Questions tagged [code]
Questions concerning computer code written or used in the context of a research project or other academic endeavour (including questions on licensing, ownership, sharing, distribution, and formatting of academic source code). For other questions on software (related to academic aspects of using the software rather then developing it), use the `software` tag instead. Generic code questions, e.g. help with debugging, are off-topic and will be closed.
316 questions
7
votes
4
answers
1k
views
For a Nature Cities submission, does sharing code on GitHub require adding a license for legal reproducibility?
I am submitting a paper to Nature Cities and will share my analysis code on GitHub to fulfill the data availability policy. My goal is straightforward: I want anyone to be able to download the code to ...
- 195
12
votes
5
answers
3k
views
What should a supervisor do with a PhD student unable to meet programming requirements? [closed]
You are a PhD supervisor in the Faculty of Chemistry. You are developing a simulation framework in Rust programming language and have made 50% progress. You chose Rust because your C++ predecessor had ...
- 6,413
9
votes
3
answers
2k
views
Adding comments to a cited paper in README.md
I finished a code-project that's based on several papers. One of those papers has many errors in its mathematical formulas, but presents an idea I believe to be unique and I have implemented.
This ...
- 217
0
votes
3
answers
729
views
Why does Zenodo reserve the right to change data secretly?
I often had Zenodo recommended as the best option for publishing code artifacts. The main advantages over GitHub seem to be that it is not dependent on a commercial company and that its DOIs refer to ...
- 125
56
votes
9
answers
8k
views
Where should I host software for individual papers when GitHub is now part of Microsoft AI?
A previous Q&A here titled "Where should I host software for individual papers" returned answers that were mostly "GitHub", plus some recommendations to additionally archive ...
- 158k
6
votes
1
answer
237
views
How to cite a work published with CC BY 4.0 that inspired visualisation of manuscript images?
We have prepared figures for a manuscript. For the purpose of transparent and reproducible research, we want to share the data and code that can reproduce the results in the manuscript.
For some ...
47
votes
3
answers
5k
views
How do I deal with a supervisor who wants to replace bioinformatics expertise with ChatGPT, especially when it comes to publishing?
My PhD supervisor who is exclusively wet-lab (in plant genetics) has recently started running scripts that ChatGPT has written for him (he has no experience whatsoever in bioinformatics, based on what ...
- 844
3
votes
2
answers
1k
views
Including code when it is the main point of the Master's project
The other questions on this matter concern computer science papers, which is not exactly the case here.
I am doing a Master's report, and a chapter revolves arround extending some open source ...
- 389
-3
votes
1
answer
336
views
Is there an authoritative source for "Obfuscated code hurts reproducibility"? [closed]
I asked a question on Security.SE about the rules regarding obfuscated or minified code. This is where someone has taken human readable source code and applied an algorithm so that it is both hard ...
- 653
19
votes
19
answers
9k
views
Should I use ChatGPT and Wolfram Mathematica as a student?
While solving mathematical equations in physics and STEM, can we take help from ChatGPT (in the same way as one would use a calculator or log tables) and use Mathematica packages instead of using pen ...
- 355
1
vote
4
answers
3k
views
Postdoc supervisor has stopped helping
I finished my postdoc and joined in a faculty position sometime back. My postdoc supervisor is not responding to my messages and not helping at all now. He is the developer of a program/code that I ...
- 43
1
vote
1
answer
203
views
Papers including non open-source code and not including non open-source code?
My question is very specific. I read papers/books that in order for the author to build the system, they need to program the hardware in IP protected code. Some papers or books publish the code. ...
- 641
3
votes
2
answers
161
views
Do you think that publishing a documented script in R (e.g. on GitHub) can increase the chance of publication?
I am involved in environmental science. The data analysis for my following scientific paper is done 100% in R. I'm wondering if I should clean up my script before submitting the article for review and ...
- 31
21
votes
3
answers
11k
views
I am not getting academic credit for code I have written for my PhD, when it was later used in other research. Should I complain?
During my PhD, I developed a data analysis code. My PI encouraged its development, expecting it to stay within the research group. The code was used in some published papers and gained attention when ...
- 311
1
vote
1
answer
169
views
Can I integrate contributing code to an open-source project as part of the curriculum?
First and foremost, I am not a lawyer. :) But I think I’ve got a tricky question: Can I integrate contributing code to an open-source project as part of the curriculum, and if so, how?
Let me provide ...
- 141