Category Archives: BioIT

The big machines

Image via Wikipedia So the latest Top 500 list is out, so why doesn’t it excite me as much as it used to. Well partly cause many of those machines are not easily accessible, while other computing resources are within reach. Perhaps partly because for a lot of the work I am interested in [...]
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Write heavy file system workloads

In a blog post last year James Hamilton wrote about workloads in large scale network file systems. In his summary about of study on the subject he writes Some of the important points that spring out for me: the percentage of random access is increasing; for those accesses that are sequential, the runs are longer; [...]
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Supercomputing Masterclass – A request for information

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 Computing, Event, Informatics, Omics | Leave a comment

High scale design patterns (missing) in the life sciences

I’ve written about software failures in the past. As I get a better understanding of scale and architectures and talk to others about some of the core design principles of systems at scale, e.g. Recover Oriented Computing (also see this talk by James Hamilton), I realize how little most of us in the life science [...]
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When software embraces failure

I recently heard someone talk about software as being operational. The context was large scale systems and how it is important not just to run hardware systems that operate at scale but also software that operates at scale. And having spent a lot of time lately in a world where operational excellence is [...]
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