<p>For emacs users there's the extremely useful <a href="http://orgmode.org/" rel="noreferrer">org-mode</a>. 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 <strong>lots</strong> 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 <a href="http://en.wikipedia.org/wiki/Distributed_Concurrent_Versions_System" rel="noreferrer">Distributed Concurrent Versions System</a>, such as git or mercurial...</p>

CC BY-SA 2.5
2010-11-15T17:26:34.880Z
2010-11-15T17:26:34.880Z
cesco
<p>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 <a href="http://www.tiddlywiki.com/" rel="nofollow">TiddlyWiki</a>. 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.</p>

CC BY-SA 2.5
2011-02-15T18:02:46.877Z
2011-02-15T18:02:46.877Z
Artem Kaznatcheev
<p>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.</p>

CC BY-SA 2.5
2010-12-11T23:00:20.617Z
2010-12-11T23:00:20.617Z
Peter Boothe
<p>I was using LaTeX files plus <a href="http://en.wikipedia.org/wiki/Apache_Subversion" rel="nofollow noreferrer">SVN</a> to keep track of my notes. </p>

<p>But recently I have stated using <a href="http://en.wikipedia.org/wiki/Apache_Subversion" rel="nofollow noreferrer">SVN</a> with a personal Wiki <a href="http://www.tiddlywiki.com/" rel="nofollow noreferrer">TiddlyWiki</a> (that Artem Kaznatcheev has mentioned above)
with a <a href="http://bob.mcelrath.org/tiddlyjsmath-2.0.3.html" rel="nofollow noreferrer">plug-in</a> for <a href="http://www.math.union.edu/~dpvc/jsMath/" rel="nofollow noreferrer">jsMath</a> 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.</p>

<p>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 <a href="http://tiddlyvault.tiddlyspot.com/" rel="nofollow noreferrer">TiddlyVault</a>.</p>

<p>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.</p>

<p>The idea came to me while reading <a href="https://mathoverflow.net/questions/1785/how-do-you-keep-your-research-notes-organized">this</a>.</p>

CC BY-SA 3.0
2011-04-29T00:55:57.953Z
How do you set up tiddlywiki to play nicely with SVN ? I'm very intrigued.
Suresh Venkat
CC BY-SA 3.0
2011-04-29T04:24:23.817Z
@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.
Kaveh
CC BY-SA 3.0
2011-04-29T07:33:12.107Z
the automatic displaying/hiding of levels in tiddlywiki seems attractive as well.
Suresh Venkat
CC BY-SA 3.0
2011-04-28T23:18:27.347Z
2011-04-28T23:18:27.347Z
2017-04-13T12:57:54.530Z
Kaveh
<p><a href="http://www.zotero.org" rel="nofollow">Zotero Firefox plug-in</a></p>

CC BY-SA 2.5
2011-02-15T18:34:16.633Z
2011-02-15T18:34:16.633Z
Pratik Deoghare
<p>I think you may like <a href="http://knowen.org/nodes/1" rel="nofollow noreferrer" title="knowen.org">knowen.org</a>. 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. </p>

<p><img src="https://i.sstatic.net/CM7Pc.png" alt="example of knowen.org"></p>

CC BY-SA 3.0
2014-12-18T15:07:46.217Z
2014-12-18T15:28:56.890Z
2014-12-18T15:28:56.890Z
Ivar
<p>There are several pieces of software that can be used for <a href="http://en.wikipedia.org/wiki/Mind_map" rel="nofollow noreferrer">mind mapping</a>. Here is <a href="http://en.wikipedia.org/wiki/List_of_mind_mapping_software" rel="nofollow noreferrer">a list</a>.</p>

<p><img src="https://upload.wikimedia.org/wikipedia/commons/thumb/7/70/Freemind-0.9x_Screenshoot.png/800px-Freemind-0.9x_Screenshoot.png"/></p>

<p>I also suggest software like <a href="http://en.wikipedia.org/wiki/Microsoft_OneNote" rel="nofollow noreferrer">Microsoft OneNote</a> or other <a href="http://en.wikipedia.org/wiki/Comparison_of_notetaking_software" rel="nofollow noreferrer">notetaking software</a>.</p>

<p>If you have a tablet PC or a graphics tablet, I suggest using <a href="http://en.wikipedia.org/wiki/Windows_Journal" rel="nofollow noreferrer">Windows Journal</a>, or other alternatives (like <a href="http://en.wikipedia.org/wiki/Xournal" rel="nofollow noreferrer">Xournal</a>).</p>

<p><strong>Edit:</strong> For <em>lab notebooks</em>, please refer to <a href="http://en.wikipedia.org/wiki/Electronic_lab_notebook" rel="nofollow noreferrer">Electronic lab notebook</a> and <a href="http://en.wikipedia.org/wiki/Open_Notebook_Science" rel="nofollow noreferrer">Open Notebook Science</a>.</p>

CC BY-SA 2.5
2010-11-15T11:35:07.020Z
However, this does not solve the last issues on the authentication of the work (as in a lab book).
Sylvain Peyronnet
CC BY-SA 2.5
2010-11-15T12:10:21.857Z
@Sylvain: You're right. I didn't point that out. Please see the updated answer.
Sadeq Dousti
CC BY-SA 2.5
2010-11-15T11:14:14.440Z
2010-11-15T12:09:07.320Z
2017-03-09T18:04:14.410Z
Sadeq Dousti
<p>This is a question in the spirit of <a href="https://cstheory.stackexchange.com/questions/2953/advice-on-good-research-practices">this one</a> 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...).</p>

<p>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?</p>

CC BY-SA 2.5
2010-11-15T15:44:32.223Z
Terence Tao's [thoughts on time management](http://terrytao.wordpress.com/2008/08/07/on-time-management/)
Aaron Sterling
CC BY-SA 2.5
2010-12-12T01:02:26.873Z
what data ? we are theoreticians ? (I kid, I kid) :)
Suresh Venkat
<soft-question><research-practice>
Research data organization
Sylvain Peyronnet
# Research data organization

(Asked by: username_0 on 2010-11-15)

This is a question in the spirit of [this one](https://cstheory.stackexchange.com/questions/2953/advice-on-good-research-practices) 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?

**Tags:** soft-question, research-practice

> **Comments:**
> **username_1**: Terence Tao's [thoughts on time management](http://terrytao.wordpress.com/2008/08/07/on-time-management/)  
> **username_2**: what data ? we are theoreticians ? (I kid, I kid) :)  

---

## 7 answers

### Answer by username_9 on 2010-11-15. Score: 7 | Accepted answer

There are several pieces of software that can be used for [mind mapping](http://en.wikipedia.org/wiki/Mind_map). Here is [a list](http://en.wikipedia.org/wiki/List_of_mind_mapping_software).

![](https://upload.wikimedia.org/wikipedia/commons/thumb/7/70/Freemind-0.9x_Screenshoot.png/800px-Freemind-0.9x_Screenshoot.png)

I also suggest software like [Microsoft OneNote](http://en.wikipedia.org/wiki/Microsoft_OneNote) or other [notetaking software](http://en.wikipedia.org/wiki/Comparison_of_notetaking_software).

If you have a tablet PC or a graphics tablet, I suggest using [Windows Journal](http://en.wikipedia.org/wiki/Windows_Journal), or other alternatives (like [Xournal](http://en.wikipedia.org/wiki/Xournal)).

**Edit:** For *lab notebooks*, please refer to [Electronic lab notebook](http://en.wikipedia.org/wiki/Electronic_lab_notebook) and [Open Notebook Science](http://en.wikipedia.org/wiki/Open_Notebook_Science).

> **Comments:**
> **username_0**: However, this does not solve the last issues on the authentication of the work (as in a lab book).  
> **username_9**: @Sylvain: You're right. I didn't point that out. Please see the updated answer.  

---

### Answer by username_3 on 2010-11-15. Score: 10

For emacs users there's the extremely useful [org-mode](http://orgmode.org/). 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](http://en.wikipedia.org/wiki/Distributed_Concurrent_Versions_System), such as git or mercurial...


---

### Answer by username_4 on 2011-02-15. Score: 5

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](http://www.tiddlywiki.com/). 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.


---

### Answer by username_5 on 2010-12-11. Score: 4

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.


---

### Answer by username_6 on 2011-04-28. Score: 4

I was using LaTeX files plus [SVN](http://en.wikipedia.org/wiki/Apache_Subversion) to keep track of my notes.

But recently I have stated using [SVN](http://en.wikipedia.org/wiki/Apache_Subversion) with a personal Wiki [TiddlyWiki](http://www.tiddlywiki.com/) (that username_4 has mentioned above)
with a [plug-in](http://bob.mcelrath.org/tiddlyjsmath-2.0.3.html) for [jsMath](http://www.math.union.edu/~dpvc/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](http://tiddlyvault.tiddlyspot.com/).

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](https://mathoverflow.net/questions/1785/how-do-you-keep-your-research-notes-organized).

> **Comments:**
> **username_2**: How do you set up tiddlywiki to play nicely with SVN ? I'm very intrigued.  
> **username_6**: @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.  
> **username_2**: the automatic displaying/hiding of levels in tiddlywiki seems attractive as well.  

---

### Answer by username_7 on 2011-02-15. Score: 2

[Zotero Firefox plug-in](http://www.zotero.org)


---

### Answer by username_8 on 2014-12-18. Score: 1

I think you may like [knowen.org](http://knowen.org/nodes/1 "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](https://i.sstatic.net/CM7Pc.png)


---

