The Xfam team in Cambridge is advertising an open curator position. Join the Xfam team, see the world! At least some of the best parts of it: Cambridge UK, Stockholm Sweden, and our beautiful, secluded, mysterious Janelia Farm on the banks of the Potomac River near Washington DC.
The National Academy of Sciences has just released the report Sequence-Based Classification of Select Agents: A Brighter Line. A committee of 13 of us, chaired by Jim LeDuc (Director, Galveston National Laboratory, University of Texas Medical Branch) and cat-herded by India Hook-Barnard (NAS), has been working on this report for the past year or so. It’s good to see it done. There is an NAS press release, and Nature and Science, among others, have already picked up the story.
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Our little Janelia lab got even smaller this week.
Sergi Castellano left to take a new faculty position in the Department of Evolutionary Genetics with Svante Paabo at the Max Planck in Leipzig, Germany. Sergi’s postdoctoral work on single-sequence-query homology searches in HMMER, the project we call “Smith/Waterman: reloaded”, is still in progress — a generative probabilistic interpretation of what all the explicit and implicit zero scores in Smith/Waterman scoring really “mean”, and the nonzero values we say they ought to have. Temple Smith has said his career was based on zero, referring to the extra step in the Smith/Waterman local alignment recursion compared to global sequence alignment. Sergi’s going to show that Temple’s career is and always should have been nonzero.
Diana Kolbe, one of our two last Washington University grad students, defended her thesis back in St. Louis yesterday. She’s worked for many (!) years on ways to accelerate the Infernal software for RNA similarity search. An important last chunk of her work, which we hope to write up for publication in addition to what’s in her thesis, established proof of principle for a structure-based heuristic acceleration that complements Infernal’s current sequence-based heuristic acceleration. It will take significant software engineering to implement her ideas in the production codebase, and she’s more than done her time in grad school already, so we’re letting her go; the proof of principle is captured in an Infernal development snapshot release. She’s off to join Laura Elnitski’s lab at NIH NHGRI as a postdoc.
The lab is getting close to completing a gradual four-year transition from its WashU configuration (where we were about 15 people, almost entirely built around me working with graduate students, and a sprinkling of postdocs and staff) to its Janelia configuration (where we are about 6 people, and the long-term plan is to have a core of staff working on software engineering in HMMER and Infernal, with me working on shiny new things with one or two postdocs). The last Washington University graduate student, Seolkyoung Jung, is now writing her thesis and her last paper; we’ve just submitted her magnum opus, a paper describing an enormous chunk of work on finding ncRNAs in Oxytricha trifallax.
A burst of new work from the lab is available over on our publications page. Summaries and backstories for three of these manuscripts, below the fold: Read more »
The NIH National Human Genome Research Institute is going through a process of making plans for the next five years of research in genomics, including computational genomics. In the past couple of months I’ve been at two planning meetings – the Cloud Computing workshop (31 March – 1 April) and most recently the NHGRI Informatics and Analysis Planning Meeting (21-22 April). Goncalo Abecasis and I got the job of trying to summarize the consensus of the Informatics and Analysis meeting. I’m not sure how good I am at identifying consensus, but I just sent off four pages of notes to Vivien Bonazzi, one of NHGRI’s informatics program officers, describing some of my personal views of the future, strongly colored by the discussions at the planning meetings. I thought I’d share the same comments here. Transparency in government and all that. Just imagine all the potential conflicts of interest here; good thing I’m paid by a dead billionaire, not so much by federal tax dollars.
Anyone with an interest in how the sausage is made at NIH might want to peek under the hood, below. Read more »
Alex’s acceptance speech for the 2010 Benjamin Franklin Award in the Life Sciences is now online at SciVee.tv. The fearless leader of Xfam, grounded by a piddly wee volcanic ash cloud and forced to videoconference to his adoring public. Meanwhile, I’m supposed to schlep over to Cambridge for the annual Xfam meeting in a couple of weeks, and I guarantee that Alex won’t accept any volcanic excuses from me.
Congratulations, Alex, and to the whole Pfam and Rfam teams in Cambridge!
Our quest is at an end.
– Monty Python and the Holy Grail
Four years in development, and a year in testing: HMMER3 has reached its first public production release. Do we have time for a beer and a small celebration before we write the manuscripts and move straight on to 3.1 development? No? Thought not.
HMMER3 is available for download as a source code tarball. Over at hmmer.org, there are also links for downloading tarballs including precompiled binaries for Linux/Intel ia32, Linux/Intel x86_64, and Mac OS/X Intel platforms.
The release notes for 3.0 follow:
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My relationship with email is fraught. On the one hand, it ravages my time and concentration; on the other hand, it’s better than the damned phone.
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The czar of Rfam in Cambridge UK, Paul Gardner, is advertising for a new co-czar. Jennifer Daub is off to New Zealand, which is great for Jen, but what will Rfam do without her? It’s a great opportunity to bring more order to the world of noncoding RNAs, for someone with interest and skill at the interface of bioinformatics and RNA biology. The officialese of the job posting is available at the Sanger Institute web site.
In a world where “a few days” means a month; in a world where “HMMER3 is ready” means another release candidate: ta-da! A release candidate!
HMMER3 release candidate two is available for download as a source code tarball. Over at hmmer.org, there are also links for downloading tarballs including precompiled binaries for Linux/Intel ia32, Linux/Intel x86_64, and Mac OS/X Intel platforms.
The release notes for 3.0rc2 follow:
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