This is your brain on Toxoplasma

August 30, 2006

Seed magazine:

Approximately one-quarter of Americans host a parasite that has been shown to affect personality in both rodents and humans. According to a recent study, this single-celled organism may be able to shape entire cultures.

(via Quantum Ghosts)


Protein models and the PDB

August 29, 2006

A post by Deepak alerts that the PDB will no longer be accepting computational models of protein structures as of this October, and notes the pressing need for a peer-reviewed knowledgebase of protein models to exist alongside the PDB. The field of “structural genomics” has envisaged a marriage of experimental and theoretical determinations since its beginnings in 1998, but since then one gets the impression that the US-funded Protein Structure Initiative (PSI) has been sidetracked by the difficulties involved in experimentally determining protein structures in a number that approaches its initial somewhat optimistic forecasts. It is encouraging to see via these press releases that computational modeling is still within the realm of the PSI. Large scale funding for protein structure modeling such as this may deliver the kind of quality protein model databases that are needed in the light of the decision of the PDB.

Global bird flu sequence database planned

August 25, 2006

According to this story in Science, a former Hollywood TV executive has been flying around the world on his own coin collecting signatures for a proposed “Global Initiative on Sharing Avian Influenza Data”, through which genomic sequences of avian influenza are made public. The executive, Peter Bogner, who bears a striking resemblance to Eric Idle, was inspired by the campaign of Italian virologist Ilaria Capua, who had called for the open sharing of H5N1 sequence data earlier this year. Mr Bogner’s motivations are unclear:

Capua says Bogner initially suggested that he was working for U.N. Secretary-General Kofi Annan. Bogner says that the U.N. is one of his clients but not on this issue; indeed, he says, he hasn’t been paid a cent for his flu efforts. “In fairness, there are some aspects of this whole story I don’t quite understand,” says Capua. “But we’re getting what we want.”

UPDATE: Here is the letter to Nature referred to in the story above, in which we find that the Global Initiative on Sharing Influenza Data (GISAID) has a website.

Google vs. Brazil

August 24, 2006

Google is in big legal trouble in Brazil for withholding information about the users of its social interaction website Orkut, some of whom may be in involved in pornography and crime. An astonishing 66% percent of Orkut members are Brazilians – this is an example of the Brazilian Internet Phenomenon, the causes of which are mysterious and intriguing.

A non-coding RNA the missing link?

August 21, 2006

Story here, and this is the Nature article it is about.

Managing structural genomics data

August 21, 2006

Neil Saunders is wondering if there is some standard software to manage the data involved in structural genomics projects. Unfortunately most structural genomics laboratories (e.g. the JCSG, the TB consortium) have had to tackle this problem independently.

A couple of years back I worked on a LIMS system for stuctural genomics, which can be read about here. In theory the SQL schema and frontend are available for anyone, but there would be a fair amount of tweaking involved if another lab wanted to use it, and I think that would be the case for other systems. There have been efforts at the EBI to develop standard data models for structural genomics, though.

This is another example of the importance of data standardization in bioinformatics / post-genomic biology. Everyone in the structural genomics community agrees that standardization of the data is very important, because data mining of the results of thousands of individual experiments along the structural genomics pipeline might yield some really important results. For example, by comparing the sets of proteins that couldn’t be crystallized with those that could, we could find those properties of proteins that are conducive to crystallization. Some attempts at this kind of retrospective data mining of experimental results have already been made. And with a view to that, the PDB has a target registration database to which all SG centres submit their data in XML format, although the flexibility of the DTD for this data is questionable, and more importantly, there is no guarantee that the data that is reported is up-to-date. It will be interesting to see how the structural genomics community will continue to deal with all their data.

Welcome to Memomics

August 21, 2006

Why “memomics”? Memomics is about the totality of memes if you like, or maybe memos, take your pick.