29 March 2006

The Name Of The Rose

I finally saved a large number of journals from the Genset Libray that were initially intended to end in the bin. Although most of those journals are now in open-access, I stored this collection in my office and I'm now looking for an academic laboratory that would be interested in getting those journals.

The Name Of the Rose

20 March 2006

The ruins of Genset

For a few years Genset has been the leader and the pride of the french biotec, it was then acquired by the Swiss pharma Serono in 2002. But this Reseach Center definitively closed this year. With a few colleagues of integragen, we've be visiting the desert building... Nobody in the corridors, the library was a mess, complete collections of scientific journals abandoned on the ground...

15 March 2006

SciFOAF cited at 4th International Semantic Web Conference

SciFOAF was cited at the 4th International Semantic Web Conference. SciFOAF is a tool that helps building FOAF profiles from pubmed.

Using the Semantic Web for e-Science: Inspiration, Incubation, Irritation by Carole Goble [abstract]

(...)Genuine “Semantic WEB” examples, with the emphasis on Web, are also starting to appear. SciFOAF builds a FOAF community mined from the analysis of authors and publications over PubMed (http://www.urbigene.com/foaf/). Scientific publishers like the Institute of Physics (http://syndication.iop.org/), publish RSS feeds in RDF using standard RSS, Dublin Core and PRISM RDF vocabularies. The Uniprot protein sequence database has an experimental publication of results in RDF (http://www.isb-sib.ch/~ejain/rdf/). YeastHub converts the outputs of a variety of databases into RDF and combines them in a warehouse built over a native RDF data store. BioDASH is an experimental Drug Development Dashboard that uses RDF and OWL to associate disease, compounds, drug progression stages, molecular biology, and pathway knowledge for a team of users.
These examples should be an inspiration to the Semantic Web community.(...)

Thanks for the citation Dr Goble, but can you explain me why my paper was refused by Bioinformatics :-) ?

There was also an interesting note about semantic-web and computer performance:

(...)Performance over medium-large RDF datasets is disappointing – the CombeChem combinatorial chemistry project generated 80 million triples trivially and broke most of the triple stores it tried (www.combechem.org)...

06 March 2006

GBrowse Genome Browser + AJAX

In a previous post I introduced a PHP script to display tracks from the UCSC Genome Browser using SVG. A week later, a mail was sent on the UCSC mailing list to introduce the GBrowse/BioPerl browser based on AJAX and written at the Ian Holmes lab (Berkeley).

Now, let's wait for a genome browser based on both technologies :-)....