Inauguration of the Pufendorf Astrobiology theme at Lund University

I participated in the inauguration of the Astrobiology theme at the Pufendorf institute, Lund University. It was truly fascinating listening to the talks on the theme “Emergence of Life”. After an introduction by Sture Forsén and David Dunér, the nobel laureate Sidney Altman presented his talk “Entering the RNA World”. John Sutherland, recently moved to MRC, LMB, Cambridge, presented an equally intriguing talk entitled “RNA: Prebiotic Product, or Biotic Invention?”. The morning session was ended by Michael Russell giving a vivid answer to the very relevant questions “Why Does Life Start, What Does It Do, Where Will It Be, And How Might We Find It?”

In the afternoon Adriana Ocampo, Planetary Science Division, NASA gave a wonderful talk on “The Role of Meteorite Impacts for Early Life on Earth: An Analogue
with Mars” and described the plans for sending a new rover to Mars.

The inauguration ended with a grand finale of Bruce Fouke,University of Illinois Urbana-
Champaign, spanning from nanometers to kilometers with his talk “Yellowstone Hot-Springs: A New Look at the Search for Ancient
Microbial Life on Mars”

 

Workshop on Comparative Genomics 2011

I am very proud to announce that the Geneco Research school (Geneco stands for Genomic Ecology) is coorganizing a top level workshop on Comparative Genomics. Check out the workshop web page http://www.molecularevolution.org/workshops/WCG.

Workshop on Comparative Genomics, Europe 2011

Cesky Krumlov, Czech Republic

9 – 21 January 2011

Application Deadline: 15 October is the preferred application deadline, after which time people will be admitted to the course following review of applications by the admissions committee. However, later applications will certainly be accepted.

http://www.molecularevolution.org/workshops/WCG

Scott A. Handley, Michael Cummings and Dag Ahrén (GENECO), Co-Directors
Naiara Rodriquez-Ezpeleta, Associate Directors

The Workshop on Comparative Genomics consists of a series of lectures, demonstrations and computer laboratories that cover various aspects of comparative genomics focusing on next-generation sequencing data. Faculty are chosen exclusively for their effectiveness in teaching theory and practice in comparative genomics. Included among the faculty are developers and other experts in the use of computer programs and packages such as AUGUSTUS, Ensembl, GMOD/GBrowse, MEGAN, MIRA, and Scripture who provide demonstrations and consultations. The course is designed for established investigators, postdoctoral scholars, and advanced graduate students. Scientists with strong interests in the uses of short-read sequence data, analytical methods, comparative structure of genomes, SNP detection and analysis, genome visualization tools and related areas are encouraged to apply for admission. Lectures and computer laboratories total ~90 hours of scheduled instruction. Admission is limited and highly competitive, with admissions decisions determined by an international committee. No programming experience is required.

Topics to be covered include:

– Sequencing technologies: short-read sequencing technologies of various types
– Assembly and alignment: basic analyses in de novo and re-sequencing studies
– Gene finding and annotation: functional description of genomic data
– Genome characterization: gene content; genome structure; synteny; SNPs
– Assigning sequences to taxonomic groups in metagenomic studies
– Evolutionary genomics
– Population genomics

2010 Fee: 1800 USD. Fee includes opening reception and mid-course dinner, but does not include other meals or housing. Special discounted pricing has been arranged for hotels, pensions and hostels.

Offered in partnership with the Graduate Research School in Genomic Ecology (GENECO) http://www.geneco.se/
For more information and online application see the Workshop web site -
http://www.molecularevolution.org/workshops/WCG

The Workshop on Molecular Evolution is also being offered immediately after the Workshop on Comparative Genomics.
http://www.molecularevolution.org/workshops/WME

Going to Joint Genome Institute today

Today I will go to JGI with my friend Victor Kunin. I will try to learn more on how JGI is handling the sample preparation for pyrosequencing. For most people (including me), the process seems straightforward, but in reality the throughput of the 454 sequencing machine is largely dependent on the technical staff feeding the sequencer. This has become very clear after a visit to the sequencing facility in Copenhagen.

IMG-ACT

The IMG-ACT of JGI is now on Twitter! Join to learn more about annotation of microbial genomes

http://twitter.com/IMG_ACT

Geneco Winter meeting 2010

The Geneco Wintermeeting 2010 started yesterday with several very good presentations mainly by the geneco PhD students. Unfortunately both invited speakers were forced to cancel their trip to Lund but we hope to invite them to one of the coming meetings. In the afternoon we also had a very interesting and fun workshop arranged by LUInnovation on making an elevator pitch as well as coming up with a research idea that could be commersialized. I was not easy but I several witty ideas emerged.

Genome Encyclopedia of Bacteria and Archaea GEBA

The bioinformatics programme at Lund University that I am heading has been selected as one of the collaborators of the GEBA project together with Joint Genome Institute (JGI) at Department of Energy (DOE). The aim of the project is to use a phylogenetic tree to guide the genome sequencing of microbial genomes.

New York Times have written about this.

Got our first 454 genome sequences today!

Finally got the pyrosequencing data from KTH. Now it is time to start evaluating the data, estimating genome size and coverage. The sequences look good!