Microbiology, Metagenomics and Bioinformatics

Johan Bengtsson-Palme, University of Gothenburg | Wisconsin Institute for Discovery

Browsing Posts tagged Workshop

The 11th annual meeting of PhD students and Postdoc researchers in Bioinformatics in Sweden will take place in Lund the 29-30 September. The workshop is an opportunity for young researchers to meet, exchange ideas, and keep up to date with the growing body of knowledge. I will go there, and you should be there too! Besides, it’s free for PhD students and Postdocs! All info can be found at the workshop website. The last time I was there (2010) really fueled some interesting discussions, and I am really looking forward to the event this year. Hope to meet you there, fellow Swedish bioinformaticians!

For those of you who are not already fed up with my writings on biology stuff on the web site, two opportunities to hear me talk in real life has popped up in May. The first is already on May 2nd, on the Open Day in Life Sciences, arranged by the Science Faculty at the University of Gothenburg. I will talk about the search for detoxification systems in metagenomic sequence data (from a collections point of view, as that is the theme for the day). There will also be an opportunity be guided in the herbarium and the botanical garden, plus having lunch and an optional after-work drink at Botaniska Paviljongen. But hurry, last day of admission is tomorrow! Register here.

The second opportunity will be at the SocBiN-2011 bioinformatics conference in Helsinki, on the 12th of May. I will present in the session called “Bioinformatics of Metagenomics”, and talk about a software tool for rRNA classification. I really look forward to this Bioinformatics conference, there are a number of highly prominent and interesting speakers, and I have heard that Helsinki in May is very beautiful. Besides, I am going there with extremely nice people, adding up to potentially being the best biology venue I will attend this spring.


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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.