ISCB BoF on open source and open data

ISCB logoMore ISMB recap.

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).

Continue reading ISCB BoF on open source and open data

ISMB/ECCB 2007 recap

ISMB2007Back 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):

I’ll write a quick post on the BoF session on open source and data sharing as well.

Todd and I took some pictures as well.

Haunted Woods

Eucalyptus is an utilitarian tree, so it’s no surprise that several organizations are interested in genetically engineering it. Indeed, its genome sequence is slated for release, which should facilitate a GE market for the species. One company in particular – ArborGen (they have a very interesting mission statement) – is using genetic engineering, cloning and classic hybridization techniques to make a cold tolerant variety. ArborGen’s grove of 355 hybrids is located in southern Alabama. While a cold tolerant genotype would enable harvest of the tree across North America, this project has been met with particular public resistance, given the species’ invasive abilities.

There may be another reason for the public to resist ArborGen’s new project: Cryptococcus gattii.   Known to associate with eucalyptus, C. gattii is a yeast-like fungus that can infect and kill mammals, including humans, that inhale its spores. Recently, a rare C. gattii genotype was the subject of an outbreak in British Columbia. Scientists and environmentalists are concerned that standing groves of eucalyptus that may be inncoulated with C. gattii could result in a subsequent health hazard for anyone living nearby. This particular risk, it should be noted, is independent of genetic engineering, but rather results from increased reliance on Eucalyptus as an industrial wood (remember, it’s not native to North America). The concerned parties have raised the issue with the US Deptarment of Agriculture and the EPA, so hopefully Cryptococcus ecologists will be afforded the opportunity to determine if the pathogen lives in ArborGen’s grove.

Final note: a special thanks to Kabir Peay, a fungal ecologist, who brought this to my attention.

Genomes on the horizon at JGI

Several more fungi are on the docket for sequencing at JGI through their community sequencing program. This includes

This complements an ever growing list of fungal genome sequences which is probably topping 80+ now not including the several dozen strains of Saccharomyces that are being sequenced at Sanger Centre and a separately funded NIH project to be sequenced at WashU.

More Cocci genomes

The Broad Institute has made available additional genomes of strains of Coccidioides immitis and C. posadasii. There are now genome sequences for 4 strains of C. immitis sequenced and 3 strains of C. posadasii including the C735 strain from the JCVI/TIGR. including the reference strain RS that is assembled into 7 supercontigs (there are probably 5 chromosomes) and annotated with ~10,000 genes. However we think at least ~1-2k of the annotated genes in strain RS are likely reptitive sequences and not real genes based on comparisons with the TIGR annotations of C. posadasii C735 strain and de novo repeat finding and analysis – John talked about this in his talk at Asilomar.

Thse available strain sequences are going to allow for some interesting analyses that have yet to be applied in fungi. This includes doing some whole genome scans for selection using more sensitive population genetic tests than the gross-level non-synonymous /synonymous ratio tests that we’ve been relegated to with the current comparisons and it is starting to feel a bit like when “all you have is a hammer…”. Now all we have to do is get the whole genome multi-strain alignment quirks worked out and probably have to do our own quick annotation since only the two reference strains are annotated.

Cocci arthrocondia