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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.

10
votes
, line 6, the word "mispell" should be "misspell". This is probably the easiest approach if the number of such comments is not too large, since it doesn't require any extra software and doesn't require the authors to search through the PDF for your annotations. …
answered Jun 28 '12 by David Ketcheson
9
votes
For the last month, I have been using Gitit for this purpose. That link goes to a live demo where you can try it out. It satisfies all your requirements: It's a wiki, so you can easily make links …
answered Apr 11 '12 by David Ketcheson
55
votes
the code. If you use proprietary software, your code probably makes use of closed source code, and therefore it cannot be verified or reproduced from scratch. If you use open source software, then … reproducibility is more achievable with proprietary, widely-used software. I am optimistic that the current trend will lead to open-source software catching up in terms of wide use (consider SAGE, for example …
answered Jul 10 '12 by David Ketcheson
3
votes
My university uses Blackboard, so I am required to use it for entering final grades. I use it for only that, because I find Blackboard to be not very user-friendly. There are alternatives that are f …
answered Aug 27 '15 by David Ketcheson
5
votes
If you use bibtex, then you can batch edit with things like sed, awk, or simple find/replace in any text editor.
answered Jun 29 '12 by David Ketcheson
23
votes
Mind maps might be what you're looking for. From the Wikipedia page: A mind map is a diagram used to represent words, ideas, tasks, or other items linked to and arranged around a central key word …
answered Feb 15 '12 by David Ketcheson
51
votes
This question has become an important one as the push for greater reproducibility in computational research grows. Use of closed-source software is an acceptable part of research in most fields … the full software environment, code and data, that produced the result. From this point of view, if you rely on closed-source code, you can't completely publish your research. Issues with closed …
answered Dec 1 '16 by David Ketcheson
21
votes
6answers
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 relia …
asked Jan 8 '14 by David Ketcheson
35
votes
Aditya's comment should be the accepted answer: Bitbucket offers unlimited private repos for academic users.
answered Nov 14 '12 by David Ketcheson