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244 votes

How can a TA help a student who is certain she sucks at programming?

When you tell her that she doesn't suck at programming, all she hears is that you don't understand how bad she sucks. The psychology is the important thing here, not pedagogy. If I were in your ...
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  • 7,752
238 votes

Outsourcing trivial authorless work

The fact that to a seasoned programmer the work is easy doesn't have anything to do with it. As you describe it, this is work that's required for the publication. Without it, you don't have a paper. ...
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  • 13.3k
236 votes

Advisor professor asks for my dissertation research source code

One of the reasons Science has been so successful is that scientists treat knowledge and tools as public goods. We don't hoard knowledge, but rather we write papers, share techniques, offer ...
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181 votes

Is publishing runnable code instead of pseudo code shunned?

There are cases where real code is preferable, and cases where pseudocode is preferable. You shouldn't rely on a simple iron rule, but rather on judgement of what is appropriate to the situation. ...
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  • 5,556
121 votes
Accepted

Is it OK to update code on repository after publication?

Absolutely yes! There is no reason to stop a project from evolving just because you've published about it. What would be good to do, however, is to identify the version current at the time of ...
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  • 182k
111 votes
Accepted

Why are papers without code but with results accepted?

For me it seems that the reasons are two: the belief that code is only a tool, a particular implementation being secondary to the idea or algorithm, the historical residue (it was unpractical to ...
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  • 25.7k
106 votes

Will a paper be retracted if a flaw in released software code invalidates its central idea?

If the main idea in the paper has been invalidated by the correction in the code, you would do well to try to retract the paper yourself. This is just a point of professional ethics. It also protects ...
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  • 271k
104 votes

Is there any way to post my code on Code Review Stack Exchange and not be worried about plagiarism?

In addition to all the good answers you received so far, I should also point out that in general people's fear of being unethically scooped is vastly exaggerated. I would imagine that there really isn'...
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  • 127k
102 votes

During peer-review, should I comment on the authors' messy code?

If the authors have provided a link to their code as a reference, then it is appropriate to offer commentary, particularly if the article is based on the code. However, I would recommend making the ...
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  • 172k
99 votes
Accepted

Academic code copied by library author

In fact something great happened: Your research did have impact in the real world and seems to be useful - not everyone can say that! When it comes to legal issues, things are usually complicated and ...
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  • 13k
87 votes

Advisor professor asks for my dissertation research source code

Ideally in this situation you would make your program publicly available. Giving others access to this code does not prevent you from using it, and will help you build reputation within your field. ...
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  • 1,292
80 votes
Accepted

Teaching a blind student MATLAB programming

Yes, this is all possible, but I recommend seeking specialist advice. Blind support organisations often have technical advisors who are aware of the latest software and hardware adaptions that are ...
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77 votes

Advisor professor asks for my dissertation research source code

As someone who works in scientific computing, I agree with what others say, and would likely take it a step further. To put it hyperbolicly: Refusing reasonable requests to code used in a published ...
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  • 4,648
76 votes
Accepted

Is it acceptable to use Mathematica to derive results in your research?

Is it okay to use Mathematica to solve the integration and use the result in my research? Of course it is. It might be useful, though, to make the Mathematica code employed for the calculations ...
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  • 52.8k
75 votes

I wrote the code based on a paper's methodology; are there any legal problems with making it open source?

You are not required to get permission to implement an idea you have read about in a paper, or to make it open source. The paper is protected by copyright, but this only protects the text and images ...
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  • 107k
75 votes
Accepted

I have found a mistake on someone's code published online: what is the protocol?

Now that I have found the problem what is the protocol for highlighting this, is emailing the author necessary? It isn't necessary, but it is the right thing to do, if you don't, you're responsible ...
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  • 40.2k
72 votes

Advisor professor asks for my dissertation research source code

If you wrote the code as part of your work as a PhD candidate, and were at all considered an employee of the institution as a PhD candidate, then the institution may well own intellectual property ...
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67 votes
Accepted

Double blind peer review when paper cites author's GitHub repo for code

Censor out the repo's name, and provide code to the referees as an auxiliary file.
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56 votes

How can a TA help a student who is certain she sucks at programming?

About her not wanting to work with her team mate -- she may have some fears such as: that she'll feel embarrassed in front of her team mate that she'll rely too much on the team mate's competence ...
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  • 38.7k
56 votes

Why say source code is available with an ArXiv paper when it is not?

There is no advantage to claiming the source code is available and then not doing that. All it will achieve is irritating the really interested readers. The most likely reason is it’s a simple mistake....
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  • 34.2k
53 votes

I have found a mistake on someone's code published online: what is the protocol?

An important point of etiquette that has been skipped in the other answers: Treat it as a suspected bug, and do not assume "I'm right, you're wrong" while presenting your fix. No matter how ...
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53 votes
Accepted

How do you manage to study and have a balance in your life at the same time?

Yes, it matters that you are in grade 9. It is probably a good thing that you are able to do what you like to do (math and computing), but it seems too early to focus yourself quite so much on narrow ...
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  • 271k
53 votes

Is publishing runnable code instead of pseudo code shunned?

In my research, I often write algorithms, which may contains statements like: Find a dominant subspace of a given hermitian matrix A with relative accuracy Ɛ. Find a nonnegative solution of this ...
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51 votes

Is it acceptable to use Mathematica to derive results in your research?

I take this question as not specific to Mathematica, but equally relevant to any other computer algebra system. You have an integral or an equation that you cannot solve. You have a piece of ...
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  • 2,156
51 votes

My code is published as original work by a different group. What should I do?

This seems to be a clear case of plagiarism, and potentially a copyright violation. The BSD license contains a line "Redistributions of source code must retain the above copyright notice, this list ...
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51 votes
Accepted

Can one demand to see code used to generate an article?

I believe you are asking the wrong question. You are asking: Can one demand to see code used to generate an article? To which I would answer: Assuming you're in a country with free speech, you can "...
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46 votes

During peer-review, should I comment on the authors' messy code?

The code is within the scope of the review, and it is appropriate to review this and offer constructive suggestions in relation to its deficiencies. Now, bear in mind that the onus is on the author ...
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  • 46.1k
46 votes
Accepted

GitHub repository ownership as a PhD student in a lab

It's fairly common for labs to have GitHub organizations. There are multiple reasons for this. First of all, it doesn't prevent the authors from getting credit. The commits will be shown as commits ...
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  • 14.1k
43 votes
Accepted

Should I be credited for my programming contribution to a dissertation?

You did work for hire for a research group. Since you say you were strictly involved in developing the tool and not in the research, authorship of subsequent publications is not to be expected. An ...
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  • 26.7k

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