Quantifying cost-effectiveness of scientific cloud computing in genomics and beyond

Biosystems Analytics

On-demand computing, often known as “cloud computing” provides access to the computing power of a large data center without having to maintain an in-house high performance computing (HPC) cluster, with attendent management and maintenance costs.  As even the most casual observers of the tech world will know, cloud computing is growing in any many sectors of the economy, including scientific research.  Cheap “computing as a utility” has the potential to bring many large-scale analyses within reach of smaller organizations that may lack the means or infrastructure to run a traditional HPC.  These organizations or individuals could include smaller clinics, hospitals, colleges, non-profit organizations and even individual independent researchers or groups of researchers.  But beyond the industry enthusiasm, how much can cloud computing really help enable low-cost scientific analyses?

There is now a veritable smorgasbord of offerings from many different vendors, but the big players are Amazon…

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Biologist Mickey von Dassow on collaboration, citizen science and ctenophores

Biosystems Analytics

Mickey von Dassow is a biologist who is interested in exploring how physics contributes to environmental effects on development. He created the website Independent Generation of Research (IGoR) to provide a platform to allow professional scientists, other scientists, non-scientists or anyone to collaborate and pursue any scientific project that they are curious about. I talked to him recently about his new site, citizen science and the future of scientific research and scholarship.

Mickey_headshot Mickey von Dassow

Can you describe your background?

My background is in biomechanics and developmental biology. My Ph.D. asked how feedback between form and function shapes marine invertebrate colonies. During my postdoc I worked on the physics of morphogenesis in vertebrate embryos, specifically focusing on trying to understand how the embryo tolerates inherent and environmentally driven mechanical variability. Since then I have been independently investigating interactions among ecology, biomechanics, and development of marine invertebrate embryos, as…

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All Big Data is equal, but some Big Data may be more equal than others

Biosystems Analytics

We are in the era of Big Data in human genomics: a vast treasure-trove of information on human genetic variation either is or will soon be available.   This includes older projects such as the HapMap, and 1000 Genomes to the in-progress 100,000 Genomes UK.  Two technologies have made this possible: the advent of massively parallel “next generation” sequencing where each individuals’ DNA is fragmented and amplified into billions of pieces; and powerful computational algorithms that use these fragments (or “reads”) to identify all the “variants” – any changes that are different to the “reference genome” – in each individual.

With existing tools this has become a relatively straightforward task.  Identification of single nucleotide polymorphisms or variants (SNVs) – single base differences between the individual and the reference genome – especially medically relevant ones –  is beginning to become routine. A project I worked on with…

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