The Uppsala and EBI CDK-teams have been working hard on finishing the rewrite of JChemPaint I started with Niels earlier. While the EBI-team focused on the applet (and Swing application), the Uppsala team, obviously, focused on the SWT side, for integration into Bioclipse.

And I just got around to grasping some more of the details of handling dependencies with plugins. Bioclipse has a product file, which uses features to run it. That works fine. It also uses Spring (version 1.0.2 in our case) in a set up where we use custom managers to do stuff, like run things from a JavaScript environment (e.g. this), but use the same methods to be run from Bioclipse GUI elements, like buttons, menus and wizards.

Dear lazyweb! I have been trying to figure out which Eclipse 3.4 feature I must install from the update site to get the org.eclipse.zest plugin in my environment. I installed the Zest feature (which I am going to use to visualize an RDF network), but my workspace still complained that I did not have the plugin.

In preparation of the CDK workshop next week, here is a small Bioclipse2 script to calculate the XLogP value for a given SMILES, using the a CDK-based XMPP service: Earlier in this series:Bioclipse2 Scripting #1: from SMILES to a UFF optimized structure in JmolBioclipse2 Scripting #2: searching PubChem

Bioclipse is an environment for handling and processing life sciences data. This data is present in files with a wide variety of formats, each of which can contain a particular data type. For example, a we can have a single molecule in MDL molfile and in CML.

While Bioclipse is much more, it could be an interesting alternative to the Jmol application.

I ran into an Eclipse Grep Console plugin (EPL license) today that takes regular expression to color output in the Console.

RDF is swiftly becoming the lingua franca of life sciences (see for example [1,2]). Bioclipse is an excellent platform to visualize results from analysis of the network, both for graph visualization (see [3]), as well of visualization of domain specific data types (e.g. sequences, molecules, ...). Yesterday I uploaded a Bioclipse feature that adds a rdf manager to handle RDF content, which includes SPARQL support.

As you might have read, Bioclipse has scripting support (see for example, Scripting JChemPaint), and that we have been collection them on Gist and indexing them on Delicious with the tags bioclipse and gist. This provides a nice overview of what you can do with the current SVN version of Bioclipse2. And, hopefully, when released, allow users to quickly learn about Bioclipse features, allow people to share scripts etc.

One advantage of using XML is that one can rely on good support in libraries for functionality. When parsing XML, one does not have to take care of the syntax, and focus on the data and its semantics. This comes at the expense of verbosity, though, but having the ability to express semantics explicitly is a huge benefit for flexibility.

Stefan, Gilleain, Arvid and I had a JChemPaint Developers Workshop in Uppsala, to sprint the development of JChemPaint3, for which Niels layed out the foundation already a long time ago. Gilleain and Arvid merged their branches into a single code base, while Stefan worked on the Swing application and applet. The Bioclipse SWT-based widget is being developed for Bioclipse2.