Ensembl Plants: A Guide to Plant Genomic Resources
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Ensembl Plants: A Guide to Plant Genomic Resources
- 1. Ensembl Plants part of Ensembl Genomes Dan Bolser, Ensembl Plants project leader, HSF 2012/01/26
- 2. What is Ensembl Plants? In the beginning, there was Ensembl…
- 3. What is Ensembl? Ensembl Suite of tools for vertebrate genomic information Genome browser Database(s) Perl API
- 4. What is Ensembl? Ensembl Suite of tools for vertebrate genomic information Genome analysis Mature code base Allows stable pipelines to be developed Community support
- 5. What is Ensembl? Ensembl Suite of tools for vertebrate genomic information Genome analysis Reference data Assembly Gene build Variation, regulation, homology
- 6. What is Ensembl? Ensembl Suite of tools for vertebrate genomic information Genome analysis Reference data
- 7. Ensembl Genomes Ensembl Ensembl Genomes Suite of tools for vertebrate Applies Ensembl technology to genomic information additional species Genome analysis Adopts existing standards Reference data Requires additional time and effort
- 9. Bacteria Ensembl Fungi Genomes Metazoa Extending Ensembl across the Plants taxonomic space Protists Pan-Compara
- 10. Why plants? Food, feed, fuel, pharma, and future technologies Crop improvement
- 12. Gramene
- 13. Ensembl Plants Current projects (grants) Barley Wheat transPLANT Future plans How to coordinate explosive growth?
- 14. Current projects Wheat Part of the genome sequencing consortium. Money for sequencing / Assembly? / A ‘gene-space’ site. One position (starting soon) Barley Part of the genome sequencing consortium. Develop resources for the community (EnsBarley). One position (starting soon)
- 15. Current projects transPLANT A trans-national computer infrastructure for PLANT genomic science Two positions Me + one developer position (currently hiring) Motivation Massive growth in data acquisition Many opportunities for crop improvement Key parts of plant infrastructure are missing
- 16. transPLANT Work Packages 7. Reference repository for genomes 8. Architecture for plant genomic complexity 9. Archive for plant variation 10. Linking genotype to phenotype 11. Information retrieval systems 12. Algorithm extension and development
- 17. Future…
- 18. How to coordinate explosive growth? Community annotation Wiki-style solutions? Genomes as a service SourceForge for genes Tools for communities and genomes? rather than a central Check out archive Modify Check in your new assembly?
- 19. Acknowledgements Paul Kersey Andy Yates Dan Staines Jay Humphry Uma Maheswari Arnaud Kerhornou All the people I’ve been Michael Nuhn nagging with endless emails…
Notas do Editor
- Brief overview of EGPlants, can’t cover much in 15 mins. Audience?
- Address the question… Background… (no screen shots).
- Launched 1999, initially developed for the human genome project.
- Interpreted informatiom
- A project based on Ensembl.
- Add some quotes…
- Future technologies such as fuel and plastics.
- NCBI. Rosids vs. Asterids. Variation data for A. thaliana, O. indica, O. sativa, and V. vinifera (grape).
- Work with the communities also to develop Ensembl Genomes.
- Crop genomes now possible.
- Standards!