Exodi

Belated congratulations to Rob Finn, who has moved to EMBL-EBI to lead the Protein Families team. The HMMER web services pilot project that HHMI has funded at Janelia, under Rob’s leadership, is now in transition to EBI, and Rob and I will write more about this in the future.

Slightly-less-belated congratulations to Travis Wheeler, who has left the lab to start his new job as an assistant professor at the University of Montana this fall. The nhmmer software project and his lead role in the Dfam mobile element database moves with him. We mourn the death of our collaborator and friend Jerzy Jurka this past July. Together with Arian Smit and others, sometime soon we hope to have more to say about the legacy of Jerzy’s seminal Repbase database.

Timely — perhaps even premature — congratulations to Eric Nawrocki, who is in process of accepting a position at the National Center for Biotechnology Information, where he seems likely to start in January. Eric will remain lead developer of the Infernal RNA homology search codebase. We’ll probably have more to say about that too, and what it means for Infernal development and the Rfam structural RNA database.

It’s getting a little underpopulated here in our Janelia monastery cells. But there’s good reason for that, all part of the master plan… another exodus story that I’ll post about soon.

Open position: Director, Advanced Computation and Technology group

Janelia has a scientific director-level position open in our computation and technology group:

“The Janelia Farm Research Campus of the Howard Hughes Medical Institute seeks an exceptional individual to lead a world-class technology effort in advanced computation, data analysis, and instrumentation design and fabrication. The Director of Janelia’s Advanced Computation and Technology group is responsible for leading an array of data-driven technology teams, ranging from data acquisition to data analysis. In collaboration with Janelia research scientists, this person must drive a strategic vision and set priorities for focused investment of effort in sophisticated engineering and computational technology, enabling Janelia’s two scientific goals:(1) understanding the basic mechanisms used by nervous systems to store and process information and (2) developing new methods for image acquisition and analysis. This individual may not necessarily be a neuroscientist or even a biologist themselves; rather, the ideal individual will have extensive technical and engineering expertise in some area of large-scale data analysis, while being excited about applying this expertise in fundamental neuroscience research.”

We’re running ads in all the usual places, and you’ll find some more information about the position there: such as this one in Nature. Please spread the word. I’ll be happy to answer questions about the position informally, for anyone who may be interested, or who may know someone who’d be interested.

Biological sequence analysis and probabilistic models: 24-27 March 2013

Registration is open for a conference on “Biological sequence analysis and probabilistic models”, 24-27 March 2013, here at Janelia Farm. Katie Pollard (UCSF), Adam Siepel (Cornell), and I are the co-organizers. Janelia Farm conferences are small (~50 people), a nice size for conversation and thought. We’re likely to select about 15 more participants from open registration. For more information, including a current list of the invited speakers and a link to registration, see the Janelia conferences web page.

Janelia Undergraduate Scholars summer program

Janelia is accepting applications for our 2012 summer undergraduate research program, deadline January 13. Janelia pays all expenses, travel, and a stipend for the 10-week program here at the Farm.

The program is particularly terrific for students interested in systems neuroscience, since Janelia is a neurosciency place, but there’s a wide range of opportunities, including computer science and applied physics projects. You can browse Janelia’s lab web pages at janelia.org. In my own lab, I’d be particularly interested in finding a summer student who wants to do some C coding in our HMMER codebase, exploring how well we might be able to get it to run on graphic processing units (GPUs). I expect we’d be able to set up a collaboration with engineers at NVIDIA, because NVIDIA have offered help to us on several occasions, but so far we’ve lacked the extra person-time to take them up on any offers. Should be a good summer experience for the right person, combining experience in computational biology with experience in software engineering and GPU programming.

For more information, see the Janelia Undergraduate Scholars program web page.