Notes from the Biomass

The NAR web server issue was published yesterday and describes 166 bioinformatics web servers.
The distribution of services is against the recent trend - many servers are "classical" sequence driven services, whereas the majority of bioinformatics (methods) articles are concerned with mRNA expression data or protein-protein interactions.

An overview of the methods published can be found at the UBiC.

The following call from Frank Gannon deserves support. So I can sign the petition - and post it here.

Scientists petition for increased EC funding for research

Dear Colleague,

The collapse of the discussions on the EU budget has been highlighted in media. What receives less attention is the fact that preparatory discussions on a new budget were pointing towards a very major reduction on the doubling of funds for Framework 7 that had been requested by the Commission. Included in this funding were increases for the Marie Curie programme, expansion of the standard Framework activities and, significantly, the funding of the European Research Council (ERC).
All of this is now at risk and the voices of scientists need to be heard. As one effort to ensure that the politicians get a message from the scientific community, we, supported by ELSF, (European Life Sciences Forum) (http://www.elsf.org) and ISE, (Initiative for Science in Europe) (http://www.initiative-science-europe.org) have opened an online petition on the EMBO website.

If you are in agreement with the petition, sign it at http://www.embo.org/petition/petition.php

Please ensure that all of the scientists in your institute are aware of it and encourage them also to sign. This is a case where numbers and a rapid reaction are very important!
Please note also that ELSO, (European Life Scientists Organization) have prepared a letter to be sent to Ministers of Research to underline the importance of the ERC. http://ultr23.vub.ac.be/petition/

This is your opportunity to influence the future of research so I suggest that you act on these initiatives now.

Prof. Frank Gannon
Executive Director, EMBO

The first issue of the latest journal - PLoS Computational Biology - was launched by Public Library of Science. Will be interesting to see whether it can become the prime bioinformatics journal - it certainly has the potential.

The current issue of Bioinformatics describes the YeastHub database , created by the Gerstein lab.

Yeast is a well sampled and organism with many high throughput data sets to integrate and several established and curated resources such as MIPS, SGD and what used to be YPD.

The new YeastHub data base connects available data using semantic web technologies such as RSS, RDF and a relational to RDF mapping. The set of technologies has the potential to solve many of the small problems one has do deal with when integrating data across many sources.

Eagerly, I tested the data base but was a little let down: While I see the obvious benefits, many small problems appear, which taken together, make the system not really very helpful to the average bioinformatics user, let alone a biologist in the the yeast community.

The lack of descriptions of formats of the data sources makes it tough to create queries and I did not really get past trivial results. I also dearly missed capabilities to browse the data sets. However, it appears as if these technologies will become more and more important and the old tab separated tables hopefully disappear one fine day.

A more recent addition to NCBI's online databases is PubChem, which aims at providing a comprehensive database for low molecular weight chemical structures. It includes the results of bioassays.
After the Slashdot feature today, I played a little with it and was little disappointed to obtain only 6 protein kinase inhibitors, 2 Caspase inhibitors and no assays for these activities. It will definitely take some time before the data base seriously competes with private efforts but let's sit back and wait and review this in September, when the service will be up for one year.

An essay in the recent issue of PLoS Biology explores the how norms or memes evolve and strikes chord here.

Food for thought for tonight for me...