PyPedia is a collaborative programming web environment.

Nice! Chanced upon this while googling for solutions to a problem
Gems I have found 
Convert impute2 to PEDMAP
Align VCF to reference
Pairwise linkage disequilibrium


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Translational Genomics Research Institute, personalised genomics to improve chemotherapy, cloud computing for pediatric cancer

I think it's fantastic that this is happening right now. Given that the cost of sequencing and computing is still relatively high, I can see how the first wave of personalized medicine will be lead by non-profit organizations. I am personally curious how this might pan out and would this be cost-effective for the patients ultimately? Would they be able to quantify it? 

Kudos for Dell for being a part of this exercise, though I wondered if they could have donated more to the data center or alternatively setup a mega cloud center and donate compute resources instead. Since i think the infrastructure and knowledge gleaned will be useful for their marketing and sales. 

http://www.hpcinthecloud.com/hpccloud/2012-02-29/cloud_computing_helps_fight_pediatric_cancer.html

Cloud technology is being used to speed computation, as well as manage and store the resulting data. Cloud also enables the high degree of collaboration that is necessary for science research at this level. The scientists have video-conferences where they work off of "tumor boards" to make clinical decisions for the patients in real-time. Before they'd have to ship hard drives to each other to have that degree of collaboration and now the data is always accessible through the cloud platform.


"We expect to change the way that the clinical medicine is delivered to pediatric cancer patients, and none of this could be done without the cloud," Coffin says emphatically. "With 12 cancer centers collaborating, you have to have the cloud to exchange the data."


Dell relied on donations to build the initial 8.2 teraflop high-performance machine. A second round of donations has meant a doubling in resources for this important work, up to an estimated 13 teraflops of sustained performance.


"Expanding on the size of the footprint means we can treat more and more patients in the clinic trial so this is an exciting time for us. This is the first pediatric clinic trial using genomic data ever done. And Dell is at the leading edge driving this work from an HPC standpoint and from a science standpoint."


The donated platform is comprised of Dell PowerEdge Blade Servers, PowerVault Storage Arrays, Dell Compellent Storage Center arrays and Dell Force10 Network infrastructure. It features 148 CPUs, 1,192 cores, 7.1 TB of RAM, and 265 TB Disk (Data Storage). Dell Precision Workstations are available for data analysis and review. TGen's computation and collaboration capacity has increased by 1,200 percent compared to the site's previous clinical cluster. In addition, the new system has reduced tumor mapping and analysis time from a matter of months to days.