ensembl plants hsf_d_bolser_2012
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Ensembl Plantspart of Ensembl Genomes
Dan Bolser, Ensembl Plants project leader,HSF 2012/01/26
What is Ensembl Plants?In the beginning, there was Ensembl…
What is Ensembl?
Ensembl
Suite of tools for vertebrate genomic information Genome browser Database(s) Perl API
What is Ensembl?
Ensembl
Suite of tools for vertebrate genomic information
Genome analysis Mature code base Allows stable pipelines to
be developed Community support
What is Ensembl?
Ensembl
Suite of tools for vertebrate genomic information
Genome analysis Reference data
Assembly Gene build Variation, regulation,
homology
What is Ensembl?
Ensembl
Suite of tools for vertebrate genomic information
Genome analysis Reference data
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
Ensembl Genomes
Extending Ensembl across the taxonomic space
Ensembl Genomes
Bacteria Fungi Metazoa Plants Protists
Pan-Compara
Food, feed, fuel, pharma, and future technologies
Crop improvement
Why plants?
Gramene
Ensembl Plants
Current projects (grants) Barley Wheat transPLANT
Future plans How to coordinate
explosive growth?
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
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
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
Future…
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?
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…
