Archive for February 2nd, 2008

Automated programming for bioinformatics algorithm deployment

Saturday, February 2nd, 2008

Automatically providing a GUI to bioinformatics algorithms by analysing the source code (and maybe some documentation comments). That is a neat idea.

Automated programming for bioinformatics algorithm deployment
Alterovitz et al.

Bioinformatics 2008 24(3):450-451; doi:10.1093/bioinformatics/btm602

I don't have any Java code around to test this on, so I don't know how well it works, but if anyone does, please let me know.

Tenfold cost reduction in exon resequencing

Saturday, February 2nd, 2008

Yesterday Roald Forsberg sent me this link: NHLBI, NHGRI Offer $12M to Cut Cost of Exon
Sequencing for Large-Scale Disease Studies
.

This is a research project that will offer four awards totalling $12M to help reduce the cost of reseqencing all exons, making this a viable approach to whole genome association mapping.

[The project will] complement the 1,000 Genomes Project that the NHGRI, the Wellcome Trust Sanger Institute, and the Beijing Genomics Institute announced last week.

Unlike that project, which aims to catalog genetic variations in human populations unbiased for disease, the resequencing technology program is geared towards studies that will correlate sequence variations with disease phenotypes.

When writing the grant proposal for my new project (that started yesterday) I argued that it was time to consider whole genome resequencing for association mapping and that we would see whole genome resequencing in association mapping within five to ten years. I am beginning to think I was being pessimistic here. Sure, this only focus on exons, but if we can sequence all exons, then the entire genome is not far behind.