Tag Archives: training

Apply for EuPathDB workshop

Dear Colleague,

We are pleased to announce the 10th annual EuPathDB workshop to be held in Athens, Georgia, USA from May 31 – June 3rd, 2015.

Learn how to effectively use EuPathDB resources and mine available data to help guide your research.

For more information and to apply, please visit: http://workshop.eupathdb.org/current/

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Databases covered: EuPathDBAmoebaDB, CryptoDB, FungiDB, GiardiaDB, HostDB, MicrosporidiaDB, OrthoMCL, PiroplasmaDB, PlasmoDB, ToxoDB, TrichDB, TriTrypDB

Costs and Fees: The course is free. Housing, all training materials and lunches are covered. Attendees are expected to provide their own transportation to the course and pay for a few of their meals. Letters of acceptance will be mailed early to facilitate the solicitation of outside travel funds.

When: 6:30pm on Sunday, May 31 to 5:00pm on Wednesday, June 3, 2015

Where: University of Georgia, Athens, GA, USA
Davison Life Sciences Building, room C128.

Application deadline: February 1, 2015. Click here to apply. NOTE: Deadline extended apply before Feb 20!

If you have any questions or concerns please email help@eupathdb.org

Lichen genome projects and the power shift prompted by next-gen sequencing

Genome Technology highlights the very cool thing about next-gen sequencing – it puts the power in the hands of the researchers to explore genome sequence and doesn’t limit them to projects only funded through sequencing centers. The Genome Technology piece highlights work at Duke to sequence the genome Cladonia grayi, a lichenized fungus, with 454 technology at Duke’s Institute for Genome Sciences and Policy through their next-gen sequencing program. This is the way of the future where sequencing core facilities will be able to generate sequence only having to wait in the queue at the own university rather than through community sequencing project or sequencing center proposal queues.

This isn’t the only lichen being sequenced. Xanthoria parietina is also in the queue at JGI, but has taken a while to get going because of some logistical problems getting the DNA (and any problems are amplified because it takes a long time to get new material since lichens grow very slow).

The transfer of the power for researchers to be able to quick exploratory whole-genome sequencing with next-gen and eventually, high quality genome sequences from next-gen sequencing is predicted to transform how this kind of science gets done. It means we’ll probably just sequence a mutant strain instead of trying to map the mutation – this is happening already in anecdotal stories in worms and in our work in mushrooms. N.B. this is done after a mutagenized strain has been cleaned up a bit to insure we’re looking for one or only a few mutations based on some crosses – but that is part of standard genetic approaches anyways.

This fast,cheap,whole-genome-sequencing is also the stuff of personal genomics, but for basic research it will also mean that a first pass exploring gene repertoire of an organism will be a multi-week instead of multi-year project. I just hope we’re training enough people who can efficiently extract the information from all this data with solid bioinformatics, computational, data-oriented programming, and statistical skills to support all the labs that will want to take this approach. You’ll need a life-vest to swim in the big data pool for a while until more tools are developed that can be deployed by non-experts.