Category: Workshops

There is currently an interesting competition going on organised by UCSC called the Assemblathon. The idea is that participating research groups will try to assemble simulated short-reads to a simulated genome, with the winner being the group doing it “best” (by some criteria set up by the evaluation team at the UC Davis Genome Center). The complete set of rules can be found here. The whole thing will culminate in a Genome Assembly Workshop at UC Santa Cruz in mid-March.

I think the competition is an interesting initiative, hopefully inspiring new, more efficient, sequence assembly ideas. Those are desperately needed in these times of ever-incresing DNA sequence generation. In addition, there are numerous already existing genome assembly programs, but (as noted on the Assemblathon site) it is not obvious which one is the best in a given situation. Hopefully the competition can shed some light on that too. The deadline for participation is the sixth of February, and even though I am not myself competent enough to participate, I hope the ones who do are successful in their work.

The time is running out if you want to attend to the workshop session on mapping signal transduction, hosted by Stefan Hohmann and Marcus Krantz, which I will take part in. Deadline is on the 15 of May, so register soon if you have not already done. You can find all important info here.

The workshop will take place on June 29:th, between 13.00 and 15.30. The goal is to show some visualisation strategies for signal transduction pathways, and how to use pathway maps as a base to create mathematical models. There will be a brief introduction to mapping and modelling and to the software used (Cytoscape, CellDesigner). This will be followed by independent work with a set of small case studies that demonstrates the basic methodology. I will take part in answering questions and assisting during the case study part.