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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5
votes
3answers
2k views

Is using Mendeley to organize my files a good idea? [closed]

My Library is already partially organized (manually) with regular filesystem folders. But it is pretty messy right now and getting unwieldy. Also several files should be renamed to something ...
2
votes
2answers
146 views

A place to host static HTML+JavaScript that can be referenced from a paper?

My PhD supervisor always told me that we write papers "for the ages". The publication system being what it is, we cannot go back and update any links, so we should not cite or reference a source that ...
0
votes
1answer
179 views

Notetaking with Latex and collapsing text for research papers [closed]

I am looking for a note-taking software with the following features, I would appreciate any advice! Collapsing or folding text (Like FoldingText or other outliners) Ability to quickly write up ...
8
votes
1answer
2k views

How and when to cite code from MATLAB File Exchange

What are the rules/etiquette to cite MATLAB File-exchange submissions on paper publications? There are different scenarios where I am curious what is best: FEX submission is clearly code from a ...
3
votes
1answer
140 views

Transitioning from PhD in biomedical engineering to software dev (have 5-6 software experience working for a team during PhD)? [closed]

My PhD is in biomedical engineering (MEMS and electronics). I also have taken some CS classes in the last 5 years (and during undergrad in electrical engineering). I was also in the software team for ...
0
votes
1answer
935 views

Do university accept a Mechatronics Engineer undergraduate to do Masters in computer science? [duplicate]

I finished my undergraduate studies in Mechatronics Engineering and have a low CGPA. The main reason is that I'd been developing web application and doing small projects (creating robots). I have ...
0
votes
7answers
1k views

How can software piracy in academia be reduced/eliminated?

Software piracy is obviously illegal as well as being wrong for a variety of reasons. However, from my experience it is extremely common to see pirated software being used by research students. This ...
5
votes
5answers
385 views

Portal for sharing a research manuscript with supervisors/advisors

I was wondering if there was a website or portal for confidentially sharing research manuscript with supervisors/collaborators whilst its being drafted. I tend to just e-mail the manuscript to my ...
7
votes
5answers
320 views

How to organize repository of common research papers for lab members?

The Problem I am a graduate student in a research lab with several other students, and as such we're all pursuing research and dissertation topics that are at least generally related in nature. We ...
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 ...
2
votes
1answer
224 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 ...
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 ...
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
220 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 ...
11
votes
5answers
296 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 ...
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 ...
1
vote
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 ...
1
vote
3answers
18k views

How do I cite a screenshot I've taken of a software program?

How to write a proper reference for an image I'm going to use for my thesis? This image is a screenshot of a software installed on my own PC and I am the one who took it myself. It's not from another ...
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?
18
votes
8answers
821 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......
1
vote
3answers
853 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, ...
14
votes
2answers
5k 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 ...
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 ...
6
votes
2answers
844 views

In performing a comparison, how can I get authors to actually respond to a request for source code?

I'm doing my PhD in computer science and am working in computer vision. I have come up with an algorithm that my supervisors consider to be promising and publishable. It took me a long time to get ...
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 ...
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 ...
11
votes
4answers
806 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 ...
9
votes
7answers
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 ...
5
votes
1answer
373 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 ...
1
vote
2answers
371 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 ...
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 ...
1
vote
1answer
229 views

How can I convince the university to apply security upgrades to the online learning system?

In my university, we've been using Moodle for many years (>5y). There was a general negative opinion on the Moodle for very different reasons, from "it's ugly" to "it's not up to date", going through "...
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 ...
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 ...
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 ...
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 ...
13
votes
3answers
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 ...
18
votes
4answers
746 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 ...
3
votes
1answer
146 views

Should I cite the author of software tool or script that I use? [duplicate]

I'm writing a paper for my Ethical Hacking class. In 'hacking', you use a lot of tools written by other people, some of them are mainstream and/or made by big teams, others are less known and made by ...
-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 ...
7
votes
1answer
401 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
602 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.
286
votes
18answers
33k 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 ...
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 ...
7
votes
3answers
922 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 ...