A message from our CEO about the future of Stack Overflow and Stack Exchange. Read now.

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.

Filter by
Sorted by
Tagged with
16
votes
6answers
4k views

How can I digitally typeset math? [closed]

I want to digitally publish a document which includes mathematical equations – including symbols for integration, summation, etc. This isn’t possible in MS Office or Notepad, which makes things ...
13
votes
2answers
608 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: ...
2
votes
1answer
223 views

Unable to grade student assignment in blackboard [closed]

I created an assignment for students using blackboard. This assignment is something that is completed externally. When going into the grading center I am unable to assign grades unless the students ...
0
votes
1answer
2k views

Mathematics or software engineering? [closed]

I am currently in a dilemma and could not decide where I am going in the future. My undergraduate and master degree is in software engineering and I am currently doing a computer science PhD. I did ...
11
votes
5answers
292 views

Are virtual machines good for reproducibility and open science?

Virtual machines (VMs) provide a way for scientists to package not only scientific software, but also data, external dependences, and even entire operating system configurations, facilitating a ...
5
votes
3answers
305 views

Receiving comments on one's article

After publishing an article, assuming that the publisher doesn't prevent you from sharing an article online in a public place, the authors might want to receive additional feedback. Are there good ...
2
votes
2answers
219 views

Naming a library or program partially after a school

I have seen several programs and libraries partially named after a school, e.g.: Berkeley Entity Resolution System MIT Information Extraction Stanford CoreNLP To name a library or program partially ...
19
votes
4answers
5k views

I want to opensource my code. Is it legal? Can I still publish?

I am a PhD (stipend) student at a Max Planck Institute (for a biological science) here in Germany. I came here to write software, but ended up spending practically all my time doing wet-lab work. As a ...
2
votes
4answers
2k views

What features does Adobe Illustrator lack compared to Microsoft PowerPoint for making posters?

I have used Microsoft PowerPoint to make posters so far, and I am considering giving Adobe Illustrator a shot for my next poster. What features does Adobe Illustrator lack compared to Microsoft ...
4
votes
1answer
923 views

If I develop a product as part of a project at university, does the university have any ownership over it?

To specify further, this is an undergraduate project, not a PhD, so (I think) that this is not directly funded by the University, and I am studying in the UK. I ask because I have a few ideas about ...
0
votes
2answers
7k views

“System”, “software”, “application” or “tool” – which to use in my paper? [closed]

I am in the field of computer science, I developed some software to solve some problems and would like to write some papers about them. But I don’t know what to call the software in each of my works. ...
36
votes
10answers
10k 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 ...
40
votes
7answers
3k 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, ...
2
votes
2answers
121 views

How to set bibliographic entry to display author only when applicable?

I'm writing my bachelor's thesis with OpenOffice Writer. Most of my sources are websites, and the author or publication year is often absent. With Writer's bibliography system, you can specify ...
2
votes
1answer
222 views

Can I host my published software at Dropbox?

I am about to publish a software in Bioinformatics Journal. May I keep the files for online availability at Dropbox as public link. If that's not a good idea what are the options?
1
vote
3answers
848 views

Which survey software to use?

I want to create a fairly long survey for my doctoral research. The target audience is teachers in the area. I have the option of using the software my institution provides (Qualtrics), Google Forms, ...
7
votes
3answers
891 views

Is there any automated way I can detect if a co-author plagiarized before our paper is submitted?

My professor, a co-author and I have been working on a paper for more than a year. I was doing the math and simulations, my co-author was responsible for the writing, and my professor was editing the ...
1
vote
2answers
120 views

Using Others Work - To What Level Is It Okay? [closed]

From September I will be starting my final year project at a UK university. I will be developing some software. However the software I wish to create has multiple "modules" to it. Approximately 16 ...
1
vote
2answers
370 views

Questions to speaker per Smartphone in University lectures

I was at the MIT-Vienna-Conference and they had a pretty nice App-System (Superevent), where Questions to the Speaker could be asked per the Superevent-app, upvoted from others and finally answered by ...
1
vote
3answers
1k views

Heard of Chamber of Chartered Java Professionals International?

I'm Java course which they said to me that they can arrange a Bachelor's degree from "The Chamber of Chartered Java Professionals International." I did a little research my own, and from what I can ...
44
votes
12answers
9k 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 ...
16
votes
2answers
442 views

Can graphics created with Wolfram Mathematica be freely used and distributed?

This is just a simple question. I would like to know if one can use graphics generated by Mathematica (for example, plots) in one's paper and then upload that paper anywhere on the internet. I would ...
61
votes
9answers
19k 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 ...
40
votes
6answers
4k 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'...
5
votes
1answer
309 views

“Internal” license for group software?

I have a question about the use and attribution of internal software tools. We have a model in our group that is very popular and has formed the basis of many student projects and publications. It ...
5
votes
1answer
372 views

Is there any system that enables online office hours?

Can anyone comment on their own implementation of online office hours, ideally with the following characteristics: Free. (I'm happy to install software on my own server if needed) Allows for live ...
14
votes
4answers
3k views

Alternatives to Word/LaTeX [closed]

I wrote my undergrad thesis using Word. Overall I managed to get the job done, but as with all WYSIWYG editors, by the end I feel like I had created a bit of a mess. It didn't show, but I know it's ...
1
vote
3answers
111 views

Collaboration tool for students and teachers

I'm looking for a tool (web application) similar to Atlassian Confluence but for academic purposes. The main purpose of that is to allow selected teachers and students from different schools ...
13
votes
3answers
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 ...
15
votes
1answer
717 views

Is there any software to regularize British vs. American spelling in a text?

This is a minor but ongoing annoyance that takes up more time than I would like, and I am wondering if anybody knows of a solution. I often write papers with foreign collaborators, and we tend to end ...
2
votes
1answer
160 views

How to integrate partial version control, data exchange and research assistants?

Currently, my coauthors and I use GitHub to collaborate in coding and writing but also in data exchange. We have a lot of data, often not in text format (e.g. pdf). Most of this is collected by ...
12
votes
3answers
1k views

Why should I format a citation manually without bibliographic software?

During a lecture (and a separate presentation) my instructor told us about bibliographic software, how it composes references automatically and is able to correctly cite articles in many formats. The ...
2
votes
0answers
95 views

Plagiarism detection software – comparing two long documents [duplicate]

I would like to find out whether one of two long documents plagiarises the other. I’m looking for software or a website that does this but does not store the documents on the server (i.e., the ...
8
votes
1answer
122 views

Software for managing departmental alumni relations

My department is looking for a CRM tool to manage its relationship with graduated students (either on BSc, MSc or PhD level). What we want to achieve: Show our candidates that you can get a well ...
18
votes
4answers
745 views

Is there evidence that open source research software produces more uptake of methods?

In recent years there has been a drive to make science more open. This includes making the software used to perform research open source. The main argument in favour of this idea is that research ...
-1
votes
1answer
62 views

Does software exist for supporting conducting SLRs

I'm conducting a (short) structured literature review to generate new hypotheses. Given the fact I'm on my own, I thought of writing a little scraper (reduces bias) to automatically download the ...
4
votes
3answers
620 views

software to organize (1) research questions (2) secondary literature (3) own notes

Is someone aware of software that can help me create certain goals and research (sub)questions (digitally) and connect these questions in an organized way with the secondary literature on my computer, ...
7
votes
1answer
397 views

What papers can you ask someone to cite for using your software?

Ofen Software authors request that users cite a paper of theirs in publications resulting from projects using their software. As such an software author, what logic governs what kind of papers you ...
-2
votes
1answer
597 views

Free Microsoft Visio for Education - Mac User [closed]

I need a Microsoft Visio-like tool that works on a Mac and is free for educational users.
4
votes
2answers
162 views

Getting credit/ownership for improved software

I recently made some changes to a piece of (proprietary) code that my group uses which has made it two orders of magnitude faster. The code I updated wasn't mine and the original algorithm IP was ...
6
votes
4answers
415 views

Release software before the accompanying publication gets reviewed or accepted?

Is common practice to release an academic software before the publication of the accompanying paper in a scientific journal? What are the pros and cons of a prior release? Edit: I am not concerned ...
2
votes
1answer
64 views

Is it necessary to provide links to the mentioned softwares' websites on my CV?

I am writing my CV and, in the Skills section, I have listed the name of the softwares that I've worked with. Some of them are well-known softwares, but some are open source codes that may not be ...
34
votes
4answers
3k 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 ...
1
vote
3answers
722 views

What are good database/grade book software?

I am in the market for a (hopefully free!) grade book software and would like to see some suggestions. This would be used for a math class and I am planning for many grades (15+) per semester. In ...
9
votes
5answers
1k 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 ...
22
votes
5answers
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....
7
votes
1answer
3k views

How can I migrate a library from Calibre to Zotero?

I've got a well organized Calibre library, but due to full text PDF search, web clipping and basic bibliography management, I decided to move to Zotero. I can import .bib records easily, but is ...
1
vote
2answers
181 views

Should I publish my software independently or publish it along with a case study in higher journal?

I have built a software that handles protein clustering data in specific format. It is able to draw several plots on that basis along with many other analyses. It has more options than its existing ...
2
votes
1answer
365 views

If a journal publishing an article about a software tool requires the software to be freely available, must the article be open access?

I am interesting in publishing a Bioinformatics software as a paid access article in a journal where they have open access as well as paid access options (Oxford's Bioinformatics). But it stated at ...
11
votes
2answers
1k views

Using proprietary software to demonstrate work in conference

I am going to conduct a workshop on my research work and for that I need to show how it is done on the software. I want to know, Is it ok to display the proprietary software (through TeamViewer) from ...