Archive for the 'Programming' Category


Friday, September 7th, 2007

It’s not uncommon for organizations to have strict policies regarding the use of GPLed code, due to the somewhat viral nature of this license.


Tuesday, June 26th, 2007

In the latest effort to make myself obsolete by the end of this year, we are looking for a software developer to help us better make our data available to both humans and machines. The main responsibilities of this position will be the further development of the UniProt web site and the UniProt RDF distribution.

Source Code Visualization

Wednesday, June 6th, 2007

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!


Friday, June 1st, 2007

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

Google Clear Button

Tuesday, March 13th, 2007

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

N-Triple Converter Comparison

Monday, March 12th, 2007

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.

Metalink for UniProt RDF

Wednesday, March 7th, 2007

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.

Fastest Java Virtual Machine?

Tuesday, January 16th, 2007

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.

Blast Google Gadget

Tuesday, November 7th, 2006

The Google Gadgets API can be used to create small applications that people can add to their personalized Google home page. Here is a simple “gadget” for blasting protein sequences.

Google Life Sciences Search Engine

Tuesday, October 24th, 2006

Google now allows you to create custom search engines. I used this to set up a search engine that searches in well know life sciences sites.