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    If the paper depends on the source code, then it ought not be published. If you can't publish the code, you can't publish the paper. A paper which says "our program does these wonderful things", and you cannot evaluate the paper without running that program, then the paper borders on being an advertizing brochure for some software. Commented Oct 25, 2012 at 15:44
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    In complete agreement with Kaz -- if to peer review the research you need something that's not available (data, code, etc), it shouldn't be accepted by a peer-reviewed journal. Almost all of the arguments that DeveloperDon mentions has pointed out holds true for data release, too ... yet there's now a rather big movement in recent years towards it. Commented Oct 25, 2012 at 16:28
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    GREAT post. I'd also add that sometimes separate scientists recreating the software on their own is PART of the repeatability of the experiment. If it only works the way 1 person coded it, but not the way others code it...then the results can be called into question and errors can be identified. Commented Oct 25, 2012 at 17:56
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    your second to the last point is the strongest Commented Oct 25, 2012 at 20:07
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    @AndresF. Code is absolutely the least important thing in a paper. A paper is "Here is what I did; here are my methods; here are my results". The code is a codification of the method, and it should produce the exact same results. If you want to reproduce the paper's results but use the paper's code, you haven't reproduced anything; what you're supposed to do is read their methods section, come up with your own implementation, and then write a paper about it when you can't reproduce their results. Commented Oct 26, 2012 at 17:24