Category Archives: Omics

Supercomputing Masterclass – A request for information

By Deepak Singh | Published: June 13, 2009
I have been invited to give a Masterworks talk on Data Challenges in Genomics for Supercomputing 09. I would like to dive into the details about the technical and scientific challenges of high throughput genomics, from microarrays to next gen sequencing and beyond and how we need to be manage these data more efficiently. [...]
Also posted in BioIT, Computing, Event, Informatics | Leave a comment

When Whole Genome Sequencing becomes passe

By Deepak Singh | Published: June 5, 2009
In a recent blog post at MassGenomics talking about the recently published sequence of a Korean individual, Dan Koboldt makes an interesting observation. He notes This week’s publication of the genome of a Korean individual in Genome Research marks the fifth individual whole genome sequenced with massively parallel sequencing platforms. The fact that this [...]
Also posted in Life Science, Publishing | Leave a comment

1000 genomes, what 1000 genomes?

By Deepak Singh | Published: March 1, 2009
Image via Wikipedia Pierre asks How !#@$* do you manage 1000 genomes ??!. Perhaps we should be asking how we are going to manage 10,000 genomes, or 100,1000 and all the variants, and links between genotype and phenotype. This is going to get harder before it gets easier, and moving that data around will [...]
Also posted in BioIT, Informatics | Leave a comment

Sage: Data from old stomping grounds

By Deepak Singh | Published: February 27, 2009
When I was at Rosetta Biosoftware, I was exposed to (mostly via others) to a lot of the work that came out of our parent company upstairs, especially the work of Eric Schadt. It looks like some of that work might be the basis for Sage. Sage is an ambitious project from the [...]
Also posted in Open Science | 7 Comments

Rewarding the analysts

By Deepak Singh | Published: December 17, 2008
Science today rewards only those who collect and distribute data. There is no reward for those who organise the data and theorise based on it — Sydney Brenner Those words are from a talk at the Indian Institute of Science in Bangalore. I disagree with a decent chunk of what Dr. Brenner had to say, [...]
Also posted in Informatics, Life Science | 2 Comments

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