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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.

150
votes
12answers
17k views

Why are papers without code but with results accepted?

I just started reading some papers (Computer Science, specifically Computer Vision) and thought "now let's look at the source code" and was quite astonished that most of the papers don't have any ...
131
votes
10answers
11k views

Best-practice models for “research” code?

I have been a professional software developer for a number of years, I'm also an academic researcher - and my research has involved lots of software development. I sometimes feel as though my ...
102
votes
10answers
18k views

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

I'm reviewing a paper in pure mathematics. A lot of results in the paper depend heavily on computer computations, and the authors have provided in the article a link to the Magma code they used for ...
66
votes
11answers
24k views

Advisor professor asks for my dissertation research source code

I am a PhD student and I wrote a computer program for my dissertation research. Recently my advisor professor got a grant and she wants to use my computer program in her grant and she asks me for the ...
61
votes
9answers
11k views

Academic code copied by library author

The papers I write contain all the source code required to reproduce results. I have written a series of papers that build on each other over the years. My intention has been to release an open-source ...
57
votes
1answer
4k views

Is it OK to update code on repository after publication?

Journals consider that is good practice to release script and codes to repeat the published results, and many of us I think agree with this practice. Code are typically deposited in software version ...
56
votes
10answers
16k views

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

I am doing my thesis-based master’s in computer engineering and am required to program a tool in C++ as a part of my research. I am quite impressed by the help offered on the Code Review website and ...
49
votes
4answers
7k views

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

I coded the methodology based on the paper "Free Water Elimination and Mapping from Diffusion MRI" and I am curious if I am legally bound to take permission from the authors or the journal in making ...
40
votes
8answers
5k views

How to share computer code?

I am writing a paper with my adviser. Some of the key contributions of our paper include: A computer simulation model of an inventory system A set of simulation experiments and results to validate ...
32
votes
4answers
16k views

Can I request the code behind a research paper from the author?

I am in the field of computer science. It is often the case when I am reading a paper I start to wonder, "Wow stunning results, however, I would like to prove that." or "How exactly did he get these ...
31
votes
5answers
6k views

Principal investigator requests transfer of GitHub repository with my code to his account

I am a senior postdoc and have recently published a bioinformatics algorithm in an academic journal. For that publication, I was listed as the first author of the manuscript, and my principal ...
29
votes
1answer
2k views

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

I've found some code that I've posted online that has a BSD license published in a supplementary material of a different group in a high impact journal. The authors have replaced the name on the ...
27
votes
13answers
14k views

Outsourcing trivial authorless work

I have worked on a problem for close to two years. I feel I have an adequate theoretical solution. However I feel to get some backing on the theory I need some quantitative hard computer data. It is ...
26
votes
6answers
6k views

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

An article is published and the results depend heavily on a piece of code that the author wrote themselves. The author has not shared the code with the community, even though they have been using it ...
26
votes
1answer
1k views

License of code accompanying a published article

Given a paper that introduces a new algorithm and upon publication copyright is transferred to the publisher. Is an implementation of the presented algorithm considered a derivative of the published ...
21
votes
5answers
4k views

Is there an open-source license that enforces citations?

I build simulations and make them open-source. Depending on the context I either license them with Apache or GPL. I publish the simulation results in paper and link to the code. However sometimes some ...
21
votes
3answers
2k views

How to deal with papers/authors that provide no details of implementation?

I was reading a conference paper relevant to my area of study, and I found it interesting - they did what I was planning to do anyways, and had some extremely promising results. Now, I don't really ...
21
votes
7answers
3k views

Knowing when the code is good enough, for research

My question is in a similar vein to this one. My research requires code. I can write code and I know some things about writing good code. Both for readability, (e.g. standardised doc string, ...
21
votes
4answers
2k views

How much effort do researchers take to publish their source code?

When publishing a paper, some researchers publish the source code used for the paper. Is there any research/study/survey/... that looked at how much effort do researchers take to publish their source ...
20
votes
4answers
2k views

Should I supply code along with my paper submission?

I am submitting a paper to a machine learning/computer vision conference. Is it worthwhile to include some source code of my implementation so that the reviewers can test it themselves or gain a ...
20
votes
2answers
87k views

Source code plagiarism detection tool that checks against online content

I asked this question on Stackoverflow and was directed to ask it here. The question is: I wanted to ask about plagiarism detection tools for source code written in C++. When I searched Google the ...
19
votes
2answers
2k views

Reference on availability of source code used in computer science research articles?

I have several questions related to open-sourcing the source code used for a research article. Is there any research/study that addresses any of the following: What percentage of research articles ...
18
votes
5answers
4k views

Can I trust a paper that hides implementation details?

In Computer Science, sometimes we're assigned to reproduce the results presented by a paper that already have been published. In many cases (most of them) the code is not available, making the task ...
18
votes
4answers
2k views

when sharing source code to more than one party, should I notify them that others also were interested

A few weeks after my work was published in a conference, I received an email from a research group from another university asking me to provide my source code. The email was very polite and explained ...
18
votes
3answers
3k views

How should I compare my algorithm to others when their code is not available?

In computer science, we usually implement our work into algorithms and codes. So in order to compare our work to others, we also need to implement their approaches as well. But the problem is that ...
18
votes
2answers
4k views

When should you publish code on GitHub? Work-in-progress or after publication? [duplicate]

What is policy are you following about publishing data analysis code on GitHub? Do you do it after publishing or as a work-in-progress? I developed a number of Python algorithms to analyse a large ...
16
votes
7answers
20k views

Proper way to format computer code included in a thesis/dissertation

I intend to include my computational model code(s) in its entirety as an appendix in my dissertation. I've gone through my university's formatting guidelines and haven't seen anything on the proper ...
16
votes
5answers
461 views

How to review a software-tool paper?

I often get asked to review papers on new software tools. This always makes me wonder how one should review such a paper, or even whether software papers should undergo a typical review process at all?...
16
votes
2answers
471 views

I've reproduced a paper: where shall I share the code and findings?

The majority of papers don't share their code. However, I sometimes want to reproduce the results, and therefore re-code the experiments to try to reproduce the papers. Where shall I share the code, ...
16
votes
1answer
284 views

Study of code share practices in science

I am searching for a study that presents statistics of how often you can get code that claims to be available in scientific communities. I found the following interesting study, which is very similar ...
15
votes
6answers
15k views

When is it useful to include the code in a thesis?

I am writing my master of science thesis and I am not sure whether I should add some of the code I have written: they are not proper programs, but more like input files to be fed to a commercial ...
15
votes
1answer
466 views

Where to draw the line for authorship for a software-announcement paper?

I am currently working on a scientific software, for which I want to publish a software-announcement paper in a pertaining journal. While I am doing and probably will continue to do the vast majority ...
14
votes
9answers
7k views

Is it possible to ask the professor to check assignment before submitting?

I have got assignments related to programming. They are tough and my friends could not get results. I wanted to ask my professor to run them to see whether I did them right or not. (the deadline is ...
14
votes
5answers
1k views

Advisor wants copy of code to give to other student

My advisor has multiple electrical engineering masters research students under him. One of them came to me asking for help, saying the advisor asked her (let's call her Jen) to write some code to test ...
13
votes
2answers
1k views

Code in journal papers

Most papers do not specify a separate license for the source code, so presumably it would be licensed under the same terms as the rest of the paper. Typically, this means that the copyright lies with ...
12
votes
3answers
2k views

How to anonymize self-citation of source code repository in IEEE double blind peer review?

I am going to submit a paper IEEE Communications letters. In the paper, I cited my source code repository to provide an open access: ... For more detail, please refer [1] ... Reference ...
11
votes
2answers
3k views

How to Properly Cite Linux Source Code?

I know, the question of how to cite source code has been asked before, but I did not found anything helpful for my specific situation. I am currently writing my master's thesis. My university does ...
11
votes
3answers
202 views

Is it appropriate to put a scientific/technical document about code developed by our group on arXiv?

Basically, I have written a tutorial for a code which performs a specific type of electronic-structure calculation. The code has been developed by the group I belong to and writing this tutorial/...
11
votes
1answer
402 views

How to handle disagreement between collaborators on licensing academic code?

A group of students including myself have developed a certain program/algorithm. I as the main coder behind this group have provided 95% of all the actual code. The other two involved parties have ...
10
votes
3answers
2k views

Making your code publicly available: Does it have to undergo review?

In cases when the authors would like to make their code available online after it is published, is it recommended for authors to make their code available for review when they submit technical papers ...
10
votes
3answers
602 views

Publishing software in a convenient way

I create a software in order to solve a step of an specific problem. The results obtained (aided by the software) are going to be published in some journal. The focus of the publication is far away ...
10
votes
1answer
359 views

Can a university restrict publication of students' work due to plagiarism fears?

My question is inspired by this question. Say a student wants to publish on GitHub some code that they've written as assignments for a programming class. The student may be motivated by a desire to ...
9
votes
3answers
468 views

Code sharing between co-authors

During a collaborative experimental project in my PhD, I developed a rather intricate simulation + data processing tool. The work was published with myself as the lead author. One of the collaborators,...
9
votes
5answers
911 views

Can I post a pre-print of my paper on ArXiv knowing the paper will go through major changes? Alternatives?

I wrote a paper with a new approach and I implemented this approach in both R and SAS. I want to put the software online on Github and ideally on CRAN too. The paper has been reviewed by my ...
9
votes
1answer
3k views

Pseudocode, in a paper — is it a figure or a table?

The question is simple: I have to insert more pseudo codes in my paper. Last year we have labeled them as Table. Yesterday, my supervisor has said me to use Figure. What is the standard for IEEE ...
9
votes
5answers
409 views

How do I comment the code I wrote for a course I am lecturing in?

I am an assistant professor for a course on audio signal processing (for engineers) and I often write snippets of code to try to help the students follow the material. In addition, I get to lecture (1)...
9
votes
4answers
1k views

How to keep code and output organized?

I am having trouble keeping organized the files for the computational component of my research project. In brief, I have written computer code which I use to run computational experiments. For each ...
8
votes
5answers
3k views

Is It appropriate to put code in slides for a technical presentation?

I am doing a technical presentation on Minimizing Real-Time Data Stream Latency: Node.js and Asynchronous Operations. I've done some thorough research on the topic and I want to add some code blocks ...
8
votes
1answer
897 views

Writing a function name in a normal paragraph in my dissertation [duplicate]

I want to mention the name of an specific function (or method) that I used in a experiment in a normal paragraph in my dissertation. What is the best way to do it? Considering that the official ...
8
votes
1answer
172 views

How should I split my code and data between an open repository and the article's supplementary files?

I am working on a paper that involves some data and a piece of code to analyse the data. I want the results of the analysis to be reproducible and the code to be open. This concept of "reproducible ...