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shandley 09-28-2011 12:34 PM

2012 Workshop on Genomics, Cesky Krumlov, Czech Republic
2012 Workshop on Genomics, Český Krumlov, Czech Republic

Core Workshop: 8 - 21 January 2012
Advanced Topics Session: 23 - 25 January 2012

Application Deadline: 15 November 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.

Registration 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.

For general Workshop information:

Direct Workshop Link:
Direct Advanced Topic Link:

Co-directors: Scott A. Handley, Naiara Rodríguez-Ezpeleta and Karin Rengefors

The Workshop on Genomics consists of a series of lectures, demonstrations and computer laboratories that cover various aspects of genomics focusing primarily on the analysis of next-generation sequencing data. Faculty are chosen exclusively for their effectiveness in teaching theory and practice. 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, using next-gen sequence data to study non-model organisms, 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
- Manipulation of sequence data using the command-line and quality assessment and control techniques
- Assembly and alignment: basic analyses in de novo and re-sequencing studies
- The use of next-generation sequence data to study non-model organisms
- RAD (Restriction site Associated DNA) sequence analysis
- Genome characterization: gene content; genome structure; SNPs
- Assigning sequences to taxonomic groups in metagenomic studies
- Transcriptome quantification and mapping for expression and gene structure elucidation
- The use of frameworks (Galaxy) for genome data comprehension and analysis
- Evolutionary genomics
- Population genomics
What’s new this year?
- New Website: Updated design, content and application forms can be found at Workshop schedules as well as other detailed information can be found at this site which is frequently updated.

- Advanced Topic Sessions: In addition to the core two-week Workshop curriculum we will be organizing 2-3 day Advanced Topic Sessions on Programming and on the use R/Bioconductor for genomic analysis.

- Scholarships: A limited number of scholarships will be provided to help off-set the costs of participating in the Workshop. More details about these opportunities will be made available very soon.

- Amazon Web Services Support: We have been awarded a grant to provide cloud computing support using Amazon Web Services. Every participant will be provided with access during their participation in the Workshop.
Offered in partnership with the Graduate Research School in Genomic Ecology (GENECO)

For more information and online application see the Workshop web site -

shandley 11-07-2011 02:16 PM

Updates and Travel Awards
I am writing to provide a remider about deadlines and provide a brief update regarding the 2012 Workshop on Genomics being held in Český Krumlov, Czech Republic being held from 8-21 January, 2012. Updated information can be found on the Workshop web site:

Additions to the schedule include:

Mike Zody, Broad Institution
Manfred Grabherr, Broad Institution
Julien Catchen, University of Oregon
Alice McHardy, Max Planck Institut Informatik

The application deadline is 15 November, 2011. If you or a colleague are considering applying please make sure to do so before the deadline. We will be reviewing applications as quickly as possible so that travel arrangements can be made. A direct link to the application site is:

We will be awarding up to five $1,000 travel awards. To be considered for a travel award you will have to be accepted to the Workshop on Genomics and submit a written essay describing how the advent of moden sequencing technologies has altered your research program. Selected essays will be published on the web site. More detail and a submission form can be found on our scholarship page at:

The application deadline for the Advanced Topic Sessions is also 15 November, 2011. In addition to 3-day sessions on BioPython and R/BioConductor, we are working with the GMOD group to bring a 3-day GMOD/gbrowse Advanced Topic Session. For those of you interested in genome annotation and visualization this should be an outstanding opportunity.

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