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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129 votes
17 answers
138k views

Software to draw illustrative figures in papers

I would like to have suggestions of good software for drawing illustrations in research papers. I already know about Xfig, but this works only on Linux and is at times, clunky when it comes to text. ...
175 votes
14 answers
35k views

Why do many talented scientists write horrible software?

I am a software engineer and I have been working with people with academic backgrounds for several years. Many times, I've noticed that (even otherwise brilliant scientists) produce code of extremely ...
Thanatos's user avatar
  • 1,931
90 votes
15 answers
28k 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 ...
user avatar
73 votes
7 answers
14k views

Why use version control systems for writing a paper?

I am following the advice of @Piotr Migdal in Is there an internet Git-like repository for collaboration on a paper?, and I want to ask about version controls: how beneficial are they (specially under ...
seteropere's user avatar
  • 13.8k
33 votes
7 answers
11k views

What is the easiest way to check for plagiarism in student essay papers?

I've had to grade quite a few essay papers in the classes I've taught, and I've suspected some may have plagiarized but I never really pursued check on them because it would be too time consuming to ...
Paul's user avatar
  • 11.4k
30 votes
3 answers
6k 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, ...
olenz's user avatar
  • 541
319 votes
18 answers
39k views

Should I share my horrible software?

After I had published my paper, some people asked me to share the software that I developed. At first, I was very happy that my paper attracted some attention, and I was happy to share not only the ...
sean's user avatar
  • 17.5k
84 votes
8 answers
30k views

Free, open-source substitutes for Mendeley?

Mendeley is (mainly) a proprietary social network to share basic citation data and research papers. see also Are there any free and open source substitutes for this service? A technical possibility:...
Jonas Stein's user avatar
  • 1,659
173 votes
12 answers
28k views

Why are papers without code but with results accepted?

I just started reading some papers (Computer Science, specifically Computer Vision) and thought "now let's look at the source code" and was quite astonished that most of the papers don't have any ...
Sam Stoelinga's user avatar
65 votes
5 answers
18k views

Should I cite all R packages I used?

Intro: R is a open-source software tool for statistical analyses and graphics, which is heavily used in different science disciplines and which is becoming more and more popular (although it is ...
hplieninger's user avatar
54 votes
6 answers
42k views

Software for extracting data from a graph without having to click on every single point?

There are many times when I am faced with the task of extracting data from a published graph (usually a bitmap image in an paper). For example, a scatter plot from which I would like to get a list of ...
F'x's user avatar
  • 73.1k
46 votes
6 answers
56k views

Is it mandatory to include the registered trademark symbol ® next to the name of a computer program?

Suppose you write a paper and you use Wolfram Mathematica to do calculations. In the article, should the program be mentioned with the registered-trademark symbol immediately following the name and in ...
User X's user avatar
  • 1,119
44 votes
6 answers
5k views

Should I write a paper on open-source software I've built?

I have been fairly active in the open-source software community with a few projects that have gotten some attention. However, my reputation in the academic/publications world is a little bit low and I'...
Luca Matteis's user avatar
  • 1,157
39 votes
6 answers
8k views

Software/App for electronic research notebooks

I want to keep a research notebook for my computational "experiments". Basically, I should at least be able to write text and attach images like plots. Other nice features to have would be linking to ...
highBandWidth's user avatar
34 votes
5 answers
5k 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 ...
Tom Kelly's user avatar
  • 2,284
28 votes
6 answers
1k views

Archiving papers, simulation and experimental data, etc?

Archiving of papers and projects is very important for most of the people, and everyone has a method of it. I, personally, try to have different folders for different papers. In the folder of each ...
antmw1361's user avatar
  • 1,173
11 votes
5 answers
3k views

Reference manager with note-taking/quote-storing capabilities

I'm looking for a reference manager with note-taking/quote-storing capabilities. I don't need a full knowledge management suite, but I want to find a program where I can store and search long notes/...
Matthew R's user avatar
  • 111
42 votes
6 answers
4k 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 ...
Piotr Migdal's user avatar
  • 26.3k
17 votes
2 answers
4k views

How does copyright work on screen captures?

I am writing an article comparing three pieces of software. I have taken screen shots of all of them and would like to use them in a non-open access article. Given the intended journal, there is a ...
StrongBad's user avatar
  • 104k
17 votes
5 answers
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 ...
marlonob's user avatar
  • 279
14 votes
2 answers
10k views

How do I correctly cite the C++ standard or its drafts?

For my bachelor thesis, I have to reference a lot to the various C++ standard documents, be it the original standard or some of the working drafts. How do I cite such documents? Many of the working ...
Daniel Jour's user avatar
13 votes
2 answers
1k views

Should I cite Papers to acknowledge usage of tools?

I've found that a few tools uses in scientific research, request that if you use them, you add the paper they were discussed in to your bibliography. For example: Theano requests you cite: "“Theano: ...
Frames Catherine White's user avatar
9 votes
7 answers
5k views

Academic writing software

General-purpose word-processing programs are OK for academic writing. But I feel the experience can be much improved with some specialized software that takes better care of the special needs of ...
ba_ul's user avatar
  • 363
66 votes
15 answers
87k views

Software to use for creating posters for academic conferences?

And how much time does it usually take? I'd like to create a poster without having to put too much time into formatting.
InquilineKea's user avatar
  • 10.8k
40 votes
7 answers
4k views

Are there specific organizational processes or tools (not necessarily software) that can help in developing and structuring research ideas?

I am doing research in computer Science as a PhD student. I have some research ideas and for months I've been continuously thinking about them, developing them and make them more specific. I mean, ...
CyberPlayerOne's user avatar
24 votes
12 answers
7k views

Software for creating hand-written slides that are revealed gradually

I am looking for software to create slides like these. I want everything to be hand-drawn/hand-written. I don't want to draw/write anything at the time of presentation, but I want parts of the slides ...
M. Winter's user avatar
  • 356
15 votes
4 answers
1k views

How to keep track of deliverables for supervised students when you supervise many students?

Background: In my area, academics often supervise a large number of students (e.g., 10, 15, 20 students). Many of these students are doing a small thesis as part of either their fourth year or ...
Jeromy Anglim's user avatar
14 votes
3 answers
4k views

Which free online academic plagiarism checker is closest to Turnitin?

Which free online academic plagiarism checker is closest to Turnitin by quality standard of rigour? Turnitin features that even somebody plagiarize the context of a passage by use synonyms or simply ...
Victor's user avatar
  • 619
13 votes
3 answers
1k views

Is development research?

I'm a Msc student, and my project is to develop a novel software tool for use in neurosurgery. There is a current tool that is considered the standard of care for the procedure, but it has low rates ...
adairdavid's user avatar
11 votes
5 answers
2k views

How does a software application idea become a research project?

As a software developer just starting out in research (working for a lab) I have this idea of a software application which is meant to target a specific need: specifically to help users query data ...
Luca Matteis's user avatar
  • 1,157
10 votes
3 answers
2k views

Are software citations indexed?

It is encouraged to cite relevant software in research papers (e.g. MIT guide). The question is, Are these citations indexed at all by any engine? I can hardly find any software on e.g. google scholar ...
Blackademic's user avatar
8 votes
2 answers
28k views

How can I cite software documentations?

As my bachelor's thesis, I'm developing some software (a mocking framework for MATLAB). As such, I often need to reference software documentation - both from MATLAB and the software which serves as my ...
VPeric's user avatar
  • 181
6 votes
2 answers
317 views

What software do you use to keep up to date on literature, and if Google Scholar, how do you avoid information overload?

I see a lot of people use Google Scholar and ResearchGate alerts, but I find those alert systems too overwhelming to the point I get inundated and treat them like spam. Perhaps I'm not using them ...
elduderino260's user avatar
1 vote
2 answers
299 views

Sharing assignments with a potential employer

I'm currently a first year information technology student majoring in software development. I applied for an internship at a software development company. I got an interview and now they're asking to ...
SameOldNick's user avatar
84 votes
14 answers
37k 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 ...
Student's user avatar
  • 911
70 votes
12 answers
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 ...
Anonymous's user avatar
  • 26.2k
58 votes
14 answers
35k 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 ...
A.Loc's user avatar
  • 777
57 votes
7 answers
3k views

Popular proprietary program or obscure open source substitute for reproducible research?

For a long time, I had been using open source software for my work to make it reproducible. I believed that if I made my code open source and the software to run the code was also open source (or at ...
user avatar
35 votes
4 answers
4k views

Why do some journals prefer MS Word?

Some journals (specifically on biology or chemistry) accept only MS Word files as manuscripts, while many journals on mathematics or physics prefer LaTeX. Even Science prefers MS Word. Why do they ...
user avatar
30 votes
2 answers
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 ...
Franck Dernoncourt's user avatar
24 votes
6 answers
15k views

Is there an open source tool for producing bibtex entries from paper PDFs? [closed]

In the desktop application for Mendeley, it's possible to import a PDF and have the bibliographic data automatically extracted (or perhaps looked up, I'm not sure). This feature is more or less ...
David Ketcheson's user avatar
24 votes
9 answers
2k views

Is it acceptable to require a student to use the supervisor's preferred software/tools?

I'm about to supervise my first bachelor student and I'm not quite sure what is acceptable and what is not. The thesis will contain math formulas, illustrations, images, graphs and tables - like any ...
Crowley's user avatar
  • 3,279
23 votes
4 answers
3k views

What is the status of foreign cloud apps in German universities?

From what I heard, in German universities there is a push against foreign cloud applications such as Microsoft Office 365, Google G Suite, Github, and even Doodle. The DFN offers some alternatives, ...
Federico Poloni's user avatar
20 votes
5 answers
1k 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?...
mattek's user avatar
  • 301
19 votes
2 answers
2k views

Useful software resources for reviewing papers

I have a paper for review and I would like to include comments (on clarifications/suggestions/errors) over specific paragraphs or statements. What are some ideal software resources that could help ...
Bravo's user avatar
  • 23k
18 votes
8 answers
868 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......
Alex's user avatar
  • 183
18 votes
1 answer
928 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 ...
Wrzlprmft's user avatar
  • 61.2k
11 votes
7 answers
2k views

Is it ethical to publish a paper about porting an existing software package to another programming language?

In short: I have ported a package in another programming environment, and I want to write a paper of my ported package. Would it be considered cheating? In details: I have implemented a package in ...
fyears's user avatar
  • 111
11 votes
4 answers
6k views

Using a software screenshot in a paper

When writing a paper which, as an aside, talks about the design of a user interface on a particular piece of software, can one insert a (correctly labeled and referenced) screenshot of the software to ...
Joe's user avatar
  • 371
10 votes
3 answers
9k views

Plagiarism checker for mathematics paper

I recently accepted to referee a mathematics paper. This is my first referring assignment and was wondering if there are free plagiarism checkers more suitable for math papers. side note: Several ...
BigM's user avatar
  • 1,023