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This is a question in the spirit of this one where I answered that it is important to keep track of what you have done something, why you have done it and what is not working. I personally use notebooks for that purpose, but it has several drawbacks: first I need a lot of storage surface, second when I travel I cannot access my data, and finally this is not collaborative. It has however a strong plus: the notebook can be used as the equivalent of a laboratory notebook (you just have to find somebody to sign each page...).

So, I am interested in knowing how other researchers proceed for that matter. For example, is there any specific software that solve all the issues I mentioned?

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There are several pieces of software that can be used for mind mapping. Here is a list.

I also suggest software like Microsoft OneNote or other notetaking software.

If you have a tablet PC or a graphics tablet, I suggest using Windows Journal, or other alternatives (like Xournal).

Edit: For lab notebooks, please refer to Electronic lab notebook and Open Notebook Science.

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  • $\begingroup$ However, this does not solve the last issues on the authentication of the work (as in a lab book). $\endgroup$
    – Sylvain Peyronnet
    Nov 15, 2010 at 11:35
  • $\begingroup$ @Sylvain: You're right. I didn't point that out. Please see the updated answer. $\endgroup$
    – M.S. Dousti
    Nov 15, 2010 at 12:10
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For emacs users there's the extremely useful org-mode. It is an emacs mode that, in plain ascii, help organizing your life or at least your research :) It has TODOs, deadlines, schedules, effort, tables with some computations capabilities, and lots of other features. It can export projects in LaTeX, html or other formats. Since it is text-based you can manage projects concurrently using some Distributed Concurrent Versions System, such as git or mercurial...

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I used to (and to a small extent, still do) have everything scatter across notebooks and binders, but recently I got fed up and moved over to a personal wiki TiddlyWiki. It can be hosted completely locally (it is just one html file), runs in your browser, and after installing a simple plug-in has LaTeX-like math support. I use it to take notes on papers I read as well as to jot down ideas and self-explanations of things that confuse me.

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I use revision control for this purpose. Running backwards in time, one can see the state of the program at a given point, coupled with the changelog which (hopefully) states why it is like that. Putting the data and papers as well as code in revision control makes everything work even better.

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I was using LaTeX files plus SVN to keep track of my notes.

But recently I have stated using SVN with a personal Wiki TiddlyWiki (that Artem Kaznatcheev has mentioned above) with a plug-in for jsMath so I can use LaTeX in my notes. It is quite easy to setup and use (it is a single html file). TiddlyWiki has tagging and search functionalities.

Typing in usual LaTeX allows copying those notes directly without modification to a LaTeX file. There also lots other plug-ins that you can find by Googling, e.g. this TiddlyVault.

The really nice thing is that you can have a copy of your notes on your laptop (so you can work with them off-line), and another one on your webpage (so you can work with them online from any place) and keep them in sync using SVN. You can also use it in a collaborative manner.

The idea came to me while reading this.

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  • $\begingroup$ How do you set up tiddlywiki to play nicely with SVN ? I'm very intrigued. $\endgroup$
    – Suresh Venkat
    Apr 29, 2011 at 0:55
  • $\begingroup$ @Suresh, I should say that I have been using this for a short time, and not collaboratively but to keep a local copy of my notes, therefore haven't had complicated conflicts and resolving them has been quite easy. At the end one needs to resolve the conflicts in the html file and they have been similar to resolving conflicts in tex files. But for more serious collaborative work tex files+SVN or more collaborative Wiki software might work better. $\endgroup$
    – Kaveh
    Apr 29, 2011 at 4:24
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    $\begingroup$ the automatic displaying/hiding of levels in tiddlywiki seems attractive as well. $\endgroup$
    – Suresh Venkat
    Apr 29, 2011 at 7:33
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Zotero Firefox plug-in

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I think you may like knowen.org. I've been using it for a while now to both keep notes and collaborate with others. Knowen allows to store notes (nodes) with all relevant attachments in a DAG, keeps history of all previous versions, has fairly convenient collaboration tools. The language of the nodes is a simple markdown + MathJax, which can be exported and converted into standard LaTeX with pandoc. It is straightforward to use, but powerful.

example of knowen.org

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