ensembl plants hsf_d_bolser_2012

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…