eric.jain.name 

There is a rather useful (but perhaps somewhat hidden) plug-in for Protege that can be used to compare two versions of an OWL file: PROMPT.

My colleagues regularly ask me if I couldn’t provide them with some graphic view of my code, looking at source code is so tedious etc. I’ve looked at various UML tools in the past, but never managed to get any truly useful visualization out of any of them. But maybe the problem with UML is that it’s so limited to two dimensions? Enter Relief, a tool that visualizes code in three dimensions!

Gave a brief talk about programmatic access to beta.uniprot.org at the EMBRACE workshop in Geneva today.

Here’s the new “Powerpuff Girls”–inspired theme for the new UniProt website.

Here is a simple Greasemonkey script that adds a Clear button to Google search result pages.

In order to bulk-load RDF data into Oracle (Spatial) 11g, the data needs to be converted to N-Triples first. If the data set is large, this step can add quite a bit of overhead, which is why I decided to benchmark and compare several options.

The UniProt RDF distribution is over 5GB large. To help people retrieve the data more efficiently, we now mirror the data and provide a Metalink file that describes all the file locations.

Being able to distinguish different meanings of a term may turn out to be the next big step forward for web search engines. There are quite a few people working on this now; here is a quick survey in which I check how well the different efforts handle the term “Kiwi”.

The best choice of virtual machine is of course dependent both on the application and on the hardware the application is running on; here are the conclusions of a performance comparison with the latest batch of Java virtual machines for a web application that makes heavy use of BerkeleyDB and Lucene on an off-the-shelf Intel machine with 64-bit extensions.

Fake ad for an “annotation robot” that could be used to replace human database curators. Shown at the Christmas dinner of the Swiss-Prot group.