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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5
votes
2answers
277 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. ...
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 ...
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
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 ...
1
vote
2answers
138 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
146 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
231 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
191 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
130 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
109 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" ...
0
votes
1answer
758 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 ...
5
votes
2answers
268 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 ...
7
votes
3answers
1k 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, ...
8
votes
2answers
304 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
272 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?
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 ...
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 ...
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 ...
17
votes
1answer
517 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 ...
3
votes
1answer
350 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
396 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 ...
5
votes
3answers
875 views

Why would a university restrict publication of work due to plagiarism fears if TurnItIn was used?

I used to host some code I'd written for university assignments publicly on my GitHub account (after the deadlines had passed, of course). Before long, I received an email from the dep't asking me to ...
0
votes
1answer
164 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 ...
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 ...
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 ...
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 ...
1
vote
1answer
218 views

How to submit code (visual studio projects, C#, OpenCL) with my IEEE paper submission

I am trying to submit a paper to IEEE (transactions on signal processing). Along with my paper I have written some code (Visual studio projects, C#, OpenCL and accompanying dlls and exes). The ...
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 ...
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 ...
1
vote
1answer
631 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 ...
3
votes
2answers
528 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 ...
5
votes
1answer
4k views

Is it plagiarism to use an online tutorial as the basis for completing a programming assignment?

Let's suppose that you were assigned a programming project, which is considered from your teacher/professor, not easy. However, you manage to find an online tutorial, that guides you step-by-step ...
13
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 ...
4
votes
4answers
280 views

Using previously developed code for research at a new place

My ex student developed a useful program while working with me and some other students/postdocs in my group. Nowadays the student is a postdoc at a European university. She has a copy of the code and ...
4
votes
2answers
281 views

Can I upload a modified version of a code from a journal paper to Github?

I am new to Github and I want to upload some scripts that I developed during my research. One of the scripts requires the use of a small external program (not mine) whose source code is included as ...
0
votes
1answer
380 views

Usage of a web application that I sold for an academic project: Copyright issues?

I am currently a master's student and really glad that I learned almost everything about plagiarism prior to my master's thesis, I really want it to be perfect. Anyway, I have an issue that has been ...
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 ...
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 ...
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 ...
14
votes
5answers
2k 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 ...
8
votes
1answer
2k views

How and when to cite code from MATLAB File Exchange

What are the rules/etiquette to cite MATLAB File-exchange submissions on paper publications? There are different scenarios where I am curious what is best: FEX submission is clearly code from a ...
3
votes
1answer
123 views

Publishing research software that was developed by professional programmers - attribution ettiquette

I wish to publish a software platform that was developed for a research project. The usage-logic and user interface design were largely specified by the academic team, but the code was written by ...
16
votes
2answers
503 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, ...
1
vote
1answer
139 views

Advantages/disadvantages of bundling source code from separate, related papers?

Say that you have several papers, each with a set of experiments, in which the source code overlaps appreciably. If you wish to release the code for each paper, which is better: isolate the relevant ...
2
votes
2answers
796 views

Is is necessary to include computer code into thesis? [duplicate]

During my research, I have developed some computer codes to optimize the coefficients of theoretical equations against the experimental data. The computer codes was developed to make things easier ...
9
votes
5answers
422 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)...
1
vote
1answer
2k views

Using code from github for own thesis

For my master thesis I should write a simulation program, and compare the results with the results I get from commercial programs. Now I found a already existing script with exact the data I need on ...