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TiddlyWiki and LaTeX – Scientific Notebooks Made Easy

tiddlywiki-logo.pngFor ages scientific notebooks have been the mainstay of scientific research and have always had one thing in common: paper. Until now that was mostly due to a lack of options. Today as science and computers have become more and more inseparable the appeal of digital notebooks is quite clear. Digital notebooks have one huge advantage over their hand-written brethren – search capabilities. Digital notebooks have one huge advantage – search! The ability to easily search for notes rather than paging through 3-ring binder after 3-ring binder is a HUGE timesaver. Digital notebooks do have their shortcomings, primarily the inability to easily write equations and draw diagrams. However, by adding LaTeX to the mix digital notebooks can handle equations with ease, and scanning in diagrams isn’t too much of a chore either. I’m going to assume some working knowledge of LaTeX, however, if you aren’t familiar with LaTeX don’t worry it isn’t required to use TiddlyWiki. Besides, typesetting simple equations in LaTex is actually very simple.

latex-example.png

There are quite a few scientific notebook applications out there, but I recently found a solution that I think quite elegant and possibly the simplest to use. TiddlyWiki is a wiki platform not unlike MoinMoin and DokuWiki. TiddlyWiki has a few advantages over these other wiki solutions, however, primarily its portability and interoperability. TiddlyWiki consists of one simple html file which makes it extremely easy to take your notebook with you on a USB memory stick. In addition, since the only program required is a standard web browser (IE6, IE7, Firefox, etc) you can take notes anywhere there is a computer (no internet required). For example I can take notes from the lab machine running Windows just as easily as I can from my iMac at home.

Download TiddlyWiki

Downloading TiddlyWiki is a snap and you can get a blank wiki here. Once you have downloaded the html file simply open in a web browser, preferably Firefox. Play around with the wiki for a bit – I’m a big fan of the different animations.

Install TiddlyWiki LaTeX Plugin

Now comes the somewhat tricky part – installing the latex plugin. Visit the plugin homepage here. Once you have read up on the plugin, re-open your TiddlyWiki (you might want to make a backup by duplicating the file first). Click backstage in the upper right corner, followed by import, and enter the URL of the jsMath plugin (see below)
latex-example.png
You might get a security warning from Firefox, click ‘Allow’ and select the default workspace. If everything worked, then you should be presented with a list of check boxes, select the jsMath plugin and click import (see below)
latex-example.png
Now download and place the jsMath folder in the same directory as your empty.html file. That should do it, save your wiki and refresh the page.

Install fonts

Depending on your system you might also need to install the Tex fonts that are available here. The webpage contains clear instructions for both PC, linux, and Mac.

Enjoy!

That is all, enjoy your new digital notebook. If I missed something or if you know of a good plugin for TiddlyWiki leave a comment below.


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