I [mentioned before](http://ptsefton.com/blog/2007/06/15/etd_2007) that
at the ETD 2007 conference I met [Prof Peter
Murray-Rust](http://wwmm.ch.cam.ac.uk/blogs/murrayrust/). We're going to
collaborate on adding support for CML
– the Chemical Markup Language to ICE, so
that people can write research publications that include 'live' data.
Here's a quick demo of the possibilities.
I went to the amazing [Crystaleye](http://wwmm.ch.cam.ac.uk/crystaleye/)
service.
> The aim of the CrystalEye project is to aggregate crystallography from
> web resources, and to provide methods to easily browse, search, and to
> keep up to date with the latest published information.
>
> <http://wwmm.ch.cam.ac.uk/crystaleye/>
Crystaleye automatically finds descriptions of crystals in
web-accessible literature, turns them into CML and builds pages like
[Acta Crystallographica Section B, 2007, issue
03-00.](http://wwmm.ch.cam.ac.uk/crystaleye/summary/acta/b/2007/03-00/index.html)
From that page I grabbed this two dimensional image of
(C~6~H~15~N~4~O~2~)~2~(C~4~H~4~O~6~^-2^),
There's a Java applet on the page that lets you play with the crystal in
3d. Here's a screenshot. of the 3d rendering.
There's lots more work to be done, but I thought I'd show how easy it is
to make an ICE document that shows the 2d view for print, with the 3d
view for the web, via the applet. Be warned, this may not work for you.
The applet refuses to load in Firefox 2 for me, but it does work in
Safari on Max OS X. If you follow the 'view this page in PDF' link above
you'll see just the picture.
[](http://ptsefton.com/files/cml/bk5044sup1_II.complete.cml.xml)
What's happening here?
My initial hack is really simple. I grab the image and paste it into ICE
like any other image, but then I link it to the [CML
source](../../../files/cml/bk5044sup1_II.complete.cml.xml). I wrote a
tiny fragment of Python in my ICE site to go through every page, and if
it finds a link to to a CML file containing an image, it adds code to
load the CML into the Jmol applet. This is a kind of
integration-by-convention, AKA microformat.
The main bit of programming only took a few minutes, but sorting out
where to put the CML files and the Jmol applet, and integrating the
changes into this blog took ages. I ended up putting the files here on
my web site which meant putting a big chunk of stuff into subversion,
something that should have been done ages ago, but the version of svn
that runs on my other server refuses to do large commits over HTTPS 'cos
of some SSL bug and I can't figure out how to update it which meant
switching the repository to use plain HTTP, and so on. It wasn't made
easier by me mucking around with the Airport Extreme router and our ADSL
modem at the same time, halting internet access at home for a couple of
hours.
To make this integration a bit more usable and robust we want to:
- Work out a workflow that lets you keep CML files in ICE and easily
drop images in to your documents, letting ICE render using the
applet when it makes HTML.
- Integrate forthcoming work from Peter & team that will provide high
quality vector graphics instead of the PNG files I'm using now.
- Investigate embedding CML in an image format such as EPS that word
processors understand.
- Generalize this approach for other e-scholarship applications. We're
working with the [Alive team](http://www.alivex3d.org/) at USQ on
this.
- Talk to the [DART & ARCHER
teams](http://www.ariadne.ac.uk/issue51/treloar-groenewegen/).