1. TRPGR Gramene: A Platform for Comparative Plant Genomics Doreen Ware USDA ARS Cold Spring Harbor Laboratory Pankaj Jaiswal Oregon State University Joshua Stein Cold Spring Harbor Laboratory www.gramene.org Workshop website http://outreach.gramene.org

2. Agenda 7.30-7.40pm Gramene Database Workshop Introduction: Doreen Ware 7.40-8.00pm Exploring the Plant Genomes (browse, search, upload personal data, analysis tools): Josh Stein 8.00-8.15pm Phylogenetic analysis tools and targeted query tools using Biomart: Josh Stein 8.15-8.35pm Exploring the Plant's Genetic Diversity: Doreen Ware 8.35-8.50pm Comparative Pathways Networks and future directions: Pankaj Jaiswal 8.50-9.00pm Q/A Exhibit 9:00- 11:00pm Q/A

3. . Principle Investigators Doreen Ware (USDA ARS) Susan McCouch Edward Buckler (USDA ARS) Pankaj Jaiswal Biological Curation Genevieve DeClerck Palitha Dharmawardhana Vindhya Amarasinghe Sushma Naithani Charles Chen A. S. (Karthik) Karthikeyan Joshua Stein Bioinformatics Developers Terry Casstevens Justin Preece Marcela Monaco Will Spooner Jim Thomason Sharon Wei Ken Youens-Clark Aaron Chuah (past) Jon Zhang Cold Spring Harbor Cornell University Oregon State University Gramene is currently funded by NSF Grant 0703908: Plant Genome Research Resource USDA, DOE, NSF (Previous funding 2001-2007 ) Past PIs Lincoln Stein, Sam Cartinhour Gramene: A Platform for Comparative Plant Genomics

4. “What are the functionally shared elements of plant genomes and how does diversity in these elements relate to agronomic traits?”

5. Physical and/or Sequence map Map-2 Polymorphism Candidate gene Gene models Transcripts Peptides Function Expression Pathway Orthologs Map-1 Markers & phenotypes (Genes and QTL) Phenotype Genotype Forward Reverse Comparative and Translational Genomics

6. A network of information 6 Genotype Phenotype Genome Map Marker Assay Location Analysis Pathway Germplasm

7. What is Gramene? What do we do? Community portal Contribute to open standards (PO, TO, GO) Create and contribute to open software (Ensembl, CMap, CPAN, Tassel) Curators and stewards of genomes, diversity & pathway data Active research using comparative resources

8. Academic and Industry users throughout US, Europe and Asia Sep 2009 – Sep 2010

9. 9 www.gramene.org Collaborators Individual Researchers EBI/Ensembl Genomes MSU TAIR JGI MaizeGDB SCRI MIPS NASC SRI (Pathway Tools) OMAP/OGE GrainGenes Gene Ontology Plant Ontology Reactome BAR iPlant