Ensembl plants hsf_d_bolser_2012


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  • 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!
  • Ensembl plants hsf_d_bolser_2012

    1. 1. Ensembl Plantspart of Ensembl GenomesDan Bolser, Ensembl Plants project leader, HSF 2012/01/26
    2. 2. What is Ensembl Plants?In the beginning, there wasEnsembl…
    3. 3. What is Ensembl? EnsemblSuite of tools for vertebrategenomic information Genome browser Database(s) Perl API
    4. 4. What is Ensembl? EnsemblSuite of tools for vertebrategenomic informationGenome analysis Mature code base Allows stable pipelines to be developed Community support
    5. 5. What is Ensembl? EnsemblSuite of tools for vertebrategenomic informationGenome analysisReference data Assembly Gene build Variation, regulation, homology
    6. 6. What is Ensembl? EnsemblSuite of tools for vertebrategenomic informationGenome analysisReference data
    7. 7. Ensembl Genomes Ensembl Ensembl GenomesSuite of tools for vertebrate Applies Ensembl technology togenomic information additional speciesGenome analysis Adopts existing standardsReference data Requires additional time and effort
    8. 8. Ensembl Genomes
    9. 9. BacteriaEnsembl FungiGenomes MetazoaExtending Ensembl across the Plantstaxonomic space Protists Pan-Compara
    10. 10. Why plants?Food, feed, fuel, pharma, andfuture technologiesCrop improvement
    11. 11. Gramene
    12. 12. Ensembl PlantsCurrent projects (grants) Barley Wheat transPLANTFuture plans How to coordinate explosive growth?
    13. 13. Current projectsWheat 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)
    14. 14. Current projectstransPLANT 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
    15. 15. 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
    16. 16. Future…
    17. 17. 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?
    18. 18. AcknowledgementsPaul Kersey Andy YatesDan Staines Jay HumphryUma MaheswariArnaud Kerhornou All the people I’ve beenMichael Nuhn nagging with endless emails…