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I'd be interested in tools helping to organize thoughts and ideas, especially in a non-linear way (i.e. not as most existing note taking tools, working with lists and bullets, but rather as a post-it application). Ideally, something like the tool they use in Minority Reports would be cool (without the fancy-touch thingy), but an important point would be the ability to visually connect different ideas/notes together.

EDIT: Maybe to make things more explicit, I have a visual memory, and it helps me a lot having a graphical disposition to classify things (like important things at the top-right, urgent ones on the middle-left, etc). Basically, I'd like to find my messy desk on my screen :)

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org-mode is tough to beat if you already use emacs (or even if you don't) –  Abe Mar 20 '12 at 5:35

12 Answers 12

up vote 10 down vote accepted

For nice graphical note editing/drawing:

If you get the hang on it, you probably could use http://prezi.com/

Your notes would look great, and you can always zoom in and out, if you want to add details.

For sharing your notes everywhere (web/smartphone):

see http://www.springpadit.com, another nice option for taking notes:

  • Take your notes on the go (clients for most smartphones).
  • Edit your notes and analyse them, on the web.
  • You can tag and label your notes, so you have some non-linear flexibility as well.
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Its an awesome stuff for presentations (I used it a few times). However, does it really work for note-taking for oneself? –  Piotr Migdal Feb 15 '12 at 21:13
Thanks, I'm not sure I would use for note taking, but I definitely have to try it for making presentations! It looks really cool, even though I guess one needs a bit of time to use correctly. –  user102 Feb 15 '12 at 21:18
yes, the first presentation took me a while. But I think after having delt with it for some hours, you can be very quick to take notes when you use the default set of containers and not draw your own stuff. –  SwissCoder Feb 15 '12 at 21:35
accepted for Springpad, which is probably the closest to what I'm looking for. I guess I will have to code my own in order to be completely satisfied :) –  user102 Feb 16 '12 at 21:15
Prezi is great, but not technically non-linear- it requires that you specify a linear path –  Abe Mar 20 '12 at 5:32

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 or idea... Mind maps are used to generate, visualize, structure, and classify ideas, and as an aid to studying and organizing information, solving problems, making decisions, and writing.

There are lots of mind mapping tools out there. I've used XMind before.

One drawback is that it's hard to put longer thoughts into a mindmap.

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Yes, they are interesting, but somehow too complex to use, especially for longer thoughts. I just tried XMind, and I've tried SimpleMind before, and it seems to lack the ability to quickly write something down, and then to later one connect it to other things (at least in a simple way). –  user102 Feb 15 '12 at 17:10
I prefer FreeMind. It is a bit bloated but once you get to know the shortcuts, its as good as writing by hand. –  user107 Feb 15 '12 at 20:31
If you think FreeMind is bloated, you can recur to FeePlane –  flow Feb 26 '12 at 8:01
@CharlesMorisset: in FreePlane and FreeMind (and probably XMind as well), you can move around a node (and all it's subnodes) by CTRL+arrow_keys. Or simply cut (ctrl+x) and paste it under the node where you want it. You can also go back/forth between nodes and regular *.txt files (it will lose formatting, but keeps the node branching intact. Note that some are annoying with URLs as they treat them differently, so exporting/reimporting make them visible twice). Usually, [Return] creates a node under the current one, and [Tab] create a "child node" underneath the current node. Ctrl+left moves up –  Olivier Dulac Sep 24 '13 at 18:00
Another option is MindNode, which comes in both Free and Pro versions. I've found it very useful, and has support for on-the-fly writing, as well as outliner export. –  Matthew G. Nov 25 '13 at 18:06

For non-linear note-taking and also collaboration I use TiddlyWiki. It is one file that stores all your notes as an interactive wiki. Through a plug-in it support LaTeX-math. If you throw it on a shared dropbox then it can even be a quick way to share ideas with colleagues. If you want something more formal than dropbox, then there are hosted options like TiddlySpace.

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I remember trying TiddlyWiki a while ago, and although I thought it was quite good, especially with the ability to use it with Dropbox, it doesn't seem that it's possible to organize in two dimensions the posts :( –  user102 Feb 15 '12 at 16:48
+1 for a personal wiki. –  kmm Feb 16 '12 at 0:38
I use a MediaWiki as a personal wiki for a while now and I’m quite happy with it. The installation is quite sophisticated though (you will need a local webserver with PHP, a MySQL database and LaTeX). –  mcb Aug 17 '13 at 0:16

I needed the same functionality for myself. I was looking for a powerful note-taking system and after considerable search concluded that the wiki format was best for dynamic unpublished notes and scribblings. I started by using desktop applications but needed some way to render math better so I shifted to web applications (running them locally you'll need an XAMP server).

Desktop Applications

Zim Desktop Wiki - A wiki notebook. Really good imo. Possible drawback: only on linux.

For windows there is an alternative

WikidPad - Described as an IDE for your thoughts. Offers same functionality.

Server Based

Mediawiki - If you're going to end up with thousands of documents being edited by thousands of users then it is the best. For personal use it is a bit of an overkill, and the spaghetti php code doesnt help.

Instiki - currently using this. Compact and simple. You can easily back it up to an USB disk. Or export all pages to html. Needs ruby to compile though.

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Thanks for you answer, but do these wikis have a functional graphical interface? I'm really interested in something that can help me visually organize things, if I want to write notes down, I can use Latex directly. –  user102 Feb 26 '12 at 12:22
@CharlesMorisset the GUI is minimal, like text editors but with advanced options. –  Approximist Mar 9 '12 at 0:11
@Approximist Check out github's wiki engine, gollum (gem install gollum is enough!). 1. Everything is stored as markdown files (no db), can be edited with your favorite text editor. 2. support latex equation by default via mathjax. –  pcr Mar 20 '12 at 13:11
Zim is available cross platform at least since it was ported to python. For Windows a native installer is available, where it is compiled into an executable (which provides better integration with the Windows desktop than running a python script). The only downside is, that it sometimes suffers issues when renaming/moving pages, presumably due to the file-system differences (e.g. you cannot rename a file or folder, while any program has opened it even for reading or as working directory). –  kdb Sep 12 '14 at 15:00

I use scapple from https://www.literatureandlatte.com/scapple.php

It does exactly what you want. You can put notes anywhere on a canvas. You can connect them if you want. And you can search them.

It costs about $15 and there is a trial for 1 month so you can see if you like it before you buy it.

It works very well if you use the Crawford slip method of brainstorming.

It's one of the best piece of software I use.

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A couple of other options for mind-mapping software:

I tried using Curio, which is a very powerful program that can do mind-mapping, as well as a whole lot of other activities. The problem I had with it was that it was, if anything, too stuffed with features: I couldn't really figure out how to get simple tasks done, because there was so much work to do just to learn how to do anything at all. However, I'm certain you wouldn't run out of features.

If what you're looking for is something a little less complicated, but still in the sense of mind-mapping, you can try something like OmniGraffle Professional, which produces diagrams and organizational charts of almost any shape or complexity. It doesn't try to be the "all things to all people" that Curio is.

Another "out of the box" solution is Scrivener, which might be a little too text-based for your needs, but is a great tool for writers.

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Thanks, Scrivener looks really good, but indeed a bit too writing-oriented. I guess a mix between Scrivener, TiddlyWiki et a mind mapping tool would be perfect :) –  user102 Feb 15 '12 at 23:05

Although the question is old, my answer may benefit future readers.

I've recently started to use Gingko App. You can hierarchically organize your notes, which are themselves written in card-like units. The possibilities are many, depending on your organizational creativity. For long-form note-taking this is better than mind maps, while providing all many of the benefits of mind-mapping.

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A nice tool I have found for this is Visual Understanding Environment (VUE), which is an open source tool that sounds very much like what you are looking for. You can position nodes how you like and sketch connections between them. It even has a nice mechanism for nonlinear presentations by setting pathways between the elements in your file. The presentation mechanism is not as polished as Prezi, but since you are looking at note-taking rather than presenting, this should not be an issue.

The only thing keeping me from using it more is that there currently is no support for equation editing, LaTeX or otherwise, which is a deal-breaker in my field. There are workarounds like using Laeqed to generate PNGs of your equations, but it can be cumbersome for large projects. If this is not a concern in your area, I would recommend giving it a look.

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Thanks for the link, I will check it out! The absence of support for equation editing might be a problem though, as I'm also using only Latex. –  user102 Apr 18 '12 at 22:01

Here is another one, which I find very helpful and intuitive: CmapTools

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SilverNote is good for taking a lot of small "post-it" sized notes. You can keep track of your notes by tagging if you like, though you can just as easily "Google" for your notes with the search bar.

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Thanks for the link, unfortunately, they only have a Windows version, so I can't try out :( –  user102 Aug 14 '12 at 8:54

Since you are asking here, I assume note taking for paper is important. Docear is a mind mapping for paper tool which based on Freeplane and Jabref, which might fit academia needs perfectly. And it supports windows, linux and mac. And it' s GPL licensed.

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TiddlyMap.org - I just found it after looking at your question... Searching through another site.

It works with TiddlyWiki - the recently developed version.

TiddlyMap will let you make a clickable graph of your wiki tiddlers, and show you real time navigation as well of where you are in your graph.


DenkWerkZeug - http://denkwerkzeug.com is an application I have been looking at for a while and learning about. It combines a Wiki with a graph and semantic principles, but is not difficult to learn, a fascinating application.

And one more named Vis-a-Wiki, that I have heard about that combines a visual approach with wiki and graph as well as Scrumban board... Vis-a-Wiki has 'context sensitive navigation'.

I include these together not take away from, but hope as to just let people know about the existence of these independent software projects.


Hope this helps... -jariell

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