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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2
votes
1answer
164 views

Quotation/reference manager for print books

What is an effective and efficient system for storing quotes and notes from print books to be retrieved later? When we read books and articles in electronic format there are easy ways to mark quotes ...
3
votes
2answers
2k views

How to evaluate a software implementation for master thesis

I have developed a software to meet a specific requirement in a research field. There is only one such software developed so far, mine is second. In the thesis, I explain the implementation of the ...
10
votes
3answers
605 views

Publishing software in a convenient way

I create a software in order to solve a step of an specific problem. The results obtained (aided by the software) are going to be published in some journal. The focus of the publication is far away ...
71
votes
8answers
21k 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 possibility:...
21
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 ...
4
votes
1answer
91 views

How do you organise scientific articles with and without annotations?

Like most of you, I read several scientific articles every week and annotate them on my tablet. Do you know of a useful way to organise "clean" vs "annotated" articles in a way that is searchable ...
57
votes
7answers
3k views

Popular proprietary program or obscure open source substitute for reproducible research?

For a long time, I had been using open source software for my work to boost "reproducible research". I believed that if I made my codes open source and the softwares to run those codes in were open ...
4
votes
1answer
90 views

How to find tools that are presented in the papers? [closed]

I just searched a couple of papers related to the subject that I'm trying to work on. And the thing is that they all presented a tool that helped them do the job. Here some of them: mapo, mica, any ...
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 ...
3
votes
1answer
131 views

What are your recommendations to organizing online streams of lectures? [closed]

What are the aspects you would recommend to pay attention to? Specifically, we're organizing a seminar series, where we would also like to make the streams available online. It is not so important ...
13
votes
2answers
883 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 ...
3
votes
1answer
218 views

How disrupting is the use of blockchain for university resources?

I came across an interesting concept. The use of blockchain technology to validate academic (and other) achievements. I could find that allegedly the office of the registrar's at Stanford is invested ...
3
votes
1answer
556 views

PhD consisting mainly of programming work

I'm currently a second-year PhD student, in computer engineering. My research area is in computer graphics and virtual reality. I currently don't have a specific goal or problem to solve, except ...
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 ...
1
vote
1answer
75 views

Example of educational theory not taken in account in e-learning software? [closed]

In some papers I read some pedagogical experts claiming that e-learning software such as Moodle, blackboard, elluminate, etc. are not good because they don't take enough of educational theory into ...
23
votes
4answers
9k 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 ...
2
votes
2answers
120 views

How can I select the best platform for organizing a book? [closed]

I'm on a team of 10 people contributing to a book organized by the department. As the only contributor under 30, I'm in charge of technical stuff. The team is comprised of members who are not ...
1
vote
1answer
110 views

In which section of the thesis should I give information about formatting? How?

I am writing my Ph.D. thesis in mechatronics field. I used some notions from mechanical engineering and control engineering, but my work is mostly about a software solution. As the content is really ...
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 ...
7
votes
1answer
1k views

Publishing a paper as the sole author (undergraduate)

I am an undergraduate student and I have been working with a computational physics group for three years. Over the past three years, the code I used for our research has grown from one simple ...
30
votes
5answers
5k 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
4answers
431 views

Should I take class time to explain software?

I'm teaching a course that introduces linguistic field methods. We have fewer lectures than a typical 3-credit course, but the students have ‘lab’ sessions eliciting data from speakers, and they're ...
-1
votes
2answers
1k views

Master thesis grade

I am not happy with my master thesis grade. I wrote down my master thesis in a company. I had three supervisors in this 6 month period, two of them from university and one of them from the company. I ...
2
votes
2answers
129 views

Reference management software to get the link of references

I use Mendeley to organize and view articles (pdf files). It is almost good, however I wish something similar with one additional feature. A software to make a link for every reference in the ...
4
votes
1answer
510 views

Is there a tool like the Open Science Framework that can be run on a private server?

I am very impressed by the Open Science Framework. Unfortunately, for some projects I cannot put any data in a cloud especially if it is not encrypted. Are there similar tools which allow me to keep ...
2
votes
0answers
80 views

Is software packaging considered as a service duty? [closed]

I create from scratch and/or maintain software packages on behalf of the Debian GNU/(Linux|kFreeBSD) distribution; Debian serving as base for other apt-distributions as Ubuntu. Most of `my' packages ...
2
votes
2answers
145 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 ...
-1
votes
1answer
887 views

open source programs for plotting? [closed]

Short version: Any suggestion on an Open-Source Software alternative to Grapher/Surfer/Origin/SigmaPlot? Details: This is not a shopping question. As a scientist I explore and plot data all the time. ...
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 ...
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 ...
31
votes
5answers
1k views

How to deploy a StackExchange-style question and answer site for a university subject?

Problems with discussion boards: After being involved with StackExchange for a couple of years, I've really grown to despise standard discussion boards. All those meandering threads, no commenting, no ...
11
votes
4answers
795 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 ...
3
votes
1answer
110 views

How to anonymize research software in an abstract?

I'm writing an abstract for submission to a conference aimed at a rather small research community. The abstract should be submitted anonymously for double-blind review purposes. The problem is that ...
1
vote
0answers
48 views

Cost-sharing for survey research

I've heard that in some social science departments, simple survey-based "experiments" are done by distributing a survey packet to some population (e.g., students in an intro psych course). This ...
1
vote
2answers
59 views

Sharing assignments with a potential employer

I'm currently a first year information technology student majoring in software development. I applied for an internship at a software development company. I got an interview and now they're asking to ...
4
votes
2answers
11k views

How can I cite software documentations?

As my bachelor's thesis, I'm developing some software (a mocking framework for MATLAB). As such, I often need to reference software documentation - both from MATLAB and the software which serves as my ...
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 ...
3
votes
4answers
567 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 ...
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 ...
71
votes
7answers
12k views

Why use version control systems for writing a paper?

I am following the advice of @Piotr Migdal in Is there an internet Git-like repository for collaboration on a paper?, and I want to ask about version controls: how beneficial are they (specially under ...
287
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 ...
19
votes
4answers
2k views

Not citing code libraries used for paper

I'm submitting a paper to a CS conference, where I've just got the feedback from my professor. He wants to delete the few lines citing the implementation libraries such as sk-learn as well as more ...
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 ...
27
votes
6answers
1k views

Archiving papers, simulation and experimental data, etc?

Archiving of papers and projects is very important for most of the people, and everyone has a method of it. I, personally, try to have different folders for different papers. In the folder of each ...
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 "...
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 ...
3
votes
1answer
139 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
914 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 ...
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 ...
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 ...