Archive for 2007

Amos Bairoch Action Figure

Tuesday, December 4th, 2007

While looking for a birthday and farewell (I was just leaving the Swiss-Prot group) present for Amos Bairoch, I came across a company that creates custom action figures. Here’s the result!


Friday, November 30th, 2007

Some pictures and notes from a one-week trip to Rwanda.

Some Java Benchmarks

Saturday, September 29th, 2007

During the last two weeks I ran some tests to answer a few questions that had been accumulating:

  1. Should I disable hyper-threading (ht)?
  2. How much does doubling the available memory improve performance?
  3. Mirror, mirror on the wall, who has the fastest JVM of them all?


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.

Swiss-Prot 20 Talks on Google Video

Friday, August 10th, 2007

One year after the amazing and memorable conference that was held at the 20th anniversary of Swiss-Prot we’ve made all the talks available on Google Video. Here’s a starting point. I heard it’s going to be a rainy weekend ;-)

ISMB 2007

Monday, July 30th, 2007

Just got back from the ISMB conference in Vienna. Turned out to be a quite busy conference — I barely managed to attend any talks :-)


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.


Sunday, June 10th, 2007

Rochers-de-Naye (near Montreux, Switzerland) is a nice place to see some Marmots up close in a nice surrounding.

Compare Ontology Versions

Thursday, June 7th, 2007

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.

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!