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
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
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…
Hinweis der Redaktion
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.