Solubility Data in Bioclipse #2: handling RDF

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, …). less than 1 minute read

Bioclipse2 Scripting #2: searching PubChem

This week I have been porting the PubChem plugin for Bioclipse 1.2 to the new manager-based architecture. While still working on the Wizards, you can run the following JavaScript in Bioclipse2 from SVN and from the next beta (*): less than 1 minute read

DBPedia enters rdf.openmolecules.net

As of tonight, rdf.openmolecules.net links to the chemistry DBPedia (1816 chemical compounds), for which I used the SPARQL given in DBPedia: lookup and autocomplete of chemistry . It’s first of several steps to extend rdf.openmolecules.net to link up various chemistry database. The below figure shows the current state, where the green nodes are fully RDF-ied: less than 1 minute read

Bioclipse for CDK Developers #1

Ola has released the second beta for Bioclipse 2.0. Things are getting along, and I will not go into details on the molecules table Arvid is working on, the 1GB+ SD file support, the validating CML editor , the support for XMPP services , or the brand new welcome page which will guide new users around in what Bioclipse has to offer. 3 minute read

Blogger Degrading...

Did others notice this too? The blogger.com Links to this post functionality seems seriously broken… once a rather useful feature, it has now degradated to a useless state: less than 1 minute read

DBPedia: lookup and autocomplete of chemistry

On the DBPedia discussion mailing list there was a post on a nice web page which allows you to look up things, and which features a autocomplete edit field. The below screenshot show lookup of molecular structures: 1 minute read

CDK 1.2 Release Candidate

I released CDK 1.1.5 today. Below is the email I sent to the cdk-user mailing list: 3 minute read