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
112 views

How detailed should I describe my actions regarding code?

I am writing a thesis about a data analysis I'm implementing and am currently describing my data preparation where I talk about what needed to be done prior to the analysis (formatting the data, ...
-1
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0answers
18 views

Research question thesis [migrated]

I am now in high school and have to do research. But I am not sure which research question to choose. I would like to talk about programming languages and therefore something within computer science. ...
2
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2answers
191 views

Does building a Python library fall in the category of research?

If a Python library is built can it be turned into a research paper? Will it be accepted?
27
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10answers
6k views

Supervisor wants me to support a diploma-thesis software tool after I graduated

During my last year of MSc. studies, I was part-time employed on the university project. The project was related to my diploma thesis, and my task was to create a data-mining software and run ...
41
votes
4answers
7k views

Double blind peer review when paper cites author's GitHub repo for code

I and my coauthor wrote a paper and the project involved creating a (small) software library. Part of the novelty of the paper is the output of the code, which is a digital object not intended for by-...
40
votes
6answers
11k views

Will a paper be retracted if a flaw in released software code invalidates its central idea?

Say I have written code that performs a physics calculation. After this, I get a paper published based on the results of the code. In the interest of advancing the progress of science, I upload the ...
40
votes
6answers
10k views

I have found a mistake on someone's code published online: what is the protocol?

I have been using an econometrics toolbox for around 2 years and it is great, very useful. It is available from someone's personal website. I have found a mistake in one piece of code which has set ...
16
votes
6answers
4k views

Should I include code in my research paper?

My paper is about a specific application of blockchain. I've developed a basic prototype for it and so far, I've described it in detail, and put screencaps of the interface for it. Should I also ...
1
vote
4answers
128 views

Should I compare my proposed work with my implementation of the previous related papers or the reported result?

In computer science, I need to compare the accuracy of my proposed method to the previous ones. There are two possible options: Implement the methods described in related papers on my own machine Use ...
1
vote
0answers
92 views

In-house code used in paper methods section but not shared

I am muddling my way through my program an stumbled upon a technique I would really want to employ in my research. The technique is well outside the realm of my PI's expertise and my PI would not run ...
2
votes
1answer
104 views

Error discovered in an accepted conference paper but not yet presented

I'm a CS student, and I discovered two code bugs that change some numerical values on a table of a paper that got accepted and will be presented at a conference very soon. The changes is very small (...
3
votes
2answers
114 views

Code hosting platform that allows sharing through link [closed]

I am finishing my thesis (Physics) and need to add a link to all the codes I created to do the analysis presented in the manuscript. The codes are not polished and they are intended to be public ...
56
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 ...
1
vote
2answers
201 views

Sharing Code In thesis

My question is about sharing code in my thesis. I ran simulations using ready data in my field from a book. After that, I compared the results with those from the book. Do I need to share my code or ...
4
votes
3answers
188 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
284 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
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 ...
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 ...
7
votes
5answers
650 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
212 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
261 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 ...
4
votes
1answer
116 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
274 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
364 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
8k 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
559 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 ...
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, ...
2
votes
2answers
186 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
913 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
229 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
1answer
102 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
262 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
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
530 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
131 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
207 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 ...
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 ...
21
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 ...
5
votes
2answers
270 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
166 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
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
142 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
224 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
90 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
186 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 ...