Now, the DOI ubiquity scripts I just blogged about, was just the beginning of things. Me exploring the environment and learning the JavaScript language.

Now, I’m really after something else, but here’s my first Ubiquity scripts. It allow you to select a DOI on any web page (which really only makes sense if it is not already a hyperlink), you hit ALT-SPACE (Linux), CTRL-SPACE (Windows), or whatever the shortcut is on your operating system, and type resolve-doi and it will automatically convert the DOI into a hyperlink to look up the paper.

Cameron, Jean-Claude and I were invited to Peter’s place in Cambridge, where we are now hacking on CMLReact for the Ugi reactions Jean-Claude has been working on. I just finished a script that uses the CDK and Sam’s interface to the InChI library to convert a list of four reactants and one Ugi product into CMLReact (doi:10.1021/ci0502698). The full BeanShell script looks like:

Definately not a first post, but here are my experiences of my first blogging conference (see also this and this , the latter using semantic markup for the event): it was fun! My suggested unconference was not chosen, because I, as I usually do, focus to much on how instead of why one wants to do something. Nevertheless, I got to say my things, so I won’t complain.

The nice thing about a hacksession, is that you have something to write about. Below a screenshot of a Ugi reaction in Bioclipse… note the source tab of the editor, which holds the CML.

Have to leave to the airport any second now for the Science Blogging 2008 in London, so nothing much I shall say. Hope to see you tomorrow at the Royal Institute!

Just a quick screenshot. Remember our use of SKOS in MetWare ? Steffen has been working on creating integrated JSF pages, while I am focusing on autogeneration of blobs. The below screenshot is such a blob, called a UI component in JSF, which allows easy embedding the the aggregations Steffen is working on.

As promised yesterday , here’s the pretty visualization of the mass spectrum, using JavaScript from the PRIDE project:

Not visually attractive, but that will be solved when Steffen gets his hands on it. For now, I’m happy with a table formatting.

I was doing some profiling (YourKit and Eclipse3.4) of the CDK atom typer, and it turns out that most time is spend on the perception of nitrogen atom types, which seems to be caused by the loadClassInternal() method of the JVM (java-1.5.0-sun-1.5.0.16 on Ubuntu Hardy):

Deepak asked me to comment on his blog post Is your web service open source?. With a slight delay, I did on FriendFeed. I’ll copy it here.