Microbiology, Metagenomics and Bioinformatics

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

Browsing Posts in Workshops

I am part of the organizing committee for the Swedish Bioinformatics Workshop (#SBW2014) that will be held October 23-24 this year in Gothenburg. I would like to invite you all, especially master/PhD students and PostDocs in Sweden, to come and share the event with us!

SBW is an annual event that has been organized by the different universities in Sweden. This year it will take place at the Wallenberg Conference Centre in Gothenburg and is arranged by both University of Gothenburg and Chalmers University of Technology. SBW2014 will, as the tradition abides, be a meeting point for PhD students and postdocs working with any kind of bioinformatics within Sweden and is therefore free of charge for these groups. We are proud to announce a program including both invited speakers – such as Mick Watson from the Roslin institute, Dawn Field from University of Oxford, and Joakim Lundeberg from KTH – along with participant presentations and poster sessions. This year, the program will also contain a number of workshop sessions where hands-on problems will be used as starting points for discussions on new bioinformatics approaches to these problems. This will provide opportunities for attendees with different methodological backgrounds to interact and work together to find synergies between fields and come up with creative solutions.

More information about the event including registration and abstract submission can be found at www.sbw2014.se.

I, and the rest of the organizers, look forward to meeting you in Gothenburg in October!

Webpage: http://www.sbw2014.se

Facebook: https://www.facebook.com/events/1450513325188910/

Google+: https://plus.google.com/events/cuhlpovcc275stut854dk5ussnk

If you want, you can spread the word, for example using this flyer!

Science for Life Laboratories (SciLifeLab) in Stockholm will host a metagenome data analysis workshop on May 21-23, in which I will participate as a tutorial assistant. Additionally, our group leader Joakim Larsson will be giving a lecture about how we use metagenomics to assess the environmental reservoir of antibiotic resistance genes (much of my recent work will likely go into that). I hope to meet you there, so don’t forget to register!

Confirmed speakers:
Lex Nederbragt, Oslo University, Norway
Saskia Smits, Erasmus University Rotterdam, Netherlands
Joakim Larsson, Göteborg University, Sweden
Paul Wilmes, University of Luxembourg, Luxembourg
Anders Andersson, SciLifeLab, Sweden
Noan Le Bescot, UPMC (Tara expedition), France

The workshop is part of the AllBio Bioinformatics initiative.

Those of you attending the Swedish Bioinformatics Workshop, this year given in Skövde, will have a chance seeing me talk about how sequencing depth influences the picture we get of the environmental resistance gene diversity. I think the topic is very urgent and interesting, and will likely come back to it in a more thorough blog post later. There are also a few other very interesting talks, for example about metagenomic gene quantification, and en masse sequencing of E. coli and H. pylori isolates. I think all attendants are in for a treat! See you there!

Those attending the Metagenomics lab (part of the basic NGS course for PhD students given at GU this week), can find the material for the lab on this page:
http://microbiology.se/ngs-metagenomics-lab/
Of course, the page is open for anyone else as well, although you won’t get the support that the GU students are given.

The newly formed bioinformatics network for PhD students in Gothenburg (GoBiG), will have an introductory meeting next week, on thursday the 26th at Chalmers. See this page for more info.

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.

I will present my master thesis “Metagenomic Analysis of Marine Periphyton Communities”, on Tuesday the 22nd of March, at 13.00. The presentation will take place in the room Folke Andreasson at Medicinaregatan 11 in Gothenburg. The presentation is open for everyone, but the number of seats are limited.

Assemblathon

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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.