Lights, CAMERA, Venter!

I'm of two minds about Craig Venter. Undoubtedly he is a egotistical glory hound who, at one point, could have seriously compromised the public human genome project (would computational genomics research today be the same if we all had to go through Celera? Probably not.... I'm thinking subscription based database access... I'm thinking HGMD... I'm thinking the amount of hair pulling and fruitless mouse clicking that was involved the last time I tried to get some information about a set of Celera SNPs off the web).

On the other hand, the man has cojones. He also has a fondness for high-throughput data collection that as a bioinformatician I have to admire.

Anyway, Venter has been in the news again recently. Bio-IT World is carrying a story about Google's involvement with Venter (first seen in the Sunday Times in November last year - Snowdeal picked up on it back then). There's also a story making the rounds about a new collaboration between the Venter Institute and UC San Diego division of the California Institute for Telecommunications and Information Technology (Calit2).

As you may know, right now Craig Venter is circumnavigating the globe on his high tech superyacht Sorcerer II, currently sitting off the coast of Madagascar. In between BBQs on the poop deck and having bikinied lovelies massage suncream onto his sensitive pate he collects litres of seawater, strains all of the living organisms out of them and then sends the resulting crates of freeze dried micro-organisms back to the States to get shotgun sequenced. It's this project that Calit2 is interested in.

As Sorcerer II is collecting vast amounts of information:

Scientists aboard the vessel are identifying about 40,000 new species at every 200-mile stop along their route, [Venter] said

it's anticipated that to store, annotate and analyse all of the sequence data that is going to be generated scientists will need a fair amount of computing power.

The proposed solution is to set up a Grid on top of the National LambdaRail (a high speed academic network that runs over fiber optic lines). Calit2 is calling this a "Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis", or CAMERA for short. Calit2 and the San Diego Supercomputer Centre will provide the hardware while the Venter Institute will contribute sequences and "community developed genome analysis software" to help researchers make sense of the new data.

The infrastructure involved isn't trivial:

the CAMERA complex will have a thousand processors of dedicated local cluster computing and several hundred terabytes of replicated data storage.

Fair enough.

The press release makes for fun reading: bombast from the Venter Institute, the natural predilection for tortured acronyms shared by all Grid researchers and the love PR officers have for making science sound complex have all come together: the whole project is swaddled in fantastically meaningless jargon. For the record, it's not a Grid, it's an environmental metagenomics data storage and computational complex run over the OptIPuter high-performance 'collaboratory'.

Oh, and it'll help cure cancer.

The new resource will greatly enhance [UCSD's] health science researchers' ability to advance the development of new drugs and therapies from the ocean's resources to combat cancer and neurodegenerative and other diseases.