Following on from the SVG experiments I've started to put some of the Javascript code for displaying phylogenies on Github. Not a repository yet, but as gists, little snippets of code. Mike Bostock has created http://bl.ocks.org/ which makes it possible to host gists as working examples, so you can play with the code "live". The first gist takes a Newick tree, parses it and displays a tree.

One visualisation method I keep coming back too is the treemap. Each time I experiment with them I learn a little bit more, but I usually end up abandoning them (with the exception of using quantum treemaps to display bibliographic data). But they keep calling me back.

One thing I'm increasingly conscious of is that I've a lot of demos and toy projects hanging around and the code for most of these isn't readily available. So, I plan to clean these up and put them in GitHub so others can explore the code, and reuse it if they see fit. First up is the code to create a HTML+Javascript clone of Nature's iPhone app, as described in an earlier post. There's a live version of the clone here here.

The bulk of the Biodiversity Heritage Library's content is available as DjVu files, which package together scanned page images and OCR text. Websites such as BHL or my own BioStor display page images, but there's no way to interact with the page content itself.

I have blogged about two Molecular Chemometrics principles so far: McPrinciple #1: access to data McPrinciple #2: be clear in what you mean Peter’s post #solo10: Green Chain Reaction; where to store the data? DSR? IR? BioTorrent, OKF or ??? gives me enough basis to write up a third principle: Molecular Chemometrics Principles #3 : We make scientific progress if we build on past achievements. Sounds logical, right?

One of the more glaring limitations of my BHL viewer described in the previous post is that it can take a while to load all the page thumbnails (there can be hundreds). Given that one of the original motivations for this project was a faster viewer, this kinda sucks. What I'd like to do is load the thumbnails only when I need them, rather than all at once at the start -- in other words I'd like to implement lazy loading.

I've just discovered Nicolas Garcia Belmonte's JavaScript Information Visualization Toolkit (JIT). Wow! This is very cool stuff (and no Flash). To quote from the web site: Nicolas also links to a talk by Tamara Munzner, which I've embedded below to remind myself to watch it.

The Bioclipse Workshop has ended and, for just three days, turned out quite productive. We have first bits of scripting support for JavaScript using Rhino. At this moment the scripting plugin needs to explicit depend on plugins to be able to access their classpath, but we plan to solve that. An example script: // to have short identifiers Array = Packages.java.lang.reflect.Array; String = Packages.java.lang.String;