Cryptogenomicon

Francis Collins became Director of the NIH in August. Eric Green has now accepted Francis’s previous position of Director of the NIH National Human Genome Research Institute (NHGRI). That means Eric’s position, Scientific Director of the intramural NHGRI research program, is now open. A search committee is forming, and I’m on it. Eric has started to canvass the community for interested candidates, and ads will soon start appearing. There is a tight timeline – Eric expects to interview for the position in March. Whom should NHGRI be considering as candidates?
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In 2005, the New Yorker published a remarkable article by Margaret Talbot called The Auteur of Anime, about the Japanese director Hayao Miyazaki.
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The final HMMER3 beta test release is available for download as a tarball. It includes precompiled binaries for Intel/Linux systems, both 64-bit (x86_84) and 32-bit (ia32) platforms, and you may just copy these into some directory in your $PATH if you like. If the precompiled versions don’t work for you, you can always compile your own version from the source.

The main additions in 3.0b3 are parallelizations and even more speed. It now includes support for multicores (POSIX multithreading) and support for clusters (MPI). For the first time, we’re seeing some searches peek above NCBI BLAST search speed. Yes, you read that right, profile HMM speeds have started to exceed BLAST speed. And we’re far from done.

The release notes for 3.0b3 follow: Read more »

Do not go gentle into that good night,
Old age should burn and rave at close of day;
Rage, rage against the dying of the light.

– Dylan Thomas

Every time I shake someone’s hand, I think of my grandfather.
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The truth will set you free. But not until it is finished with you.

– David Foster Wallace, Infinite Jest

With the release of Pfam 24, HMMER3 beta test code has been pressed into service just a bit earlier than we’re comfortable with. Though the 3.0b2 code seems to be holding up reasonably well, we are aware of six bugs — two in how H3 handles Pfam GA/NC/TC cutoffs, two in how H3 handles the ‘*’ nonresidue character that some sequence files use to represent stop codons in translated DNA, one in hmmscan’s tabular domain output (”domtbl”) format, and one in sequence description lines with % characters causing crashes in jackhmmer. All six are fixed in the development trunk. We are starting our test/release cycle for 3.0b3 (the third and probably final beta release) now. The fixes will be included in 3.0b3, along with some important new functionality I’ll discuss on the blog soon.

More details on the six bugs are below the fold.
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Writing and drawing are slow, deliberate activities, so I tried to keep distractions to an absolute minimum, and I did everything myself. I liked this control, as it fostered a sense of craftsmanship. There was great personal satisfaction in attending to detail and quality, and I remain very proud of the standards the strip met day after day. I also liked the responsibility of knowing that, succeed or fail, it was all my own doing.

– Bill Watterson, Calvin and Hobbes

Besides writing code all day, one of the more interesting things about the job is what I get to do on the side. Technically, Janelia expects me to be physically present for nine months a year, and it gives me three months to do whatever I want — skiing in New Zealand, NIH study section, visiting some university and giving a seminar, swine flu, it all counts against my three months of “vacation time” as far as Janelia’s concerned. So. Mild-mannered software/bio geek by day; advisor to US government agencies by… uh, well… seemed like pretty much the whole summer, this year. Two big time commitments with serious committee reports to help write. One report is finished for the Department of Defense, and another is well underway for the National Academy of Sciences. That, plus three weeks in Spain for the Benasque RNA conference, plus some review work for NIH all pretty much enforced a personal vacation away from the HMMER code. Probably good, because the code was making me cross-eyed, not to mention cross. I needed a break from it.

Nonetheless, despite a few months of radio silence, things have been moving forward for HMMER3. Especially on the Grand Long Term Strategy front. HMMER now has a development team.

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This is wrong on so many levels. I taught two of these young whippersnappers computational biology at WashU — I should’ve stopped them when I had a chance. (I hope that old dude at the end isn’t supposed to be me.)

An Interview With Cofactor Genomics from Grant Essig on Vimeo.

Some bugs crept through testing and into the 3.0b1 release of HMMER3. They’re fixed, and the link in the “3.0b1″ release post below was quietly updated to the 3.0b2 tarball available for download on our FTP site.

I fixed a bug with the new code that deals with fragment-rich alignments (sometimes hmmbuild was failing, complaining about a failed “trace validation”). I also added the –tblout and –domtblout options to hmmscan, which should’ve been there in the first place.

it is not necessary to accept everything as true, one must only accept it as necessary.
– Franz Kafka, The Trial

As the unearthly whine of the Janelia compute cluster subsides after testing the beta1 release, power and lights are flickering back to life in Virginia, and I have a quiet moment to talk about failure.
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The alpha test is complete, and the beta test phase begins today. HMMER3 beta test code is publicly available as a tarball available for download on our FTP site. Besides source code, the tarball also includes a binaries/ subdirectory with precompiled binaries for Intel/Linux systems, both 64-bit (in binaries/intel-linux-x86_64) and 32-bit (in binaries/intel-linux-ia32), and you can just copy these into some directory in your $PATH if you like. These should work on a wide variety of platforms but if you have any trouble, you can always compile your own version from the source code.

My attention is now going to turn toward writing up some papers on all this, and writing the HMMER3 documentation, because (of course) nobody’s going to find any bugs in the beta test, right?

The release notes for 3.0b1: Read more »