Blog Feeds

DSLs for High Performance Computing

Image via Wikipedia In the past I’ve written about Dan Reed’s post about a Ruby on Rails for HPC. Pan Hanrahan at Stanford has a similar article in the summer issue of Biomedical Computation Review. Dr. Hanrahan argues that in the age of multicore, grids and clouds, parallel computing is ubiquitous. This is, or at [...]

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Chemicalize

It’s ACS time in Boston, and there is a steady stream of tweets from the conference which you can track. Prior to the conference there were a couple of topics related to chemistry on the web which I’ve been meaning to write about. Better late than never I guess. The first one is Chemicalize, a [...]

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Strategic innovation

Ready two blog posts back to back, and realized just how much of a change in approach the biopharma industry needs. In post #1 Derek Lowe reproduces a letter from someone at a big pharma companies with a lot of analogies and metaphors comparing pharma to Hollywood. Part of the thrust of the letter is [...]

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Geospatial mashups. A blueprint for genome browsers?

I’ve talked about my jealousy of geospatial apps before. One of the things about the geo space that I really like is the number of mashups around, enabled by companies like SimpleGeo. Brady Forrest has a great post on O’Reilly Rradar highlighting some of the mashups enabled by the Polymaps, a collaboration between SimpleGeo and [...]

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A library for information retrieval

The blogging is slow these days cause I am completely swamped, leaving little time for any serious thought that isn’t work related. I’ve been thinking a lot about information retrieval these days, specifically in the context of scientific literature. Don’t know if anyone in that space reads bbgm, but they might want to take a [...]

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Data geeks and biology

Image of Matt Wood I’ve had the luxury of working in some very interesting areas; large scale protein structure prediction, physics-based approaches to drug discovery, data management for all kinds of molecular profiling data, and high-scale distributed infrastructure. I also have had the fortune of meeting some of the brightest people in the world at [...]

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Folding it, video game style

It’s been two years since I first wrote about Foldit. By now you’re read all about how Foldit was used to solve structures, probably a first for game play. Does this mean that computation sucks? Not really. Folding is a hard problem, and no method out there really does a good job because our functions [...]

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Twenty queries

Image via Wikipedia I am reading up a lot of Jim Gray these days, so a lot of his ideas are quite fresh in my head. Also had an interesting discussion with Nancy Parmalee on Twitter about software, informatics, bench scientists and small labs. One thing that jumped out, and is hardly a surprise, is [...]

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The internet, publishing, and data

A few days before Jim Gray sadly disappeared, I exchanged emails with him on a set of slides which are now a chapter in the Fourth Paradigm. There’s one slide in there that I wanted to share click for full size In this slide (the narrative can be found in the Fourth Paradigm), Jim states [...]

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Tenure

Megan McArdle has an interesting article on tenure in her blog at The Atlantic. She believes we should do away with tenure altogether.  She has another post on the costs of tenure Tyler Cowen has an different viewpoint on this subject (he is a tenured professor). I don’t know if that was the intent, but [...]

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