Hear the BBC radio program on Fungi: The Fifth Kingdom
Suzanne Leal wrote a very touching tribute in PLoS Genetics to Marcy Speer who passed away this summer. Marcy was one of the reasons I went to grad school at Duke and was a wonderfully generous and brilliant scientist, mother, and friend. I had the great opportunity to know her both when I worked at the CHG during and after college (where she would later become the director) and in her leadership role in my grad Program in Genetics (and Genomics) at Duke. Her smile and bright outlook is missed but her scientific legacy will continue to influence a great many.
Ed Louis at Nottingham sent out an email today outlining plans for publishing analyses of the Saccharomyces Genome Resequencing Project. They are in process of analyzing the data and ask that people respect their use of the data, but also invite collaborations and companion papers.
“If anyone has done or plans on doing a global analysis with a tight clean result which you think should be included in the overview paper, please contact us [Richard Durbin and Ed Louis; emails available through above links]. The analysis would have to be complete by 14 December and you would have to be willing to have the details transparently displayed on the web pages associated with the project.”
The Senate is expected to vote on the Fiscal Year 2008 Labor, Health and Human Services and Education (L-HHS) appropriations bill the week of October 15.
For the NIH, the Senate bill provides $29.9 billion, $250 million more than the House-passed L-HHS bill and $1.2 billion more than the President’s FY08 request. President Bush has threatened to veto the L-HHS bill because the House and Senate bills are $12 billion and $10 billion, respectively, more than the President proposed in his FY08 budget.
Strong, bipartisan support of the Senate bill is our best hope in the Congress to achieve a meaningful increase for the NIH. Otherwise the NIH will be forced to make further cuts in research as it has for the past few years.
Nature has an overview of what goes in and out of next generation sequencers with an interview with a smiling Chad Nusbaum from the Broad Institute. Most of these have been out and about for a while, but it seems that the hayride/bandwagon is starting to pick up more steam as GT‘s Genome Scan has several posts about sequencing referencing J. Craig V, George Church, and the Nature news article (not free).
Note that Solexa is no longer the cool name – “Genome analyzer” being the name for the machine that was previously called Solexa 1G. I’m holding out hope for funnier names in the future. I do feel that ABI’s choice of SOLiD is more exciting than 310/3700/3730 that is as inspiring as HAL9000.
If all went well you didn’t even notice… We migrated wiki and blog to new web server in Berkeley out of its kind hosting at OBF servers in Boston area. We’ve started the process of rebuilding the genome browser data similar to what was deployed at fungal.genome.duke.edu server, but we are redeveloping the data dumping and importing scripts to be more automatic. We hope this will result in a useful resource for fungal genome data including browsing and downloading annotation that is systematic and consistent across genomes. If all goes well beyond that we’ll deploy the ideas for comparative tools across the set of genomes for the kindgom. It will initially be to support our research interests in filamentous fungi, but we hope it will be a general enough system for other questions.
There was also a bit of a stir at the Open Data and Software BoF which centers around the ISCB’s statement about guidelines for open source software (you should provide feedback if you feel strongly about this and are an ISCB member: policy<-at->iscb.org).
The discussion was prompted in part because Mike Eisen and Sean Eddy both turned down their complementary ISCB memberships stemming from recent publications in PLoS CompBio (oh the benefits of publishing in PLoS CompBio) because of their disagreement with the policy. The Board took notice enough to organize a BoF at the conference. Unfortunately it was during lunch so you had to either choose between food and session or wolf down food very fast and run over to the room.
Some usual suspects were there that had a variety of opinions on open source – I don’t have the complete list written down though. There was an open-mic session after a panel of ISCB directors presented their opinions. It seemed like most of the audience members were in support of revising the statement to be more supportive of open-source although not everyone wanted to make it a requirement that source code be available commiserate with publication. To me there are a lot of messy ends here rather than having a discussion about the principals it ended up being about individuals personal stories that supported or discouraged a requirement of open source. Some people see it as too much of a burden to release their software (it is written either poorly or too hard-coded for their internal compilation system).
Back from ISMB/ECCB and a mountain of things left undone that somehow still need doing … including a quick entry about what was interesting at the conference.
I heard many good talks and only a few bad ones – maybe I guessed properly in darting between the multiple sessions. The meeting itsself was much better than past ones I had attended. The combination of Special Interest Groups meeting (BOSC, AFP, and Microbial Comparative Genomics being the ones I spent my time in). I got to give my talks and tutorial during the first few days and was able to just try and soak up the rest of the meeting (when my brain wasn’t melting from the heat). Particularly good was Carole Goble’s presentation on 7-deadly sins of bioinformatics software development.
Some general evolutionary talks that I found really interesting (some of these are probably biased since I count many of the presenters as friends):
- Mike Eisen’s keynote on evolution of regulatory sequences in Drosophila and other flies. Was a wild ride with a couple of different points he has made in the past, but was great to see it all come together.
- Alan Moses presented his work on predicting CDK targets through similar methodology that he pioneered in Eisen lab on cis-regulatory binding site clustering.
- Alex Hartemink gave two incredibly lucid presentations in that I really understood what he was trying to accomplish and how they did it. I wasn’t lost in the algorithm complexities but still understood the approach they were taking. One on Neuronal Information Flow using songbird brain profiling data and a second talk on their work in the epigenetics session on predicting imprinted genes.
- Pilpel Yitzhak presented a summary of published work on selection on translational efficiency and found some very interesting patterns in codon biases in aerobic and anaerobic fungi.
- Ilan Wapinski talked about his approach to building orthologous groups of genes that seems to be quite robust among the ascomycete fungi he used as benchmarked against the YGOB. I’m excited to work with him to apply it to larger sample of fungi as well as other particular clades of fungi.
- Ines Hellmann from Rasmus Nielsen’s group talked about some very cool work to look at population genetic analyses based on whole genome tiling data.
I’ll write a quick post on the BoF session on open source and data sharing as well.