If you need help with online teaching or other challenges in academia arising from the COVID-19 crisis, we have prepared this FAQ to get you started.

Questions tagged [software]

Queries related to various software used in academia. Questions shall not address highly technical aspects of the software but shall address features/issues highly relevant to academia. For 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), use the `code` tag instead.

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1answer
46 views

How to publish review of commercial software

I really like software product X and been using it for >6 years. I am unaffiliated and never have been linked to company or anyone involved with X. I would like to publish a paper that explains why ...
2
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0answers
110 views

Remote lecturing: best software approach [duplicate]

With the recent outbreak of covid-19 many of us will need to think about remote means of teaching. The option for me that seems ideal would be the capacity to broadcast exactly what is on my screen ...
1
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1answer
108 views

In addition to the grammerly software, are there other better tools in English writing?

For non-English speakers, are there other useful tools besides grammerly software in English writing? Mainly check whether the sentence is authentic.
12
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3answers
2k views

I used a fork of a GitHub repository whose paper I cited – should I also cite the fork?

I want to cite a GitHub repository in scientific publications. The repository that I used is a fork version of the original GitHub repository which is accompanied by a paper. Both repositories are the ...
4
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2answers
178 views

How to work in academic research as an outsider/experienced software engineer?

I would like to have advice on how a software engineer with a decent (>10 years) of industry experience can join a team doing academic research in the areas of physics, chemistry, biology or climate ...
0
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0answers
39 views

Are there software libraries or registries like ASCL.net for other fields in the physical sciences, Physics in particular?

The question Roadmap and possible pitfalls for a first-time software author to publish a paper on a Python package? explains the road I've started on. I just noticed that Skyfield, a software package ...
6
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1answer
384 views

Potential consequences for a PhD student using a cracked software

A friend of mine, along with ~10 of their colleagues, recently received an email from the IT department saying the department is investigating those students for using two pieces of cracked software. ...
32
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5answers
4k views

Can open-source software be peer-reviewed and published?

My colleague and I have developed a software tool and intend to release it open-source. This tool is specifically for tasks in my field but we think it would be helpful for the wider community. Our ...
4
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1answer
127 views

Roadmap and possible pitfalls for a first-time software author to publish a paper on a Python package?

I'm not a software developer by trade but I am in the process of writing a Python package which models an experimental apparatus and physical process and generates simulated data. Results can be used ...
1
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2answers
108 views

How to work authorship of software developed with another University

I am supervising a PhD student, enrolled at another University, where the co-supervisor is employed. We developed some useful software in her thesis and published 3 papers. In this development another ...
39
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6answers
3k views

Is there an internet Git-like repository for collaboration on a paper?

I've just started using git for tracking changes in a LaTeX paper I'm writing, and for collaboration with co-authors. However, I cannot find easily private git repositories with reasonable plans for ...
1
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3answers
199 views

Can I use open-source code for a simulation for my research?

I am working on a paper and I found open-source code that I could use for running a simulation. Should I write my own code for that simulation? Will it be enough if I refer to the code in my citations/...
0
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1answer
87 views

What will be the research methodology if you are developing a generic software [closed]

I'm developing a generic software for the unorganised retail sector. The design is completely based on the literature review that has been conducted. The only problem is that since I'm not doing any ...
2
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1answer
209 views

Is it possible to work full time and do a part time PhD in software engineering in England?

Is it possible to work full time and do a part time phd in the area of software engineering in England saying that I want to use my job earnings to pay my tuition fees? And if I start a part time PhD ...
21
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3answers
2k views

What software to cite in a manuscript, and how?

When writing a manuscript for a scientific article, I often wonder what software I should cite or acknowledge, and how. The first problem is to make a choice which software to cite. On the one hand, ...
2
votes
2answers
249 views

What are the main practical complications/challenges to using Linux as your full time OS, particularly as faculty in Biology/Ecology?

I am an ecology post-doc and considering switching from Windows to Linux for my main work computer (I am not a mathematical modeller). I have used Linux before and I am aware that, with effort, one ...
57
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10answers
6k views

How can a software developer best volunteer to help childhood cancer research? [closed]

I have 30 years of professional experience as a software engineer and I'm at the point in my career where I can volunteer lots of time. I have helped with several childhood cancer organizations over ...
2
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2answers
84 views

How to do a literature review on practical research (thesis)?

Some background, for my bachelor of science degree I have to do a practical research (thesis) for a company that develops software. At the end of my Introduction chapter I arived at the following ...
1
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1answer
166 views

How can multiple people grade assignments online so that different graders don't see each others' grades?

this question is related to how you do your double blind marking for assignments, we are looking at the coursework plugin for moodle but are interested in how other other institutions do this. a ...
-3
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1answer
156 views

What are good methods for clarifying student uncertainty? [closed]

A primary task of professors is communication with their students. Communicating typically involves lecturing, clarifying uncertainties, and receiving feedback. Lecturing happens at fixed times, but ...
3
votes
1answer
115 views

Which authors to cite for open source software

While I have worked on open source software myself I'm, strangely, uncertain about how to cite it in a paper. I do know how to cite software itself, I'm just uncertain which author(s) to attribute it ...
18
votes
8answers
822 views

I'm looking for an application or workflow which integrates data values into the writing process

Currently, on all of my projects, I do my data analysis, create my figures, put them into a word document, and then I start writing. I say things like "We saw a 35% reduction in the effectiveness of......
13
votes
4answers
2k views

Is it safe to use pirated software for Doctoral research?

I am using unlicensed simulation software (downloaded from torrents) for Doctoral Thesis (and Research papers) on my personal laptop without the knowledge of my institution as the university doesn't ...
2
votes
0answers
59 views

Best tool for digitally marking assignments? [closed]

I was wondering if anyone could recommend a good piece of software for marking digital (PDF) assignments. Specifically, I am marking a first-year mathematics course, and need to do the following for ...
7
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3answers
302 views

Managing lab funds

I am very fortunate to have several sources of research fundings to run my lab. Like many other skills needed for running a lab, I have no background in accounting (?). Different funds come through ...
3
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1answer
100 views

Listing (peer reviewed) software article on CV

I am a contributor to an R package, and we are preparing a submission to the Journal of Open Source Software (JOSS). Submissions are peer reviewed (guidelines available here), and articles are ...
2
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0answers
71 views

Citing contributors to open source project when publishing to Zenodo

appleseed, our open source (MIT) physically-based rendering software, is used in various circles, one of them being academia. We have been asked to obtain a DOI so that our software could be cited. ...
0
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1answer
127 views

what is the best software for drawing mechanical mechanism? [closed]

I want a software which I can use to draw mechanisms like this picture: Update: the author told me that : "the figure was made in Adobe Photoshop/Illustrator by tracing the hand-drawn kinematic ...
4
votes
3answers
447 views

Git repo in shared folder or multiple cloned repos in each researcher individual folder for collaborative data analysis? [closed]

We are four social scientists working on a dataset that is in a secure server accessible via remote desktop. We have a shared folder where we put our code and datasets: root -functions -data -...
72
votes
13answers
18k views

Is there any efficient non-linear note-taking software?

I'd be interested in tools helping to organize thoughts and ideas, especially in a non-linear way (i.e. not as most existing note taking tools, working with lists and bullets, but rather as a post-it ...
15
votes
5answers
2k views

Searching for a quotation manager

I’m looking for a way to manage the text of the quotations that most certainly I will use (i.e. quote) in the future. I’m a philosopher, so this is specially handy —and even required— for the ...
3
votes
0answers
159 views

Have there been attempts to get around “DeWitt clause”-like license restrictions?

(This is a complementary question to: Has the DeWitt Clause, which prevents publication of named DBMS benchmarks, ever been successfully defended in court?) Several commercial database vendors ...
29
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2answers
1k views

Has the DeWitt Clause, which prevents publication of named DBMS benchmarks, ever been successfully defended in court?

Several commercial database vendors include an end-user license agreement provision, known as the DeWitt Clause, that prohibits researchers and scientists from explicitly using the names of their ...
0
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2answers
151 views

Work for college affecting assignment

For an assignment, I was paired up with a professor who also has an administrative role within my college. The assignment was unique to me, with a competitive process to be chosen for the assignment (...
5
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3answers
402 views

Software to create repositories of students' software projects

I want to be able to store the software projects my students submit so I can catch plagiarism. Some students copy work from previous years and it would be really helpful if I could find a way to store ...
2
votes
1answer
107 views

Can I develop software that solves a problem as a Master's thesis?

I have designed and developed software that solves a problem (In healthcare if it matters) for my master's degree, and I'm having some doubts about whether it could be considered an actual research to ...
15
votes
4answers
3k views

How to make a software documentation “officially” citable?

We are currently finishing the implementation of a scientific software library. It's the first project of this type for me and I'm curious, how to make the software citable in a similar way to Molpro ...
1
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0answers
84 views

Cheaper alternative citation managers for Mendeley [duplicate]

I am using Mendeley for paper and citation manager. Mendeley have 2 thing I need: index, searchable in all paper (title, author, content, ...) auto-lookup all information (title, author, conf, ...). ...
1
vote
0answers
97 views

Experience with paid English grammar and style software for writing papers?

I'm looking to suggest to our institute to invest in a paid software for helping writing, along the lines of Grammarly Premium, Antidote 10 or something similar. Does anyone have any experience with ...
25
votes
5answers
702 views

Issue tracking when writing a paper

When writing papers (and even more - when revising after collaborators', or reviewers', remarks) it's hard to keep track what is done, what needs to be fixed, what cannot be fixed, when opinions of ...
71
votes
12answers
11k views

Why do faculty use the software “Blackboard”?

It is becoming apparent to me that, outside my field, use of Blackboard and other LMS software is becoming extremely common. Indeed, a rash of technical problems here is making it apparent students ...
40
votes
7answers
8k views

A team member of a coursework software development project didn't contribute in any way. Can I remove his name from the project?

I am the project manager of a small team of five undergraduate developers who have been working for months on a large system for our Senior Capstone project. Four members of the team, including myself,...
6
votes
3answers
230 views

When is a not updated software considered deprecated in the academic world?

Currently I'm writing a thesis in Computer Science for which I need to introduce and compare several open source tools that are available for performing a certain type of testing (mutation testing) on ...
0
votes
2answers
142 views

License for research projects

What is a good way to license your research projects? Diving into the details of most licences, a lot of their wording and concerns seem centered around 'redistribution', and are not so much driven ...
1
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1answer
98 views

Why not design the proposed online survey using the actual survey tool? [closed]

Question: Assuming no school prohibitions on doing so, why would you not design the proposed survey in the proposed survey tool, and include screenshots of the survey in the proposal? Background: I ...
55
votes
14answers
31k views

Lab colleague uses cracked software. Should I report it?

I've just (accidentally) found that one of our colleagues in the lab (who is a graduate student) uses a cracked piece of software on his personal laptop (We were talking near his station and a pop up ...
84
votes
14answers
36k views

Can a lecturer force you to learn a specific programming syntax / language?

My class is currently further learning our relational database / SQL as part of the course. The lecturer we have currently is restricting us to learning specifically Oracle SQL syntax rather than ...
5
votes
1answer
175 views

Is there a tool to visualize the citation network which works with Google Scholar?

I know about tools like CitNet Explorer and VOSviewer, but they only work with Web of Science, which doesn't contain many papers I'd like to have in the network. Is there any software, which does the ...
4
votes
4answers
2k views

What software license allows me to have GPL for academic use and paid use by industry for my open-source project?

I have spend many years during my PhD developing a code base and decided to open-source the code when I finished. It's currently under GPL. The code is used by many different research group around the ...
13
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4answers
1k views

Software for tracking next manuscripts to submit

I manage a research group and need to track, for all manuscripts I am going to submit soon, things like funding agency I need to add for that manuscript, authors for the other, potential journals for ...

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