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.

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8
votes
2answers
131 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 ...
9
votes
1answer
134 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 ...
2
votes
2answers
185 views

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

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 ...
2
votes
2answers
99 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 ...
82
votes
10answers
7k 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 ...
12
votes
1answer
199 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 ...
24
votes
4answers
2k 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 as "Wolfram Mathematica" or "Wolfram Mathematica®" (with the "registered ...
0
votes
2answers
102 views

What is the best way to publicise an on-line survey for research?

I am doing my graduation project to become a Software Engineer. The project aims to study the behavior of freelance developers to subsequently design a process that allows more quality and efficiency. ...
27
votes
4answers
1k 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 ...
5
votes
4answers
1k 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 ...
27
votes
6answers
2k 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 ...
1
vote
1answer
144 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
99 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 ...
69
votes
11answers
4k views

Why do many talented scientists write horrible software?

I am a software engineer and I have been working for years with people hired from academic background. Many times I've noticed that (even otherwise brilliant scientists) produce code of extremely low ...
14
votes
2answers
199 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
161 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 ...
6
votes
1answer
154 views

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

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 ...
9
votes
2answers
140 views

Should I cite Conference 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: ...
19
votes
7answers
459 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 ...
1
vote
1answer
169 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 ...
3
votes
1answer
103 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 ...
1
vote
1answer
83 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, ...
2
votes
1answer
153 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
112 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
177 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
2answers
239 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 ...
4
votes
2answers
180 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, ...
6
votes
4answers
268 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 ...
2
votes
1answer
203 views

Do you find a computer-assisted qualitative data analysis tool useful?

I do a lot of qualitative coding and assessment as part of my research activities. Usually my colleagues and I simply use generic tools for this process like text editors and spreadsheets, but I know ...
18
votes
6answers
3k views

Software for extracting data from a graph

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 ...
19
votes
9answers
1k 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, ...
19
votes
3answers
349 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 ...
47
votes
7answers
4k views

Why use version control systems for writing a paper

I am following the advice of @Piotr Migdal in this question, and I want to ask about version controls: how beneficial are they (specially under LaTeX settings) for writing papers compared to DropBox ...
19
votes
3answers
926 views

Internet Git 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 ...
10
votes
3answers
349 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 ...
16
votes
4answers
2k 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 ...
26
votes
5answers
935 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, ...
19
votes
5answers
3k 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 ...
4
votes
1answer
69 views

Identifying new references when appending to existing reference list

I am building a database from several online sources like Engineering Village. Everyday I am searching different/close/related keywords that pertains to my research topic. Then, I am (everyday) ...
9
votes
2answers
162 views

Strategy for using a Virtual Learning Environment (aka Blackboad/WebCT/Moodle)

My university is switching its Virtual Learning Environment (VLE). Specifically, we are moving from WebCT to Moodle, but I don't think this matters. This means I need to spend some time learning how ...
9
votes
3answers
285 views

Batch editing references

I imported many pdf articles into Mendeley but saw that Mendeley did not capture all the fields correctly. So, I needed to change them manually. It would be a tedious job to do so with many documents. ...
16
votes
2answers
869 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 ...
11
votes
1answer
286 views

Publishing paper using an open-source software

Can someone publish a paper on the mathematical model of the open source software i.e. parameter analysis of the model (i.e relevant to specific area) which is the backbone of the software. Is it ...
28
votes
11answers
7k 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.
18
votes
4answers
3k 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 ...
64
votes
13answers
14k 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. ...
27
votes
7answers
3k 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 ...
5
votes
1answer
94 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 ...