Overview
Background and Objectives
In 2006, the North East IDeA states (VT, NH, ME, RI, DE) launched an initiative now called the North East Cyberinfrastructure Consortium (NECC). Two related collaborative efforts were initiated: to identify and promote the shared use of research facilities across the region, and assess and address cyberinfrastructure needs. This led to the development of the Little Skate Genome Sequencing & Annotation Project, which provides a model for highly collaborative approaches to use specialized resources and expertise in an integrated process.
Collaborative Use of Specialized Resources & Expertise
The project builds on the expertise and resources provided by the Bioinformatics Cores of the five northeastern states that form the NECC, which includes:
- Little Skate (Leucoraja erinacea) Clones: MDIBL – Mount Desert Island Biological Lab (ME)
- Next-Generation Sequencing: UD DNA Sequencing & Genotyping Center (DE)
- Sequence Assembly: Vermont Genetics Network (VT) with ME, RI
- Sequence Analysis/Annotation: pipeline at DE, ME, RI, NH and VT
- Storage & Access Of Sequence/Annotation Data: UD shared data center (DE)
- Public Dissemination: UD CBCB (DE), MDIBL (ME), skatebase.org (VT), NIH
Skate Genome Annotation Workshops
The Skate Genome Annotation Workshops and Jamborees are intended to offer training and opportunities for faculty and students to work with and annotate genome sequences. The workshops include lectures, tutorials and exercises annotating the genome of the little skate, Leucoraja erinacea.
Little Skate Mitochondrial Genome Jamborees
September 2011
Each state held a Mitochondrion Genome Annotation Jamboree bringing together past workshop participants to annotate the complete sequence of the little skate mitochondrial genome sequence. Annotation results from the five states will be combined and reviewed by the organizers. The final annotation and DNA sequence will be submitted to GenBank, and the annotation activities have been summarized and reported in a sumitted manuscript.
http://www.bioinformatics.udel.edu/SkateMitochondrion
Third Skate Genome Annotation Workshop
May 23-27, 2011
This is the final workshop and will be held at the University of Delaware. Topics will include genome annotation basics, overview of automated annotation, GenBank submission tutorial and hands-on annotation exercises.
http://skatebase.org/Workshop_content#ThirdSkateGenomeAnnotation
Second Skate Genome Annotation Workshop
October 12-15, 2010
With nearly two dozen participants, the primary goal of this Skate Genome Annotation Workshop was to train participants in how to annotate skate transcriptome sequences to facilitate annotation of skate genome sequences. This workshop was held at the Mount Desert Island Biological Laboratory.
http://skatebase.org/Workshop_content#SecondSkateGenomeAnnotation
First Skate Genome Annotation Workshop
May 24-28, 2010
The first workshop was held at the University of Delaware and drew 27 student participants and 11 faculty from seven different universities and colleges. Topics included Genome sequencing using Next-Gen, Genome Assembly and Analysis, introduction to sequence, gene and protein resources, sequence similarity searching, genome sequence analysis, gene finding, genome browsers, genome annotation platform and protein bioinformatics.
http://skatebase.org/Workshop_content#FirstSkateGenomeAnnotation
Workshops are sponsored by the IDeA Network for Biomedical Excellence (INBRE) Program from the National Center of Research Resources at the National Institutes of Health (grant number 3P20RR016472-09S2).
Related News
CBCB Hosts Third Skate Genome Annotation Workshop
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.
Cyberinfrastructure project featured as a success story by federal agency
Jan. 3, 2011 A multi-institutional project that includes the University of Delaware was highlighted in a recent publication by the National Center for Research Resources (NCRR) at the National….
University of Delaware Participates in Second Skate Genome Workshop
Oct. 20, 2010 The Skate Genome Project is sponsored by IDeA (Institutional Development Award) Network for Biomedical Research Excellence (INBRE) Program from National Center for Research Resources at NIH, which funded North East Cyberinfrastructure Consortium to enhance cyber-enabled research and workforce development in the North East states. The second workshop took place in Mount Desert Island Biological Laboratory Oct. 12-15. Faculty members from CBCB co-organized and participated as instructors.
University hosts hands-on skate genome bioinformatics workshop
June 1, 2010 The Center for Bioinformatics and Computational Biology (CBCB) at the University of Delaware hosted the first Skate Genome Annotation Workshop at Clayton Hall from May 24-28.
CBCB to host 1st Skate Genome Annotation Workshop in May
On May 24, 2010, CBCB will host Skate Genome Annotation Workshop at the University of Delaware. The workshop will last 5 days.
UD awarded funds for cyberinfrastructure development
November 23, 2009 The University of Delaware is part of a multi-state team that has been awarded a total of more than $14 million from the National Science Foundation (NSF) and the National…