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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9
votes
3answers
696 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 ...
22
votes
3answers
1k 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
votes
0answers
56 views

Can I get into Aeropace engineering without going for A-levels or College? [closed]

this is my first post so I hope it is correctly labelled and in the right place. I have just started an apprenticeship in software development. However, I have changed my mind about what I want to do ...
2
votes
0answers
61 views

Software to regularize British vs. American spelling

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 ...
0
votes
1answer
76 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, ...
4
votes
1answer
74 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
votes
0answers
16 views

MS Word Formatting Question [migrated]

There does not seem to be a SE for MS Office? I have a Word document with a signature line (name printed underneath). Is there a way to force that paragraph to always be at the bottom of the page? I ...
20
votes
2answers
301 views

Has the DeWitt Clause, which prevents researchers for publishing DB benchmarks explicitly using a DBMS name, 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 ...
0
votes
1answer
82 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 ...
3
votes
0answers
82 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 ...
16
votes
3answers
254 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 ...
8
votes
2answers
858 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) ...
1
vote
2answers
143 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 ...
0
votes
2answers
103 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 ...
8
votes
2answers
161 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
169 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
358 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
119 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 ...
86
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 ...
13
votes
1answer
210 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 ...
26
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
107 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 ...
29
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
0answers
76 views

Automatic analysis of audio recordings of group tutoring wanted to reduce tutor “talk time.”

I occasionally provide training resources to the peer tutoring program on campus. The upper-division tutors meet regularly with groups of lower-division students who are taking large gateway science ...
1
vote
1answer
159 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
105 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 ...
74
votes
11answers
5k 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
225 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
180 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 ...
9
votes
3answers
301 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
151 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
479 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
197 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
110 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
90 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
177 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
119 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
180 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
269 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
208 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, ...
9
votes
4answers
344 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
213 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 ...
19
votes
6answers
4k 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 ...
20
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
365 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 ...
48
votes
7answers
5k 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
996 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
393 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 ...