GSoC/IDEA 10

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Here is a space for more details and project coordination.

Email 01

As I see it there are two main strands, a) create a data model to for the "environment/trait/SNP/propensity/citation/opinion" tuples, and b) put a user-friendly wiki-style interface on top.

Sadly, I really can't commit that much mentoring time to the project (sorry, but I'm just being realistic). So the main requirement would be for you to be able to work independently with only perhaps a few hours of high level guidance per week from me. However, you're welcome to work on this project with anyone.

If you are interested, you could try playing with Semantic MediaWiki and Semantic Forms, which I see as two useful tools for this project: http://scratchpad.referata.com

Email 02

You're absolutely right, genes (or specifically, the proteins they encode) are the functional workhorses of biology, doing the 'work' of the cell and the body. The biological differences between individuals are often attributable to changes in proteins or their regulation (such as changes in their expression level). These differences are evident at the DNA level, as DNA encodes the proteins and their regulatory elements. Now the interesting thing is that specific SNPs often serve as markers for particular blocks of DNA (called haplotypes) - when 'shuffling the deck' of human DNA, their are fewer cards than you imagine, because DNA is only mixed in these large blocks. So... by measuring SNPs, you can predict a lot of biology by association.

This principle underlies the science of 'genome wide association studies' (GWAS). If you like I can put together some reading on this topic for you, as it's something I'd like to understand better too!