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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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-1
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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
405 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
617 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
34k 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
163 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
928 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 ...
6
votes
4answers
417 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 ...
5
votes
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 ...
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 ...
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 ...
8
votes
2answers
2k views

What are the drawbacks of HTML5 presentation software?

I use pdf files, generated with Beamer/LaTeX, and whatever pdf viewer is available on the computer I am presenting on. While I like the Beamer/LaTeX/PDF combination better than PowerPoint type ...
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....
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 ...
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 ...
15
votes
1answer
749 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 ...
4
votes
3answers
621 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
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 ...
29
votes
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 ...
2
votes
1answer
370 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 ...
5
votes
1answer
310 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 ...
48
votes
4answers
11k 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 ...
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 ...
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 ...
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 ...
17
votes
2answers
2k 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 ...
12
votes
1answer
411 views

How to handle disagreement between collaborators on licensing academic code?

A group of students including myself have developed a certain program/algorithm. I as the main coder behind this group have provided 95% of all the actual code. The other two involved parties have ...
1
vote
2answers
16k views

How to find a university without min. GPA requirement for Master degree (any state/US)? [closed]

I am an international student who is able to self-finance his master degree education in the US. I looked at a relatively big number of schools that offer a master degree in software engineering and ...
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 ...
155
votes
12answers
19k 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 ...
4
votes
3answers
518 views

Should I cite sources about a technology description?

I want to add some description of a technology (Node.js = server-side JavaScript) in my thesis. The description is about what exactly this technology is, how it works, what it can do etc. I want to ...
16
votes
2answers
459 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 ...
43
votes
6answers
35k 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 ...
36
votes
4answers
14k 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 ...
11
votes
7answers
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 ...
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'...
1
vote
1answer
388 views

Fastest way to browse journal papers (from Web of Science)?

The search engine which I typically use to browse journal papers is WebofScience. It allows me to sort by times cited, and check out who cited what. The problem is that to get to the actual article ...
3
votes
1answer
278 views

Mapping connections between topics covered in academic papers - does such a tool exist?

I'm interested in learning about how to go about writing a paper, and obviously, an integral part of this process will be to read papers written by others, and study those. I'm curious about the idea ...
151
votes
14answers
25k 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 ...
20
votes
2answers
1k views

Are there opportunities to support cancer research through volunteer IT or software development?

Several friends and acquaintances have recently died from cancer. The chemo treatments are crude and destroy quality of life. Furthermore, chemo treatments depend on the efficacy of antibiotics for ...
5
votes
2answers
578 views

Tools for data organising and processing

Suppose we perform experiments with input parameters (temperature, humidity, processing time...) and collect resulting data (thickness, structure, mech. properties...). Is there a tool (or set of ...
22
votes
6answers
8k 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 ...
13
votes
2answers
610 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: ...
24
votes
9answers
1k 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 ...
5
votes
2answers
533 views

Software to make illustrative videos explaining a research topic

What are some good (preferably open-source) software for making illustrative videos to explain one's research? I am currently looking for software to make a small video on my research topic that could ...
4
votes
1answer
173 views

Creating an central multi-purpose dictionary / database

I am trying to organize my workflow and make it more effective. As non-native English-speaker studying in a foreign country I often need to look-up domain-specific translations (in 3 languages). As ...
2
votes
1answer
181 views

What are issues to consider when making your code for an experimental paradigm, which was conceived by someone else, publicly available?

General background In the cognitive sciences, it is often necessary to program/script experimental paradigms to conduct your studies. Basically, these programs present stimuli and collect responses, ...
3
votes
4answers
578 views

Note taking software: referencing text to searchable keywords

I'm looking for software for macs geared towards organizing and referencing the text in notes. I'm currently studying pathology and would like to be able to "tag" a topic/heading within my notes (not ...
2
votes
1answer
493 views

Management after Software Engineering undergraduate degree or separate management masters degree?

I am currently an undergraduate student studying BEng (Hons) Software Engineering at University of Greenwich. I want to do masters but I am not sure what to do. I am a very talented software architect ...
6
votes
4answers
323 views

Research paper about an enhancement to algorithm

A question that has been bothering me for so long about research work is, what level of work can be called research and is worthy of publishing in a research paper? Let's say I am working with JPEG ...
1
vote
3answers
735 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 ...