Farrar's striped SIMD Smith/Waterman

Michael Farrar's striped SIMD Smith/Waterman source code [swsse2; Bioinformatics, 2007], is now available under an open source license for the first time. You can download it [here].

In 2007, Michael Farrar introduced a beautiful method for speeding up sequence alignment algorithms. Farrar's "striped" algorithm rearranges dynamic programming matrix indices …




mistakes were made

No one really knows how the game is played
The art of the trade
How the sausage gets made
We just assume that it happens

A while back Elena Rivas and I posted a response to a bioRxiv preprint (Tavares et al, 2018) that challenged some of the conclusions in …




'tis the season

Harvard's Quantitative Biology Initiative is searching for a new tenure-track assistant professor. This is a broad search -- we don't have any particular focus areas in mind. We are interested in people studying fundamental biological questions using quantitative, computational, theoretical, or experimental methods. The Initiative emphasizes cross-departmental interaction among our life …




HMMER 3.2.1

HMMER 3.2.1 is now available, fixing some small issues, mostly portability issues having to do with compilation on PowerPC machines and ancient x86 machines.

Thanks to the GCC Compile Farm folks for access to ppc64be and i686 machines that I'm using for testing now!




HMMER 3.2 release

The glorious master plan was to finish HMMER4 while hoping that HMMER3 stayed stable. Alas, HMMER4 development has been even slower than expected, and bugs and bitrot have accumulated on HMMER3. Here's a new HMMER 3.2 release to tide us all over. I'm managing HMMER releases again, with Travis …




Graeme Mitchison

Astronomy began when the Babylonians mapped the heavens. Our descendants will certainly not say that biology began with today's genome projects, but they may well recognize that a great acceleration in the accumulation of biological knowledge began in our era.

Graeme Mitchison wrote those opening lines of our book Biological …




Fall 2018 MCB112 teaching fellows

I'm looking for four teaching fellows (TFs) for my course MCB112 Biological Data Analysis in the fall 2018 semester. TFs are typically Harvard G2 or G3 students (second- or third-year PhD students, in Harvard-speak), but can be more senior students or even postdocs. I teach the course in Python and …




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