The deadline for application to the Medical Mycology course held in the summer at Woods Hole is April 1st. This is a great hands-on course for practical laboratory techniques with medically relevant fungi. I am including an email from the course directors below.
Registration opens today for the 25th Fungal Genetics conference at Asilomar. The preliminary program is also available with a great slate of speakers already lined up and plenty of opportunity for many students and postdocs to present their work.
The 24th conference help in 2007 was great and expect a similar great opportunity for sharing science and networking with the fungal genetics community.
If you are interested in fungal genetics and genomics, comparative biology, and of course dancing with fungal geneticists, plan to attend the 25th Fungal Genetics Meeting held at the beautiful Asilomar Conference Grounds in Pacific Grove, California. Below is info sent out from the Policy Committee and registration opens in a little over a month. Budding (and conidiating) artists can also submit a Logo design so we have cool T-shirts to wear.
25th Fungal Genetics Conference Registration and Program
The Fungal Genetics Policy Committee invites you to attend the 25th Fungal Genetics Conference, sponsored by the Genetics Society of America. The meeting will be held March 17-22, 2009 at the Asilomar Conference Center, Pacific Grove, California (near Monterey, California).
The FGSC is pleased to announce that the scientific program and registration information are available online at the FGSC website
Registration for the meeting will take place online at the FGSC and GSA websites from October 27th-December 12th.
Financial aid applications are due November 14th.
Abstract submission deadlines are the same as the registration deadlines, from October 27th to December 12.
LOGOS – Please Submit your artwork
We are also pleased to invite the submission of logos for the meeting. Past logos are available for review
The winner will receive a complimentary t-shirt.
Please send logos to the FGSC by October 17, 2008.
Just finished attending Genetics and Cell Biology of Basidiomycetes in Cape Girardeau, MO which was an intimate gathering of basidiomycetaphiles. I learned about systems that are used for studying fruiting body development, genetic mapping, pheromone and mating genes, kinesin dynamics, meoitic gene regulation, and a host of topics. I’m happy I got a chance to meet more folks in the community and learned about where informatics and computational approaches are really needed to push along some of the interpretation of the more than a dozen basidiomycete genomes. In particular it sounds like the Pleurotus, Schizophyllum, Agaricus bisporus, and Serpula genomes are all marching along to completion with some already in 4X assembly or further.
So we’ll further have more samples from of key model and some less-model species to assist researchers working on many different mushroom-forming fungi that range from brown and white-rotting saprophyte fungi to mycorrhizal fungi that associate with plants. I’m excited about the work to make transformation and knockouts more readily in these systems too to push the genetics and cellular biology of these systems even further. The genome sequences will be another tool in these endeavors.
The last day ended with a discussion about genome annotation and future support for curating gene models. Basically everyone is unhappy with computational predictions and want to be able to go in and fix things. (I think people remember the ones that are gotten wrong more readily than the ones that were right, but computational prediction definitely performs poorly in some situations). In this Web 2.0-land we live in, this is still not something easily done with any of the freely available genome browsing tools. The JGI’s browser was lauded for its ability to handle these kinds of requests, but how do we proceed when genomes are not sequenced by that center or when (not too distant future) communities are able to sequence a genome themselves using 454/Illumina-Solexa/Helicos/Pacific Biosystems approaches in their own lab? There is still a huge lag in what kinds of tools researchers can use to annotate genomes to fix gene models and add functions. Hopefully projects like GMOD will continue to develop useful tools for solving these needs, but there is certainly a need for better support of distributed community annotation of genomes where this little direct money for supporting curators from a single place.
I got this announcement this in the mail
taking place at
A few of the summer meetings that relate to fungal biology and evolution.
- Genetics and Cell Biology of Basidiomycetes, May 28-June 1, Southeast Missouri State University, Cape Girardeau, MO. Registration deadline April 25.
- North American Pombe Meeting, June 6-8, Los Angeles, CA. Registration deadline May 14.
- Cellular & Molecular Fungal Biology Gordon Conference, June 29-July 4, The Holderness School, Holderness, NH. Registration deadline June 8 (if it doesn’t fill up sooner).
- Yeast Genetics and Molecular Biology Meeting, July 22-27, Toronto, Canada. Abstract deadline April 7, registration deadline June 20.
- Ecological Society of America, Aug 3-8, Milwaukee, WI.
- Mycological Society of America‘s 2008 meeting Aug 9-13, The Pennsylvania State University, State College, PA. Abstract deadline April 30.
- More meetings linked from the SGD Community page.
Hope to see you at some of these.
I’m not at AGBT, but Jonathan and Anthony both have coverage of Pacific Biosciences’s new sequencing technology that uses detection of DNA polymerase activity to determine sequence. I believe some of the details are in the paper “Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures“, but I’ve not had a chance to read it.
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.
I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.
If there was any theme in the conference it was “Hey we are all using these genome sequences we’ve been talking about getting”. I only found the overview talks that solely describe the genome solely a little dry as compared to those more focused on particular questions. I guess my genome palate is becoming refined.