NoSQL Distilled by Pramod J. Sadalage and Martin Fowler

07 Jun 2014 - Ethan Cerami

For those of us in the bioinformatics and genomics space, the advent of NoSQL databases offer multiple opportunities for storing "Big Data". However, many of us are still grappling with the same set of questions: when (if ever) does it make sense to switch over to NoSQL? how much data does one need to justify a migration to NoSQL? what types of genomic data sets and applications are ripe for NoSQL? and, given the hundreds of NoSQL databases which now exist (see nosql-database.org), which do you go with?

None of these questions are easy, but if you are looking for a starting point to answering these questions on your own, I highly recommend NoSQL: Distilled, by Pramod J. Sadalage and Martin Fowler. Martin Fowler is the author of several well-known computer software books, including a co-author of one of my favorites: Refactoring: Improving the Design of Existing Code.

At just 192 pages, NoSQL: Distilled provides a concise,...

IntOGen - Interview with Nuria Lopez-Bigas

25 Oct 2013 - Ethan Cerami

This week marks a slightly different direction for biobits.org. For some time, I have been thinking of interviewing practitioners in the world of cancer genomics, and getting their perspectives.

The first installment is an interview with Nuria Lopez-Bigas, from the Biomedical Genomics group at the University Pompeu Fabra in Barcelona.

I talked with Nuria about her recent work in building IntOGen (Integrative OncoGenomics), which was recently published in Nature Methods.

What motivated you to build IntOGen in the first place? What specific problem were you trying to solve?

NLB: Numerous independent projects are re-sequencing cohorts of tumor genomes and identifying the mutations found within them, including projects from the TCGA, ICGC, as well as independent initiatives not linked to...