ensembl plants hsf_d_bolser_2012
DESCRIPTION
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Ensembl Plantspart of Ensembl Genomes
Dan Bolser, Ensembl Plants project leader,HSF 2012/01/26
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What is Ensembl Plants?In the beginning, there was Ensembl…
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What is Ensembl?
Ensembl
Suite of tools for vertebrate genomic information Genome browser Database(s) Perl API
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What is Ensembl?
Ensembl
Suite of tools for vertebrate genomic information
Genome analysis Mature code base Allows stable pipelines to
be developed Community support
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What is Ensembl?
Ensembl
Suite of tools for vertebrate genomic information
Genome analysis Reference data
Assembly Gene build Variation, regulation,
homology
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What is Ensembl?
Ensembl
Suite of tools for vertebrate genomic information
Genome analysis Reference data
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Ensembl Genomes
Ensembl
Suite of tools for vertebrate genomic information
Genome analysis Reference data
Ensembl Genomes
Applies Ensembl technology to additional species
Adopts existing standards Requires additional time
and effort
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Ensembl Genomes
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Extending Ensembl across the taxonomic space
Ensembl Genomes
Bacteria Fungi Metazoa Plants Protists
Pan-Compara
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Food, feed, fuel, pharma, and future technologies
Crop improvement
Why plants?
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Gramene
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Ensembl Plants
Current projects (grants) Barley Wheat transPLANT
Future plans How to coordinate
explosive growth?
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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)
Current projects
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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
Current projects
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transPLANT Work Packages
7. Reference repository for genomes
8. Architecture for plant genomic complexity
9. Archive for plant variation10.Linking genotype to
phenotype11.Information retrieval systems12.Algorithm extension and
development
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Future…
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How to coordinate explosive growth?
Community annotation
Genomes as a service Tools for communities
rather than a central archive
Wiki-style solutions? SourceForge for
genes and genomes? Check out Modify Check in your new
assembly?
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Acknowledgements
Paul Kersey Dan Staines Uma Maheswari Arnaud Kerhornou Michael Nuhn
Andy Yates Jay Humphry
All the people I’ve been nagging with endless emails…
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