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.
315
questions
319
votes
18
answers
40k
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 ...
- 17.6k
177
votes
12
answers
29k
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 ...
- 1,839
175
votes
14
answers
36k
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 ...
- 1,939
128
votes
17
answers
144k
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. ...
89
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 ...
user102
87
votes
12
answers
13k
views
Is it ethical to use proprietary (closed-source) software for scientific computation?
I have data from an ordinary scientific experiment. Now, in order to analyse the data, the most convenient way for me is to use some proprietary, closed-source software.
Is it ethical to use such ...
- 801
85
votes
8
answers
31k
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:...
- 1,669
83
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 ...
- 909
72
votes
7
answers
15k
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 ...
- 13.9k
71
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 ...
- 26.3k
68
votes
6
answers
13k
views
Popular software used in research is incorrectly reporting solution is optimal: what to do?
I have an example demonstrating the solution produced by a popularly used software package is not the optimal solution, despite the software claiming that it is. Several recent papers published from ...
- 919
66
votes
15
answers
88k
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.
- 10.9k
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 ...
- 775
61
votes
8
answers
21k
views
Is it immoral to show new students how to use Wolfram Alpha?
Currently, I'm working as an assistant at the mathematics department of my university. My job consists of sitting for 20 hours a week in an office to which students come with doubts regarding all the ...
- 641
58
votes
14
answers
36k
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 ...
- 777
57
votes
10
answers
7k
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 ...
- 521
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 ...
user107
56
votes
6
answers
43k
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 ...
- 73.7k
46
votes
6
answers
57k
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 ...
- 1,119
45
votes
5
answers
36k
views
How should I reference my Github repository with materials for my paper?
I am writing a paper describing some of the research I have done. As part of my work I have developed an open-source library and made it available on Github.
How should I link to it?
Should I cite ...
- 553
44
votes
12
answers
10k
views
Do résumés written in LaTeX show more promise when applying to graduate schools?
I am a computer science student from India. I noticed that most of the résumés and thesis papers etc. I see are written in LaTeX.
If I write my résumé in Word (say) rather than LaTeX, will it have a ...
- 949
44
votes
6
answers
6k
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'...
- 1,157
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 ...
- 26.5k
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, ...
- 541
39
votes
6
answers
9k
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,...
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 ...
- 576
38
votes
10
answers
11k
views
How can I sell independently created software to my university?
I am in a situation that I think is not uncommon nowadays.
I wrote software on my own time, by my own decision, and with my own resources during my undergrad career at a university in the US, and ...
- 481
36
votes
11
answers
14k
views
Students admit illicit behavior in private communication: how should I proceed?
I am an adjunct professor at a University for a course where the students have to use a certain software "X" during the course. The software is distributed under a proprietary license; our ...
- 951
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 ...
user23048
35
votes
4
answers
7k
views
Conference management software (preferably open source) with custom fields
I've been told to set up software to organize a workshop. Is there (preferably an open source) conference solution that allows for:
Abstract Submission
Event Planning
Arbitrary user data-fields
...
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 ...
- 2,286
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 ...
- 11.5k
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, ...
- 541
30
votes
5
answers
1k
views
How to deploy a StackExchange-style question and answer site for a university subject?
Problems with discussion boards: After being involved with StackExchange for a couple of years, I've really grown to despise standard discussion boards. All those meandering threads, no commenting, no ...
- 20.4k
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 ...
29
votes
9
answers
8k
views
What tried and tested possibilities are there to create a poster without using LaTeX? [duplicate]
What tried and tested possibilities are there to set up a (nice) poster for a conference without using LaTeX?
I find LaTeX always cumbersome for that purpose and I am curious about alternatives.
- 5,615
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 ...
- 1,193
26
votes
1
answer
4k
views
Why did SoftwareX’ impact factor drop from 4.5 SJR to 0.4 last year?
I planned to submit one of my long-developed software pieces to the prestigious journal SoftwareX. I was preparing for this for a while and making my code ready, and was just about to submit and ...
25
votes
6
answers
16k
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 ...
- 36.7k
25
votes
4
answers
10k
views
Use cases of org-mode as a scientific productivity tool for academics without programming needs
I am a social scientist working primarily on Linux, but also at times required to work on Windows systems at the University. I have been looking to improve my productivity in the academic workflow ...
- 1,632
25
votes
5
answers
795
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 ...
- 26.5k
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 ...
- 3,395
24
votes
12
answers
8k
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 ...
- 356
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, ...
- 47.2k
23
votes
5
answers
2k
views
Ignored Requests Open-Source Software from a Research Group
For more than 6 weeks now, I have been attempting to contact a post-doc or their (former?) PI to request access to either the source code or software of a tool that was published in BMC Bioinformatics....
user479
23
votes
9
answers
5k
views
Saving handwritten notes for future reference
I have more than one hundred pages of handwritten notes.
I made these notes while writing different chapters of my PhD dissertation. The notes include summaries of journal articles, my thoughts, ...
- 5,517
21
votes
5
answers
1k
views
Selling/Buying software in academia
I have written multiple opensource programs as part of my PhD, and some of these programs require a dedicated server somewhere on the internet to work. Mainly it is online databases, but also things ...
- 6,119
21
votes
4
answers
4k
views
Not citing code libraries used for paper
I'm submitting a paper to a CS conference, where I've just got the feedback from my professor. He wants to delete the few lines citing the implementation libraries such as sk-learn as well as more ...
- 905
20
votes
12
answers
11k
views
With a software engineering bachelor's (BE), how can I work on finding a cure for cancer?
I am in my last year of studies for a bachelor's degree in software engineering and I am currently considering different options for my career path. I don't have any background in medicine, but I ...
- 319
20
votes
4
answers
5k
views
Tutoring Unfamiliar Material
Context: I've been tutoring in software development for the better part of this year. I've been a hobbyist and student software engineer for the last 3 years and I have decent experience in a few ...
- 321