Science is running a poll titled “The Well-Behaved Scientist” this week that asks “how should we promote publication of data that can be replicated and reproduced?” Of the ideas on their list — more funding from funding agencies, more rewards from institutions — conspicuous in its absence is the rather fundamental idea that the purpose of scientific journals, including Science, is to publish reproducible research.
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Most scientists get to have their research programs reviewed quietly behind closed doors. But if your upcoming contract review gets featured in Nature under a title “A roll of the dice”, um, is that a good sign, or bad?
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.
Have you ever wondered how a new protein family would look in context of other Pfam domains? Well, look no further than the hmmer website! At the end of last week we released a new way of visualizing search results according to ‘domain architecture’ (applies to both phmmer and hmmsearch). Read more »
We’ve had a couple of reports of some less-than-intuitive behavior of HMMER3 on poor-scoring sequences. As one correspondent described it, HMMER3 is stubborn. It will refuse to score and align certain low-scoring sequences no matter what options you try to set. It’s probably worth explaining this behavior in public, partly because it’s an opportunity for me to briefly describe the fact that H3 has two processing pipelines: the “acceleration” pipeline, and the “domain postprocessing” pipeline. Only the acceleration pipeline is written up for publication, reasonably well documented, and well controllable by options. The domain postprocessor is ad hoc, not terribly satisfying, not well documented, not easily configurable — and it kicks back a side effect that drops some poor-scoring sequences entirely.
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Goran and our systems wizards will be upgrading Janelia’s network and some of our filesystems over the holiday weekend. We expect web services hosted by our lab will be unavailable at least sporadically from Friday evening ~8pm through Sunday ~4pm. This includes hmmer.org and HMMER RESTful computing services, access to software and publications at our lab home page, and the Janelia mirrors of Rfam and Pfam, etc. You won’t notice, it’s a holiday weekend, you shouldn’t be working anyway, right? We should be back to normal by Sunday evening.
I’ve written parts of HMMER’s code in the shadow of a massive Tyrannosaurus, and this week I’ll get to do it again. I’m on an advisory committee for the Field Museum of Natural History in Chicago, surely one of the few places you can sit in a cafe amongst dinosaurs. We’re meeting this Thursday and Friday at the museum. Getting a backstage pass to one of the great museums of the world is an awesome perk, but we’ve also got a serious job to do. In an age of iPads and ubiquitous information and entertainment, what should the future of a great natural history museum be?
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Peter Lawrence and Michael Locke wrote an essay that made an enormous impression on me (“A Man for Our Season”, Nature, 1997). For a long time a copy hung on the wall of the lab. I was reminded of it last week when I read a recent interview with Lawrence (“The Heart of Research is Sick”, Lab Times, 2011).
When it’s hard to reach me because I’m busy with my own research work; when I have to decline to travel to give seminars; when postdocs in my lab publish their own independent work without my name on their papers; when our papers go to open-access journals that do a good job of delivering substantive content regardless of that journal’s supposed “impact”; when I spend time on the details of a constructive peer review; when I help HHMI recruit and mentor younger scientists — and indeed when I moved to Janelia Farm, to be part of the idealistic culture that we want to build here — it’s principles much like Peter Lawrence’s that I’m aspiring to.
Real lives and white lies in the funding of scientific research
PLoS Biology, 2009
Retiring retirement
Nature, 2008
The mismeasurement of science
Current Biology, 2007
Men, women, and ghosts in science
PLoS Biology, 2006
The politics of publication
Nature, 2003
Rank injustice
Nature, 2002
Science or alchemy?
Nature Reviews Genetics, 2001
A man for our season
Nature, 1997
Over at our publications page, I’ve posted a preprint of Elena Rivas’ latest paper on RNA secondary structure prediction, which she submitted for review today.
From today’s email…
Suppose, for example, you want to search 300 million metagenomic sequence reads, each about 200nt long, against the Pfam database. What’s the best way to do that task with HMMER3? The bottom line: use hmmsearch, not hmmscan. For the numerology of why (and chapter and verse on how hmmsearch and hmmscan scale to large multithreaded and MPI tasks, their limitations, advice on how we do it, and some clues about what’s coming in the future), keep reading…
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