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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.

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2
votes
2answers
195 views

Can I use code from a supplementary material and publish it as part of my own paper?

Someone published a paper whose supplementary material contains source code. Can I include part of that code (I would mark it as copied in the source and the manuscript) in my own code, which is ...
3
votes
2answers
517 views

How to ask for code from authors who have proposed algorithms in computer science? [duplicate]

I am developing an algorithm, and I want to compare its performance with various existing state-of-the art methods. I would like to contact the authors of these methods and ask if they can send me the ...
19
votes
2answers
3k 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 ...
8
votes
1answer
918 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 ...
0
votes
1answer
283 views

What is the standard way to refer to shared code in conference papers? [duplicate]

Say I have a github repository with the shared code and data used for that conference paper? What is the standard way to refer to it in the paper itself? Write something like. The code is available ...
1
vote
3answers
267 views

How to provide codes to reviewer without making it public

I wish to provide codes and data to reviewer along with manuscript at the time of submission. I can upload the codes on a public repository, but it will bring it in public domain, I want to provided ...
1
vote
1answer
106 views

Handling computer files in simulation-based research with multiple storage drives [closed]

Can somebody give me an advice about how to efficiently handle data files, source codes, documents, and manuscripts of research projects based on numerical simulations? My problem is that I use ...
3
votes
1answer
76 views

Review-only supplemental material

I am at a difficult position. I work in a major software/telecommunications company, and pursue a doctoral degree at the same time. The company has strict policies against competing behavior. I have ...
18
votes
5answers
591 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?...
0
votes
2answers
135 views

Best license for an applied research project

I am looking to incorporate a license in the source code of a research project of University A, in which I was the last contributor. Historically the computer-science school has not forced researchers ...
1
vote
1answer
217 views

How to cite my own code in an academic paper?

I’m about to submit a research paper to the Intel STS competition. I am basically finished with everything about my paper, but I need to cite a certain algorithm that I invented in my own paper. I do ...
15
votes
6answers
18k 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 ...
-1
votes
2answers
120 views

How to refer to a Method that is to be re-implemented in my thesis?

I am writing my thesis (computer sience) and wonder how to refer to an algorithm which i reimplement as a part of the thesis. There is a paper describing the original algorithm and I am only ...
23
votes
5answers
5k 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 ...
2
votes
0answers
169 views

Is it disadvantageous to my research career in bioinformatics if my PhD work is mainly software development? [closed]

I am in the fourth year of my Ph.D. studies in bioinformatics. I have published two articles, one in my second year on the comparative genomics of a group of bacteria as a co-first author. Since ...
5
votes
2answers
274 views

Can I write a paper on software that I published a year ago?

I am a bachelor-level (software engineering) student. I made a GitHub repository more than a year ago, where I use machine learning and deep learning to identify movements in accelerometer signals. ...
17
votes
1answer
512 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 ...
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 ...
1
vote
2answers
136 views

What to do if I have a good proposal for experiment but don't have an ability to fully conduct it?

I've recently began working on machine learning, and I was a mathematician before then. Despite such background, as ML is a fast moving area, since I have studied the recent progress considerably and ...
1
vote
1answer
145 views

Citing author of visualization source code?

I've found some source code that creates a visualization I like. I've (slightly) modified it and used exclusively my own data in it. Is it right to cite the github repository I acquired the original ...
7
votes
1answer
228 views

Requesting a trained Neural Network model from an author?

A bit of background: I am working in a R&D department of quite a big name in the IT industry, and we are trying, clashing and combining different ideas and cutting-edge inventions to tackle our ...
1
vote
1answer
94 views

Citable code snippets as gists

I have several code snippets shared as gists in GitHub. How to make them citable with a DOI? I know whole repositories in GitHub can be made citable using Zenodo or Figshare (guide). But as I have ...
3
votes
1answer
190 views

Re-implementing one's own proprietary code as open-source

I wrote some software as part of an internship. It worked well for the task and we published a paper on it. However, because the internship was at a company, not my graduate institution, the code is ...
0
votes
1answer
128 views

Scientific publications and related software sourcecode

I want to create a dataset (offline, only for my research purposes) based on scientific publications (research papers), which are somehow connected to software source code (for example given by a git-...
0
votes
1answer
108 views

How do I use internet comments in my research?

I want to use comments on the internet to gather user requirements. I plan to collect these comments, read them and decide what the person wants based on what they've written. These list of "wants" ...
4
votes
2answers
263 views

Reproducible and exact calculations vs. approximate and slightly random results in experiment

When experiments are performed and reported in an academic article, I learned that reproducibility is important. I am implementing a system where I stand between the choices to use GPU acceleration to ...
0
votes
1answer
743 views

How to reference Source Code

I'm writing a paper on a technique which I have implemented in open source software. I'd like to reference the location of the open source software and the code I implemented for the technique so as ...
7
votes
3answers
966 views

How should I reference a repository of data and resources created to accompany my publication?

I'm writing a research paper and there's a large amount of code and data related to the study which may be of use to those who would read the study. They can confirm the correctness of the techniques, ...
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 ...
16
votes
1answer
289 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 ...
8
votes
2answers
301 views

Should licensed code be acknowledged in Thesis

When some function library licensed under BSD is used in simulations, should it be acknowledged in Bachelors/Masters Thesis, which have no length restrictions? In this particular case the functions ...
3
votes
1answer
271 views

Do reviewers review the code submitted with papers?

In computer science, when submitting a paper, it is common to submit some code to reproduce the experiments performed in the paper. Is it common for the reviewers to review that code?
6
votes
1answer
131 views

Submit other people's code together with a paper

I am submitting a paper to a computer science conference. In this paper I compare experimentally a method A (mine) with a method B (from other people). I found the code for method B on git-hub by an ...
154
votes
12answers
19k 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 ...
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 ...
9
votes
5answers
1k 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 ...
3
votes
1answer
336 views

Is source code provided in the appendix of a thesis copyrighted? [US]

I'm contemplating including source code in the appendix of my thesis. Although, I will not be strictly required to, I think this would be something that my committee would like to see. Will I run ...
10
votes
1answer
389 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 ...
0
votes
1answer
163 views

Documenting code for thesis [closed]

I'm making my degree thesis on applied maths. An important part of the work is the implementation of some algorithms and simulations so code is part of the work. And I mean a lot of code. I don't ...
65
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 ...
10
votes
3answers
606 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 ...
3
votes
3answers
173 views

Protocol emailing R Package creators [closed]

I have found an R Package written up that does exactly what is required but cannot figure out a bug that has presented itself. I have gone through the code and source code for the function and cannot ...
4
votes
2answers
608 views

I need some code that was made available by a student 15 years ago, but is no longer online. How can I contact someone in the group to get the code?

I need Matlab code of a method to compare it with the results of my proposed method. The method which I want to use happened to be available online by a research group in a university in US in 1997 [...
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 ...
9
votes
2answers
607 views

Pedagogical pros and cons of requiring undergraduate students to follow open/reproducible research practices?

I regularly teach an undergraduate course in which students are expected to complete projects that involve writing code. I also supervise undergraduates in other project and thesis work that involve ...
1
vote
1answer
628 views

Is it plagiarism to hire a freelance programmer for an assignment but change a lot of it before you submit it?

I took freelancer tutor help for a Python programming coursework during my MS but did not submit the exact code he gave, I refracted it and changed a lot of it. Is it considered plagiarism? I am ...
1
vote
1answer
107 views

Can I get code reviewed if it might be published or referenced in a publication?

I am a recently-graduated high school senior in the United States who is currently doing research with a professor in a lab at the university that I will attend. One of the components of the project ...
4
votes
3answers
1k views

Amount of pseudo code in the thesis body

I'm writing my undergraduate thesis (~25 pages) on a computer program I've developed. Naturally, I'm expected to explain what the program does and how it is implemented. However, the algorithm is ...
11
votes
3answers
213 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/...
4
votes
2answers
337 views

What license to choose for a model which we will freely distribute?

My research team has developed a model, analyzed data, and generated results. We are currently in the process of publishing the results -- the article is in review -- and we are preparing to make our ...