June 14, 2011–The Center for Bioinformatics and Computational Biology (CBCB) at the University of Delaware hosted the Third Skate Genome Annotation Workshop at Clayton Hall from May 23-26.

The four-day, hands-on bioinformatics workshop was sponsored by the North East Cyberinfrastructure Consortium (NECC), which is aimed at developing cyberinfrastructure across New Hampshire, Maine, Rhode Island, Vermont, and Delaware and using this broadband network for cyber-enabled research programs. In particular, this workshop is supported by the grant Delaware INBRE (grant number 3P20RR016472-09S2).

The workshop, which drew 28 participants and 8 instructors from 11 universities and colleges in the NECC states, was the final of three bioinformatics workshops planned to annotate the genome of the little skate, Leucoraja erinacea. The first one-week intensive workshop in May 2010 at University of Delaware covered all aspects of genome sequence analysis required to annotate eukaryotic genomes. The second workshop focused on annotating the emerging skate sequence data and was held in Oct 2010 at MDIBL. The skills learned through the three workshops apply broadly to many areas of research.

Participants learned valuable bioinformatics skills in this four day hands-on bioinformatics workshop together with a one-day scientific symposium on May 27. They learned how to use common bioinformatics applications and gained experience completing hands-on protein/gene annotation exercises.

“Learning the various applications for sequencing and getting to meet other people interested in bioinformatics” was considered the most useful about the workshop, said a participant. Another participant mentioned “learning the new tools and loved getting ‘big picture’ lectures from NCBI and Jason Moore to tie in with the project focus”.

Some highlights of the Annotation Workshop included two keynote presentations (Jason Moore, Dartmouth and Deanna Church, NCBI), reception (Tuesday evening), dinner banquet (Thursday evening), and poster presentation by all NECC participating teams (Thursday afternoon). Furthermore, the over fifty genes/proteins annotated in the workshop will be later submitted to GenBank and UniProt for public release.

As part of the workshop agenda, participants had the opportunity to visit DBI’s DNA Sequencing and Genotyping Center, where center director Bruce Kingham provided hands-on demonstrations of the high-throughput sequencing capabilities of the newly installed Illumina HiSeq 2000.

The workshop tutorials are available online at the CBCB website for students and researchers who are interested in learning more about genome annotation.

Article by Qinghua Wang