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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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
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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
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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 ...
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
493 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
731 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 ...
17
votes
7answers
24k 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 ...
5
votes
2answers
7k views

How to format code for IEEE Journals

I'm working on a paper for IEEE Transactions on Computers, and I can't find any guidelines on how to format code (C++) that is included in the paper. I found some other papers with short code ...
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 ...
10
votes
3answers
514 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,...
7
votes
1answer
51 views

Why don't grants from publicly-funded organizations systematically demand code and data to be released?

I wonder why publicly-funded grants do not systematically demand from the recipients that code and data to be released, and results/papers to be publicly accessible. (put aside data that raise privacy ...
5
votes
5answers
1k views

How to demonstrate programming knowledge in CV, while applying to academia and industry?

I'm currently looking for both postdoc position(preferred) and industrial position in areas where I'd need to do programming in the language(s) my lab/company will need me to. The academic areas I'm ...
1
vote
4answers
741 views

Is it acceptable to put programming code as proof in paper?

I used statistical language R to fit probability distribution to acquired data. Instead of doing it by hand I relied on code. I wrote something like "probability density function was computed using ...
13
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 ...
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 ...
2
votes
0answers
229 views

Reference on the time it takes for a source code used for a research article to be released

Is there any research/study/survey/... that looked at how much time it takes for the authors of a research article to release the source code? Ideally I'm looking for an approximation distribution. ...
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 ...
3
votes
1answer
626 views

Can I use map, fold, filter in publications?

I have to write down algorithms in my thesis, and these are getting way shorter if I use "map," "fold," and "filter" heavily. This generally results in a "map, fold, filter"-chain with a depth of 3. ...
1
vote
2answers
192 views

How do I cite or reference code that has not been officially published?

Let's say I go to someone's website, look up the source and use some of the JavaScript idea/pattern/code that is not a part of the wider framerwork/something similar, but a unique code that was ...
1
vote
0answers
96 views

Do the reviewers ask the authors to send their programming codes for the paper? [duplicate]

I am writing a paper for a Elsevier journal in optimization field. I was curious to ask, Do the reviewers ask the authors to send their Matlab or,.. codes of paper to proof their validness or honesty? ...
8
votes
1answer
2k views

When should I cite, if using code from Stack Overflow?

I already found a question handling the case if you got some information from Stack Exchange for my thesis. Unfortunately I did not find anything about the case that I get a solution (not necessarily ...
1
vote
3answers
879 views

Does writing code for an assignment after seeing similar code online count as plagiarism?

In my compilers class assignment, we were asked to write some MIPS code. One of the problem involved implementing fact() function as a sub-problem. I wanted to implement the standard recursive version ...
9
votes
4answers
2k 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
1answer
178 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 ...
4
votes
5answers
790 views

Is it realistic to deal with a huge undocumented code base for master's project?

I'm currently pursuing a Master's degree in a STEM field and working on a thesis. For my master's thesis, my advisor suggested I expand the code of the group's software and add new features to it. ...
3
votes
1answer
2k views

How to make a paper's author willing to help me with his source code like a semi-supervisor?

I am really in trouble. I am doing my MA thesis on wireless sensor networks, and I have a source code with more than 16 files and each one more than 5000 lines. It's very complex and has no ...
5
votes
1answer
2k views

Are there general guidelines for including code in a research paper?

I'm a beginning researcher trying to write a research paper , so please bear with some of the really basic questions I might have. I've already looked around for some help online, but the websites I ...
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 ...
6
votes
1answer
2k views

Is it OK to contact authors of the research paper requesting an implementation? [duplicate]

Given the research paper itself and having a complete understanding of the proposed system, I could implement the system on my own. If my intention is not to re-implement it myself, but rather study ...
12
votes
1answer
410 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 ...
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 ...
4
votes
2answers
219 views

Improve software code when reviewing paper

When reviewing a manuscript describing a new software tool, reviewers are often asked to assess its utility, quality, novelty, ... I was wondering if, in addition to the classic comments on the ...
1
vote
2answers
285 views

Including many pages of serialization code and generated source code in Master's thesis?

I'm working on my Master's thesis in Computer Science. Shortly, I am "drawing" a diagram, which is then serialized and from the serialization I generate some source code. So, my question is not about ...
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 ...
2
votes
1answer
199 views

May I modify the code/program for my undergraduate thesis project?

I have a project for undergraduate thesis. Then, I found this Chapter VBI-6. Hand and Finger Detection. In the Downloads section, there's code that we can download and launched. I want to use it and ...
7
votes
3answers
4k views

Inclusion of `computer code` in a thesis

During the compilation of thesis (MSc or PhD) in a case we wanted to include some program codes as chapters: We prefer to put heading to all program codes everywhere they appear as complete source to ...
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 ...
8
votes
3answers
556 views

How can we change things so more researchers are willing to share their source code?

This is a followup to Why are CS researchers reluctant to share code and what techniques can I use to encourage sharing?. That question specifically asked how one can succeed in obtaining researcher'...