you run with it.  You just need plain old incompetence.</htmltext>
<tokenext>Nobody said conspiracy , just plain crappy code .
You do n't need a conspiracy if you are " trying to prove " something , your crappy code spits out what you want to see and you run with it .
You just need plain old incompetence .</tokentext>
<sentencetext>Nobody said conspiracy, just plain crappy code.
You don't need a conspiracy if you are "trying to prove" something, your crappy code spits out what you want to see and you run with it.
You just need plain old incompetence.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071954</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31077204</id>
	<title>Impediments to releasing scientific code.</title>
	<author>SETIGuy</author>
	<datestamp>1265707080000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>
<i>Damn slashdot and its awful posting interface.</i>
</p><p>There are benefits and drawbacks to releasing code. First, let me say I am a scientist, and I do release my code, primarily under the GPL unless I am contractually obligated by license agreements to do otherwise. The exception would be trivial single use code or limited use code. Despite that, I don't get a lot of eyes looking at my code.
</p><p>
Some people here have claimed that journal policies are a part of the problem. Not as far as code releases go. Journals don't publish code. I think there are real impediments to code release, even when most scientists would claim that the release is a good idea.
</p><ul>
 <li>A large amount of code is written by students with limited programming experience. Therefore it is difficult to read, poorly commented, and poorly optimized. That's a strong argument that it should be released. But a lot of people would be embarrassed if that code was released. So there will be some push back. Especially by established, famous, and respected professors who really don't want their crappy code to be a source of ridicule.</li>
  <li>A lot of large bodies of code are controlled by scientific consortia. A library for simulating particle accelerator collision products might have several hundred authors. In many of the files the authors will have placed a copyright statement naming themselves as the copyright holder, in others they may have named the institution they work for as the copyright holder. Since the code was donated to the consortium, the consortium can claim its members have the implied right to used the code. But the consortium probably can't release the code to the public, since it would need the permission of all authors (many of them deceased) and the institutions they were working for when they developed the code in question.</li>
   <li> A lot of scientific programmers use code that they don't have a license to release. For example, we've all pulled a routine out of Numerical Recipes, because it was easy, did the job we wanted, and was fast enough. Oops, sorry, can't distribute that code. We've all used a GPL library in an application linked to closed source or limited distribution libraries. Oops, sorry, it's illegal to distribute that code. (Don't tell my University about this, because they'll make me consult with a lawyer before releasing any code.)</li>
    <li> Scientists may, in general, be intelligent and well informed, but when it comes to the intricacies of licensing agreements and copyright law most don't have more than a very limited understanding.</li>
    <li> A lot of scientists don't want to be scooped by competitors.</li>
    <li> There are some people who think releasing code or making it available to colleagues works against the scientific method by discouraging reimplementation of an application for the purpose of replicating earlier results.</li>
</ul><p>
In the case of climate modeling code, I'm guessing that #2 is probably the biggest hurdle. In my code, #3 is probably the biggest hurdle, and it does take significant effort to work around it.
</p></htmltext>
<tokenext>Damn slashdot and its awful posting interface .
There are benefits and drawbacks to releasing code .
First , let me say I am a scientist , and I do release my code , primarily under the GPL unless I am contractually obligated by license agreements to do otherwise .
The exception would be trivial single use code or limited use code .
Despite that , I do n't get a lot of eyes looking at my code .
Some people here have claimed that journal policies are a part of the problem .
Not as far as code releases go .
Journals do n't publish code .
I think there are real impediments to code release , even when most scientists would claim that the release is a good idea .
A large amount of code is written by students with limited programming experience .
Therefore it is difficult to read , poorly commented , and poorly optimized .
That 's a strong argument that it should be released .
But a lot of people would be embarrassed if that code was released .
So there will be some push back .
Especially by established , famous , and respected professors who really do n't want their crappy code to be a source of ridicule .
A lot of large bodies of code are controlled by scientific consortia .
A library for simulating particle accelerator collision products might have several hundred authors .
In many of the files the authors will have placed a copyright statement naming themselves as the copyright holder , in others they may have named the institution they work for as the copyright holder .
Since the code was donated to the consortium , the consortium can claim its members have the implied right to used the code .
But the consortium probably ca n't release the code to the public , since it would need the permission of all authors ( many of them deceased ) and the institutions they were working for when they developed the code in question .
A lot of scientific programmers use code that they do n't have a license to release .
For example , we 've all pulled a routine out of Numerical Recipes , because it was easy , did the job we wanted , and was fast enough .
Oops , sorry , ca n't distribute that code .
We 've all used a GPL library in an application linked to closed source or limited distribution libraries .
Oops , sorry , it 's illegal to distribute that code .
( Do n't tell my University about this , because they 'll make me consult with a lawyer before releasing any code .
) Scientists may , in general , be intelligent and well informed , but when it comes to the intricacies of licensing agreements and copyright law most do n't have more than a very limited understanding .
A lot of scientists do n't want to be scooped by competitors .
There are some people who think releasing code or making it available to colleagues works against the scientific method by discouraging reimplementation of an application for the purpose of replicating earlier results .
In the case of climate modeling code , I 'm guessing that # 2 is probably the biggest hurdle .
In my code , # 3 is probably the biggest hurdle , and it does take significant effort to work around it .</tokentext>
<sentencetext>
Damn slashdot and its awful posting interface.
There are benefits and drawbacks to releasing code.
First, let me say I am a scientist, and I do release my code, primarily under the GPL unless I am contractually obligated by license agreements to do otherwise.
The exception would be trivial single use code or limited use code.
Despite that, I don't get a lot of eyes looking at my code.
Some people here have claimed that journal policies are a part of the problem.
Not as far as code releases go.
Journals don't publish code.
I think there are real impediments to code release, even when most scientists would claim that the release is a good idea.
A large amount of code is written by students with limited programming experience.
Therefore it is difficult to read, poorly commented, and poorly optimized.
That's a strong argument that it should be released.
But a lot of people would be embarrassed if that code was released.
So there will be some push back.
Especially by established, famous, and respected professors who really don't want their crappy code to be a source of ridicule.
A lot of large bodies of code are controlled by scientific consortia.
A library for simulating particle accelerator collision products might have several hundred authors.
In many of the files the authors will have placed a copyright statement naming themselves as the copyright holder, in others they may have named the institution they work for as the copyright holder.
Since the code was donated to the consortium, the consortium can claim its members have the implied right to used the code.
But the consortium probably can't release the code to the public, since it would need the permission of all authors (many of them deceased) and the institutions they were working for when they developed the code in question.
A lot of scientific programmers use code that they don't have a license to release.
For example, we've all pulled a routine out of Numerical Recipes, because it was easy, did the job we wanted, and was fast enough.
Oops, sorry, can't distribute that code.
We've all used a GPL library in an application linked to closed source or limited distribution libraries.
Oops, sorry, it's illegal to distribute that code.
(Don't tell my University about this, because they'll make me consult with a lawyer before releasing any code.
)
     Scientists may, in general, be intelligent and well informed, but when it comes to the intricacies of licensing agreements and copyright law most don't have more than a very limited understanding.
A lot of scientists don't want to be scooped by competitors.
There are some people who think releasing code or making it available to colleagues works against the scientific method by discouraging reimplementation of an application for the purpose of replicating earlier results.
In the case of climate modeling code, I'm guessing that #2 is probably the biggest hurdle.
In my code, #3 is probably the biggest hurdle, and it does take significant effort to work around it.
</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073470</id>
	<title>Re:This is not science.</title>
	<author>Anonymous</author>
	<datestamp>1265736840000</datestamp>
	<modclass>Troll</modclass>
	<modscore>-1</modscore>
	<htmltext><p>Since Phil Jones and CRU had released a long time ago ALL THE DATA HE WAS LEGALLY ALLOWED TO DO and PUBLISHED his algorithms and code what is is your complaint?  If you have a bitch with CRU TELLING YOU THAT YOU CANN'T HAVE Indian data talk to prime minister  Manmohan Singh who insists that the Indian government be paid for it's met data in violation of it's agreement with the WMO. May be your talking about McIntyre who sent Briffa of CRU a collection of tree ring data and then spewed bullshit in the denialosphere that CRU  and Briffa were with holding self same tree ring data Maybe your talking about Tony Watts and his surfacestations.org. You know the one where Watts claimed that all the surface data stations were located badly and that CAUSED THE TEMPERATURES TO BE TO HIGH, except when Menee et al used Watts data and software Menee et al found that poor siting of stations UNDERESTIMATED THE TEMPERATURE</p></htmltext>
<tokenext>Since Phil Jones and CRU had released a long time ago ALL THE DATA HE WAS LEGALLY ALLOWED TO DO and PUBLISHED his algorithms and code what is is your complaint ?
If you have a bitch with CRU TELLING YOU THAT YOU CAN N'T HAVE Indian data talk to prime minister Manmohan Singh who insists that the Indian government be paid for it 's met data in violation of it 's agreement with the WMO .
May be your talking about McIntyre who sent Briffa of CRU a collection of tree ring data and then spewed bullshit in the denialosphere that CRU and Briffa were with holding self same tree ring data Maybe your talking about Tony Watts and his surfacestations.org .
You know the one where Watts claimed that all the surface data stations were located badly and that CAUSED THE TEMPERATURES TO BE TO HIGH , except when Menee et al used Watts data and software Menee et al found that poor siting of stations UNDERESTIMATED THE TEMPERATURE</tokentext>
<sentencetext>Since Phil Jones and CRU had released a long time ago ALL THE DATA HE WAS LEGALLY ALLOWED TO DO and PUBLISHED his algorithms and code what is is your complaint?
If you have a bitch with CRU TELLING YOU THAT YOU CANN'T HAVE Indian data talk to prime minister  Manmohan Singh who insists that the Indian government be paid for it's met data in violation of it's agreement with the WMO.
May be your talking about McIntyre who sent Briffa of CRU a collection of tree ring data and then spewed bullshit in the denialosphere that CRU  and Briffa were with holding self same tree ring data Maybe your talking about Tony Watts and his surfacestations.org.
You know the one where Watts claimed that all the surface data stations were located badly and that CAUSED THE TEMPERATURES TO BE TO HIGH, except when Menee et al used Watts data and software Menee et al found that poor siting of stations UNDERESTIMATED THE TEMPERATURE</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072052</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072134</id>
	<title>Absolutely</title>
	<author>RandCraw</author>
	<datestamp>1265731500000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Aside from logistics, there is no excuse for not doing this.  In my experience, software innovations are notoriously sensitive to subtleties in input data (e.g. data mining, AI, image processing).  Posting both code &amp; data (and a test driver, of course) should be mandatory for all publications that claim to have found a signal in data, better or faster.</p><p>The question is, how to maintain code &amp; data long after the publication publishes?  IMHO, any peer-reviewed publication should be required to maintain such a repository for perhaps 20-30 years, ideally under a GPL (or its kin) so access to it would be free in perpetuity.</p><p>Maybe such a service would finally justify peer reviewed pubs' exorbitant fees for non-subscriber access.</p></htmltext>
<tokenext>Aside from logistics , there is no excuse for not doing this .
In my experience , software innovations are notoriously sensitive to subtleties in input data ( e.g .
data mining , AI , image processing ) .
Posting both code &amp; data ( and a test driver , of course ) should be mandatory for all publications that claim to have found a signal in data , better or faster.The question is , how to maintain code &amp; data long after the publication publishes ?
IMHO , any peer-reviewed publication should be required to maintain such a repository for perhaps 20-30 years , ideally under a GPL ( or its kin ) so access to it would be free in perpetuity.Maybe such a service would finally justify peer reviewed pubs ' exorbitant fees for non-subscriber access .</tokentext>
<sentencetext>Aside from logistics, there is no excuse for not doing this.
In my experience, software innovations are notoriously sensitive to subtleties in input data (e.g.
data mining, AI, image processing).
Posting both code &amp; data (and a test driver, of course) should be mandatory for all publications that claim to have found a signal in data, better or faster.The question is, how to maintain code &amp; data long after the publication publishes?
IMHO, any peer-reviewed publication should be required to maintain such a repository for perhaps 20-30 years, ideally under a GPL (or its kin) so access to it would be free in perpetuity.Maybe such a service would finally justify peer reviewed pubs' exorbitant fees for non-subscriber access.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072742</id>
	<title>Re:This is not science.</title>
	<author>Anonymous</author>
	<datestamp>1265734200000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext><p>Shit like this is why I'm hesitant about going along with Climate Change. I'm in no way qualified to review scientific data, but I can tell when someone is shady, and I don't trust shady people.</p></htmltext>
<tokenext>Shit like this is why I 'm hesitant about going along with Climate Change .
I 'm in no way qualified to review scientific data , but I can tell when someone is shady , and I do n't trust shady people .</tokentext>
<sentencetext>Shit like this is why I'm hesitant about going along with Climate Change.
I'm in no way qualified to review scientific data, but I can tell when someone is shady, and I don't trust shady people.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072052</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072688</id>
	<title>Re:Conspiracy?</title>
	<author>xtracto</author>
	<datestamp>1265734020000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>3</modscore>
	<htmltext><p>Agreed 100\%.</p><p>You would not believe the amount and crappy quality of the code performed during "research projects", specially when the research is in a field completely unrelated to Comp. Sci. or Soft. Eng.</p><p>I have personally seen software related to Agronomy, Biology (Ecology) and Economics. The problem with a lot of that code is that sometimes researchers want to use the power of computers (say, for simulation) but do not know how to code, they then read a bit about some programming language and implement their program s they are learning.</p><p>The result? you can imagine.</p></htmltext>
<tokenext>Agreed 100 \ % .You would not believe the amount and crappy quality of the code performed during " research projects " , specially when the research is in a field completely unrelated to Comp .
Sci. or Soft .
Eng.I have personally seen software related to Agronomy , Biology ( Ecology ) and Economics .
The problem with a lot of that code is that sometimes researchers want to use the power of computers ( say , for simulation ) but do not know how to code , they then read a bit about some programming language and implement their program s they are learning.The result ?
you can imagine .</tokentext>
<sentencetext>Agreed 100\%.You would not believe the amount and crappy quality of the code performed during "research projects", specially when the research is in a field completely unrelated to Comp.
Sci. or Soft.
Eng.I have personally seen software related to Agronomy, Biology (Ecology) and Economics.
The problem with a lot of that code is that sometimes researchers want to use the power of computers (say, for simulation) but do not know how to code, they then read a bit about some programming language and implement their program s they are learning.The result?
you can imagine.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072148</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31076944</id>
	<title>Re:Not a good idea</title>
	<author>khallow</author>
	<datestamp>1265706120000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><div class="quote"><p>The point about reproducible experiments is not to provide your peers with the exact same equipment you used</p></div><p>If that could be done easily and cheaply, then it would be required that you provide the experiment as it was run as part of your publication. Imagine if you will, that you could put on page 34 of your paper, the lab set up, not a facsimile or drawing, the actual lab as it was set up when you were gathering data and the very actions you followed as you went. All someone had to do was take the lab out of the paper and watch the experiment unfold exactly.<br> <br>

That's what you can do with computer programs and why they should be included as part of any publication.</p></div>
	</htmltext>
<tokenext>The point about reproducible experiments is not to provide your peers with the exact same equipment you usedIf that could be done easily and cheaply , then it would be required that you provide the experiment as it was run as part of your publication .
Imagine if you will , that you could put on page 34 of your paper , the lab set up , not a facsimile or drawing , the actual lab as it was set up when you were gathering data and the very actions you followed as you went .
All someone had to do was take the lab out of the paper and watch the experiment unfold exactly .
That 's what you can do with computer programs and why they should be included as part of any publication .</tokentext>
<sentencetext>The point about reproducible experiments is not to provide your peers with the exact same equipment you usedIf that could be done easily and cheaply, then it would be required that you provide the experiment as it was run as part of your publication.
Imagine if you will, that you could put on page 34 of your paper, the lab set up, not a facsimile or drawing, the actual lab as it was set up when you were gathering data and the very actions you followed as you went.
All someone had to do was take the lab out of the paper and watch the experiment unfold exactly.
That's what you can do with computer programs and why they should be included as part of any publication.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072364</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072140</id>
	<title>That's all wrong</title>
	<author>Gadget\_Guy</author>
	<datestamp>1265731560000</datestamp>
	<modclass>Interestin</modclass>
	<modscore>2</modscore>
	<htmltext><p>The scientific process is to invalidate a study if the results cannot be reproduced by anyone else. That way you can eliminate all potential problems like coding errors, invalid assumptions, faulty equipment, mistakes in procedures, and 100 of the other things that can produce dodgy results.</p><p>It can be misleading to search through the code for mistakes when you don't know which code was eventually used in the final results (or in which order). I have accumulated quite a lot of snipits of code that I used to fix a particular need at the time. I am sure that many of these hacks were ultimately unused because I decided to go down a different path in data processing. Or the temporary tables used during processing is no longer around (or in a changed format since the code was written). There is also the problem of some data processing being done by commercial products.</p><p>It's just too hard. The best solution is to let science work the way it has found to be the best. Sure you will get some bad studies, but these will eventually be fixed over time. The system does work, whether vested interests like it or not.</p></htmltext>
<tokenext>The scientific process is to invalidate a study if the results can not be reproduced by anyone else .
That way you can eliminate all potential problems like coding errors , invalid assumptions , faulty equipment , mistakes in procedures , and 100 of the other things that can produce dodgy results.It can be misleading to search through the code for mistakes when you do n't know which code was eventually used in the final results ( or in which order ) .
I have accumulated quite a lot of snipits of code that I used to fix a particular need at the time .
I am sure that many of these hacks were ultimately unused because I decided to go down a different path in data processing .
Or the temporary tables used during processing is no longer around ( or in a changed format since the code was written ) .
There is also the problem of some data processing being done by commercial products.It 's just too hard .
The best solution is to let science work the way it has found to be the best .
Sure you will get some bad studies , but these will eventually be fixed over time .
The system does work , whether vested interests like it or not .</tokentext>
<sentencetext>The scientific process is to invalidate a study if the results cannot be reproduced by anyone else.
That way you can eliminate all potential problems like coding errors, invalid assumptions, faulty equipment, mistakes in procedures, and 100 of the other things that can produce dodgy results.It can be misleading to search through the code for mistakes when you don't know which code was eventually used in the final results (or in which order).
I have accumulated quite a lot of snipits of code that I used to fix a particular need at the time.
I am sure that many of these hacks were ultimately unused because I decided to go down a different path in data processing.
Or the temporary tables used during processing is no longer around (or in a changed format since the code was written).
There is also the problem of some data processing being done by commercial products.It's just too hard.
The best solution is to let science work the way it has found to be the best.
Sure you will get some bad studies, but these will eventually be fixed over time.
The system does work, whether vested interests like it or not.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31075016</id>
	<title>hmmmm.</title>
	<author>jafac</author>
	<datestamp>1265742600000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>Does this include the "science" of Economics?<br>If so - I think that would be a VERY good thing.<br>Particularly in the area of derivatives trading.</p><p>It's estimated that 20\% of the global economy now relies on trading derivatives, whose valuation is based on formulae, that are considered "proprietary" - and therefore, you're supposed to just trust the seller on the valuation.  (by the way, I've got this bridge I'm selling, in Alaska . . . )</p><p>Ironic that Climate science is regarded with such skepticism, yet people in the high institutions of banking or the University of Chicago, Economics department so feverishly cling to the belief in some "invisible hand".</p></htmltext>
<tokenext>Does this include the " science " of Economics ? If so - I think that would be a VERY good thing.Particularly in the area of derivatives trading.It 's estimated that 20 \ % of the global economy now relies on trading derivatives , whose valuation is based on formulae , that are considered " proprietary " - and therefore , you 're supposed to just trust the seller on the valuation .
( by the way , I 've got this bridge I 'm selling , in Alaska .
. .
) Ironic that Climate science is regarded with such skepticism , yet people in the high institutions of banking or the University of Chicago , Economics department so feverishly cling to the belief in some " invisible hand " .</tokentext>
<sentencetext>Does this include the "science" of Economics?If so - I think that would be a VERY good thing.Particularly in the area of derivatives trading.It's estimated that 20\% of the global economy now relies on trading derivatives, whose valuation is based on formulae, that are considered "proprietary" - and therefore, you're supposed to just trust the seller on the valuation.
(by the way, I've got this bridge I'm selling, in Alaska .
. .
)Ironic that Climate science is regarded with such skepticism, yet people in the high institutions of banking or the University of Chicago, Economics department so feverishly cling to the belief in some "invisible hand".</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072268</id>
	<title>Observations...</title>
	<author>Anonymous</author>
	<datestamp>1265732220000</datestamp>
	<modclass>Informativ</modclass>
	<modscore>4</modscore>
	<htmltext><p>As it happens, my students and I are about to release a fairly specialized code - we discussed license terms, and eventually settled on the BSD (and explicitly avoided the GPL), which requires "citation" but otherwise leaves anyone free to use it.</p><p>That said, writing a scientific code can involve a good deal of work, but the "payoff" usually comes in the form of results and conclusions, rather than the code itself.   In those circumstances, there is a sound argument for delaying any code release until you have published the results you hoped to obtain when you initiated the project, even if these form a sequence of papers (rather than insisting on code release with the first published results)</p><p>Thirdly, in many cases scientists will share code with colleagues when asked politely, even if they are not in the public domain.</p><p>Fourthly, I fairly regularly spot minor errors in numerical calculations performed by other groups (either because I do have access to the source, or because I can't reproduce their results) -- in almost all cases these do not have an impact on their conclusions, so while the "error count" can be fairly high, the number of "wrong" results coming from bad code is overestimated by this accounting.</p></htmltext>
<tokenext>As it happens , my students and I are about to release a fairly specialized code - we discussed license terms , and eventually settled on the BSD ( and explicitly avoided the GPL ) , which requires " citation " but otherwise leaves anyone free to use it.That said , writing a scientific code can involve a good deal of work , but the " payoff " usually comes in the form of results and conclusions , rather than the code itself .
In those circumstances , there is a sound argument for delaying any code release until you have published the results you hoped to obtain when you initiated the project , even if these form a sequence of papers ( rather than insisting on code release with the first published results ) Thirdly , in many cases scientists will share code with colleagues when asked politely , even if they are not in the public domain.Fourthly , I fairly regularly spot minor errors in numerical calculations performed by other groups ( either because I do have access to the source , or because I ca n't reproduce their results ) -- in almost all cases these do not have an impact on their conclusions , so while the " error count " can be fairly high , the number of " wrong " results coming from bad code is overestimated by this accounting .</tokentext>
<sentencetext>As it happens, my students and I are about to release a fairly specialized code - we discussed license terms, and eventually settled on the BSD (and explicitly avoided the GPL), which requires "citation" but otherwise leaves anyone free to use it.That said, writing a scientific code can involve a good deal of work, but the "payoff" usually comes in the form of results and conclusions, rather than the code itself.
In those circumstances, there is a sound argument for delaying any code release until you have published the results you hoped to obtain when you initiated the project, even if these form a sequence of papers (rather than insisting on code release with the first published results)Thirdly, in many cases scientists will share code with colleagues when asked politely, even if they are not in the public domain.Fourthly, I fairly regularly spot minor errors in numerical calculations performed by other groups (either because I do have access to the source, or because I can't reproduce their results) -- in almost all cases these do not have an impact on their conclusions, so while the "error count" can be fairly high, the number of "wrong" results coming from bad code is overestimated by this accounting.</sentencetext>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071954</id>
	<title>Re:Why release it?</title>
	<author>Anonymous</author>
	<datestamp>1265730600000</datestamp>
	<modclass>Insightful</modclass>
	<modscore>2</modscore>
	<htmltext>Please apply <a href="http://en.wikipedia.org/wiki/Hanlon's\_razor" title="wikipedia.org">Hanlon's razor</a> [wikipedia.org] before leaping to conspiracy theories. Or <a href="http://en.wikipedia.org/wiki/Occam's\_razor" title="wikipedia.org">Occam's razor</a> [wikipedia.org] might inform you that a conspiracy among thousands of scientists is a highly improbable occurrence; look for a solution that doesn't involve a perfect lid of secrecy among a group of (frequently) socially inept people.</htmltext>
<tokenext>Please apply Hanlon 's razor [ wikipedia.org ] before leaping to conspiracy theories .
Or Occam 's razor [ wikipedia.org ] might inform you that a conspiracy among thousands of scientists is a highly improbable occurrence ; look for a solution that does n't involve a perfect lid of secrecy among a group of ( frequently ) socially inept people .</tokentext>
<sentencetext>Please apply Hanlon's razor [wikipedia.org] before leaping to conspiracy theories.
Or Occam's razor [wikipedia.org] might inform you that a conspiracy among thousands of scientists is a highly improbable occurrence; look for a solution that doesn't involve a perfect lid of secrecy among a group of (frequently) socially inept people.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31071884</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31082808</id>
	<title>Re:This is not science.</title>
	<author>MadMagician</author>
	<datestamp>1265056320000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p><div class="quote"><p> <i>"Why should I make the data available to you, when your aim is to find something wrong with it?"</i> </p><p>That used to be what Science was. Of course, that was when truth was the goal.</p></div><p>That's still the goal of Science.</p><p>But it's not the goal of everyone. Just as with tobacco and cancer, there are a lot of people with vested interests.</p><p>But the ice <em>is</em> melting.</p></div>
	</htmltext>
<tokenext>" Why should I make the data available to you , when your aim is to find something wrong with it ?
" That used to be what Science was .
Of course , that was when truth was the goal.That 's still the goal of Science.But it 's not the goal of everyone .
Just as with tobacco and cancer , there are a lot of people with vested interests.But the ice is melting .</tokentext>
<sentencetext> "Why should I make the data available to you, when your aim is to find something wrong with it?
" That used to be what Science was.
Of course, that was when truth was the goal.That's still the goal of Science.But it's not the goal of everyone.
Just as with tobacco and cancer, there are a lot of people with vested interests.But the ice is melting.
	</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31073330</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31077792</id>
	<title>Re:Peer Review / publication process</title>
	<author>drizzd</author>
	<datestamp>1265709660000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext>That is not always possible for practical reasons, such as proprietary software that was used to find the results. Besides, submissions which describe a black box with the only value being supposedly correct simulation results will not be accepted anyways. Simulation is often simply a means to visualize and quantize results which are already expected from the theory developed by a publication. Simulation results prove a theory neither right nor wrong.</htmltext>
<tokenext>That is not always possible for practical reasons , such as proprietary software that was used to find the results .
Besides , submissions which describe a black box with the only value being supposedly correct simulation results will not be accepted anyways .
Simulation is often simply a means to visualize and quantize results which are already expected from the theory developed by a publication .
Simulation results prove a theory neither right nor wrong .</tokentext>
<sentencetext>That is not always possible for practical reasons, such as proprietary software that was used to find the results.
Besides, submissions which describe a black box with the only value being supposedly correct simulation results will not be accepted anyways.
Simulation is often simply a means to visualize and quantize results which are already expected from the theory developed by a publication.
Simulation results prove a theory neither right nor wrong.</sentencetext>
	<parent>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31072826</parent>
</comment>
<comment>
	<id>http://www.semanticweb.org/ontologies/ConversationInstances.owl#comment10_02_09_1336250.31083242</id>
	<title>Yay for public research code</title>
	<author>Frigo</author>
	<datestamp>1265017740000</datestamp>
	<modclass>None</modclass>
	<modscore>1</modscore>
	<htmltext><p>I did always wonder what would happen if we feed random data into these proggies they use to calculate temperature anomalies. Would they still produce the hockey stick?</p></htmltext>
<tokenext>I did always wonder what would happen if we feed random data into these proggies they use to calculate temperature anomalies .
Would they still produce the hockey stick ?</tokentext>
<sentencetext>I did always wonder what would happen if we feed random data into these proggies they use to calculate temperature anomalies.
Would they still produce the hockey stick?</sentencetext>
</comment>
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