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. Generic code questions, e.g. help with debugging, are off-topic and will be closed.

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1answer
567 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 ...
3
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2answers
411 views

How to Approach Students with Different Expectations on Coding Lab Sessions as a TA

I am a TA for undergraduate Introduction to Programming class at freshman level. I usually have around 30 students per semester who have two hours of lecture earlier during the week with their ...
151
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14answers
31k views

How can a TA help a student who is certain she sucks at programming?

I am a TA for an undergraduate Signals and Systems class (Electrical Engineering). As part of this, I lead a lab session, where we teach students how to code up various signal transforming operations ...
1
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1answer
124 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
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3answers
460 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
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1answer
90 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
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5answers
930 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
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2answers
541 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
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1answer
343 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
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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 ...
1
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2answers
82 views

collaboration in phd project from an undergrad student

Actually I am making my PhD studies that is in the field of Computer Science and its algorithms related. There is one part in which for proving my ideas I have to program a web related extensive set ...
28
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5answers
7k 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
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2answers
288 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
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0answers
182 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 ...
30
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6answers
8k 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
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2answers
121 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 ...
2
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2answers
320 views

How much programming experience is needed before contacting a college professor for research/internship?

I'm currently a sophomore in high school looking to work with a college professor in the near future. I'm interested in the computer science field, and I was wondering how much programming I should ...
2
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2answers
193 views

Automatically checking retracted papers in bibliography

Is there a program or online service to automatically check if there is a retracted paper in the bibliography of a pdf file?
1
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2answers
149 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
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1answer
171 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
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1answer
283 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 ...
4
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3answers
1k views

Should I quit my Ph.D. program in scientific computing to become a software developer? [closed]

I’m three years into a Ph.D. program in scientific computing and I’ve just received my M.S. I’m thinking about leaving school to go to a programming bootcamp and become a software developer. I’ve done ...
1
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1answer
106 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
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1answer
214 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 ...
7
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1answer
191 views

Is there a programmatic way to check that a journal submission follows a style guideline?

Does anyone know of a programmatic way to check if an article submission matches a style guideline? Submitters are likely to be humanists, so LaTeX is not an option. Assume the journal has a Word ...
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3answers
596 views

Is following video tutorials online of programming plagiarising?

For my dissertation, I have decided to create a program which involves multiple mini games such as a snake game, tic tac toe, maze game and a puzzle game. Although, I liked programming, I struggled ...
0
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1answer
151 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-...
1
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1answer
148 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
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1answer
1k 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
306 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
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3answers
2k 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, ...
1
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3answers
3k views

Can I hire someone to write code for my dissertation (if I've designed the algorithm)?

Barring any extremely unfortunate disaster, I am five weeks away from a final defense and a Ph.D. At this point, we are in the re-write stage ("of my unforgivably horrible and weak thesis") but it ...
8
votes
2answers
419 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
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1answer
314 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?
30
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1answer
3k 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 ...
-1
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2answers
126 views

Is it possible to contribute a native speaker for editing the paper and add him/her as authors? Is there anyone? [closed]

I'm working on SIMDization and Optimization. I usually do some great jobs. But writing a good article needs a good knowledge of writing skill. I've implemented many programs. I can write and organize ...
6
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1answer
143 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 ...
10
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
669 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
518 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
491 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 ...
8
votes
3answers
1k 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 ...
16
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1answer
290 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 ...
3
votes
0answers
268 views

Value of a online masters degree in computer science to aid a slight career detour [closed]

I'm a software professional with 9+ years of experience. I've been working most of my career (6.5 years) on the server side, and middleware with only about 5% exposure to programming (Java). The ...
8
votes
3answers
1k views

How to make programming lectures more effective and stimulating?

I've been assigned the position of Teaching Assistant for the programming part of my university courses in Bayesian Inference, at the MS level. I previously taught a course, a few months ago, in ...
11
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3answers
626 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 ...
4
votes
1answer
661 views

PhD consisting mainly of programming work

I'm currently a second-year PhD student, in computer engineering. My research area is in computer graphics and virtual reality. I currently don't have a specific goal or problem to solve, except ...
68
votes
11answers
25k 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 ...
66
votes
3answers
7k views

Teaching a blind student MATLAB programming

I teach a first year undergrad class in MATLAB programming, and one of my students is completely blind. Quite amazingly, the student memorises the whole chapter before class and regurgitates with the ...