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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 ...

3
votes
3answers
175 views

Is there a default license for code libraries that accompany scientific research papers

I read a scientific paper, which is accompanied by a code library published by the authors. I couldn't find anything about its license. Could I just reuse the code? Is there a default license for ...
1
vote
4answers
239 views

Code plagiarism by teacher at renowned university [duplicate]

As a post-graduate student at a renowned university, I am supposed to make an assignment (see attached images) which is obviously inspired on this licensed scikit tutorial. Since the assignment (code)...
27
votes
13answers
13k 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 ...
60
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 ...
7
votes
5answers
517 views

Can you publish a paper Simply Implementing another Paper's Algorithm?

There was a highly cited paper published earlier this year in my field which introduced a highly theoretical, non trivial, algorithm that relied on extremely heavy theory. The algorithm was exact (...
4
votes
4answers
154 views

How to cite or refer to programming codes in a non Computer Science Master's Thesis?

I am writing my Thesis in finance field and I am using Machine learning methods. Therefore, I wrote many Python and R scripts for collecting data, cleaning it and applying some statstics. should I ...
4
votes
3answers
233 views

Should I use a personal github account or a new one to publish academic code?

When I want to publish academic code, should I use my personal account with a pseudonymous username or create a new one with a username based on my real name? My current account uses a pseudonym as ...
101
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 ...
3
votes
1answer
92 views

R Code attachment

Hello academia community, I'm writing a paper in Finance on Portfolio optimization and stock returns. For this, I'm using R code to compute optimal portfolio allocation, histograms, boxplots etc. My ...
3
votes
2answers
220 views

Who Owns the Code I Write (Graduate Student)? [closed]

As a graduate student in a CS program, "Who Owns the (rights to the) Code I Write"? I know that the answer is different depending upon: (Case-1) I work for the University or am supported in some way ...
1
vote
2answers
299 views

Thesis in use, potential employer wants to see source code

EDIT: Let me clarify things and specify my concerns: I wrote a program for my thesis that solved a problem for the target establishment. The establishment now uses the program with my consent but ...
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 ...
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 ...
8
votes
1answer
310 views

Are there any citable Github repositories not published in journals, that receive a lot of citations?

I wish to know whether there is some way, or maybe even some standard, for making a GitHub repository citable in a way that is recognized by academics. Many options have been suggested here, e.g., ...
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 ...
20
votes
5answers
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, ...
3
votes
2answers
155 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 ...
8
votes
1answer
892 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
99 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 ...
0
votes
1answer
61 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 ...
1
vote
3answers
235 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 ...
3
votes
1answer
72 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 ...
16
votes
5answers
434 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
93 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
170 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 ...
55
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 ...
20
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 ...
5
votes
2answers
259 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
159 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
118 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
124 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
135 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
210 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
87 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 ...
4
votes
1answer
172 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
122 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
98 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
401 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 ...
4
votes
2answers
207 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
306 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, ...
7
votes
2answers
212 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 ...
4
votes
1answer
253 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
129 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
866 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 ...
15
votes
1answer
437 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 ...
4
votes
1answer
229 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
351 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
627 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 ...