Ensembl Developers Meeting

1. Ensembl Developers Meeting Xosé Mª Fernández European Bioinformatics Institute September 2008

2. In case of fire • A continuous alarm will sound • On hearing the fire alarm evacuate the building immediately using the nearest fire exit • Report to fire assembly point under the EBI oak tree

3. Evacuation procedure You are here Fire Assembly point (under EBI oak tree) Toilets

4. Meeting Outline • Today • Introduction • Ensembl release cycle • Update: Genebuild, Compara, Functional genomics, Web • Ensembl Genomes • Tomorrow • Gene build • Core: mapping xref • Compara: Multiple genomic alignments with Pecan • Functional genomics: Annotation pipeline • Tuesday • Ensembl Genomes • Ensembl Outlook

5. Hands on • Gene build Bronwen Aken & Jan-Hinnerk Vogel • Ensembl CoreIan Longden • Ensembl Compara Javier Herrero • Ensembl funcgenNathan Johnson

6. Ensembl - Project • Joint project • EMBL – European Bioinformatics Institute (EBI) • Wellcome Trust Sanger Institute • Produce accurate, automatic genome annotation • Focused on selected eukaryotic genomes • Integrate external (distributed) biological data • Presentation of the analysis to all via the Web at http://www.ensembl.org • Open distribution of the analysis the community • Development of open, collaborative software (databases and APIs)

7. Ensembl - Project • Joint project • EMBL – European Bioinformatics Institute (EBI) • Wellcome Trust Sanger Institute • Produce accurate, automatic genome annotation • Focused on selected eukaryotic genomes • Integrate external (distributed) biological data • Presentation of the analysis to all via the Web at http://www.ensembl.org • Open distribution of the analysis the community • Development of open, collaborative software (databases and APIs)

8. Ensembl - Project • Joint project • EMBL – European Bioinformatics Institute (EBI) • Wellcome Trust Sanger Institute • Produce accurate, automatic genome annotation • Focused on selected eukaryotic genomes • Integrate external (distributed) biological data • Presentation of the analysis to all via the Web at http://www.ensembl.org • Open distribution of the analysis the community • Development of open, collaborative software (databases and APIs)

9. Ensemblv50

10. The family is growing!

11. Ensembl - Project • Joint project • EMBL – European Bioinformatics Institute (EBI) • Wellcome Trust Sanger Institute • Produce accurate, automatic genome annotation • Focused on selected eukaryotic genomes • Integrate external (distributed) biological data • Presentation of the analysis to all via the Web at http://www.ensembl.org • Open distribution of the analysis the community • Development of open, collaborative software (databases and APIs)

12. Integration

13. Release process

14. Ensembl - Project • Joint project • EMBL – European Bioinformatics Institute (EBI) • Wellcome Trust Sanger Institute • Produce accurate, automatic genome annotation • Focused on selected eukaryotic genomes • Integrate external (distributed) biological data • Presentation of the analysis to all via the Web at http://www.ensembl.org • Open distribution of the analysis the community • Development of open, collaborative software (databases and APIs)

15. Ensembl - Project • Joint project • EMBL – European Bioinformatics Institute (EBI) • Wellcome Trust Sanger Institute • Produce accurate, automatic genome annotation • Focused on selected eukaryotic genomes • Integrate external (distributed) biological data • Presentation of the analysis to all via the Web at http://www.ensembl.org • Open distribution of the analysis the community • Development of open, collaborative software (databases and APIs)

16. Ensembl - Project • Joint project • EMBL – European Bioinformatics Institute (EBI) • Wellcome Trust Sanger Institute • Produce accurate, automatic genome annotation • Focused on selected eukaryotic genomes • Integrate external (distributed) biological data • Presentation of the analysis to all via the Web at http://www.ensembl.org • Open distribution of the analysis the community • Development of open, collaborative software (databases and APIs)

17. Ensembl’s roadmap

18. It ain’t a simple thing

19. Gene build Release coordination Software Team Compara Team Variation Team Web team Gene build Release coordination Software Team Compara Team Variation Team Web team Gene build Release coordination Software Team Compara Team Variation Team Web team Gene build Release coordination Software Team Compara Team Variation Team Web team Gene build Release coordination Software Team Compara Team Variation Team Web team Gene build Release coordination Software Team Compara Team Variation Team Web team Putting the blocks together

20. Ensembl – release cycle

21. Hardware upgrade Performance improvement New look & feel Design changes Control panel across all pages Hidden goodies: Store your own data http://beta.ensembl.org Ensembl from inside

23. Bronwen & Jan Running the Ensembl gene build pipeline

24. Javier Multiple Alignments with Pecan Constrained elements Conservation scores

25. Nathan Functional Genomics Annotation pipeline

26. Ian Mapping xrefs

27. Anne Web update

28. API Network User API Layer Database Variation PerlApplications Variation Compara Core Compara Ensembl Web Site Functgen FunctGen Pipeline EnsemblPipeline Core martp Perl Apollo BioMart BioDas Perl JavaApplications ProServer Dazzle LDAS ensj Java* BioConductor martj Java biomaRt

29. Paul will outline some developments in the pipeline for the new year (Tuesday) And some of you will share your Ensembl experiencewith us… Wrap up

30. Ensembl Team July 2006

31. Ensembl Team September 2008