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

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 Fire Assembly point (under EBI oak tree) Fire Assembly point (under EBI oak tree) You are here Toilets

4. 4 of 30 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 Meeting Outline

5. 5 of 30 Gene buildBronwen Aken & Jan-Hinnerk Vogel Ensembl Core Ian Longden Ensembl Compara Javier Herrero Ensembl funcgenNathan Johnson Hands on

6. 6 of 30 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. 7 of 30 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. 8 of 30 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. 9 of 30 Ensembl v50

10. 10 of 30 The family is growing!

11. 11 of 30 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. 12 of 30 Integration

13. 13 of 30 Release process

14. 14 of 30 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 athttp://www.ensembl.org Open distribution of the analysis the community Development of open, collaborative software (databases and APIs)

15. 15 of 30 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. 16 of 30 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. 17 of 30 Ensembl’s roadmap

18. 18 of 30 It ain’t a simple thing

19. 19 of 30 Putting the blocks together 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

20. 20 of 30 Ensembl – release cycle

21. 21 of 30 Hardware upgrade –Performance improvement New look & feel –Design changes –Control panel across all pages Hidden goodies: Store your own datahttp://beta.ensembl.org Ensembl from inside

22. 22 of 30

23. 23 of 30

24. 24 of 30 Bronwen & Jan Running the Ensembl gene build pipeline

25. 25 of 30 Javier Multiple Alignments with Pecan Constrained elements Conservation scores

26. 26 of 30 Nathan Functional Genomics Annotation pipeline

27. 27 of 30 Ian Mapping xrefs

28. 28 of 30 Anne Web update

29. 29 of 30 Perl Applications Compara Pipeline ensj Java* martj Java martp Perl Ensembl Pipeline Ensembl Web Site Apollo Java Applications Variation Compara BioMart UserAPI Layer Database Core BioDas Perl ProServer Dazzle LDAS Variation Functgen FunctGen API Network BioConductor biomaRt

30. 30 of 30 Wrap up Paul will outline some developments in the pipeline for the new year (Tuesday) And some of you will share your Ensembl experience with us…

31. 31 of 30 Ensembl Team July 2006

32. 32 of 30 Ensembl Team September 2008 EnsemblPaul Flicek (EBI), Steve Searle (Sanger Institute) Vertebrate GenomicsMario Caccamo, Laura Clark, Jonathan Hinton, Zam Iqbal, Vasudev Kumanduri, Ilkka Lappalainen Software Glenn Proctor, Syed Haider, Andrew Jenkinson, Andreas Kähäri, Stephen Keenan, Rhoda Kinsella, Eugene Kulesha, Ian Longden, Daniel Rios Comparative GenomicsJavier Herrero, Kathryn Beal, Benoît Ballester, Stephen Fitzgerald, Leo Gordon, Albert Vilella Functional GenomicsNathan Johnson, Stefan Gräf, Steven Wilder VariationFiona Cunningham, Yuan Chen Analysis and AnnotationBronwen Aken, Julio Banet, Susan Fairley, Jan-Hinnerck Vogel, Simon White, Amonida Zadissa Web TeamJames Smith, Eugene Bragin, Anne Parker, Bethan Pritchard, Steve Trevanion (VEGA) ZebrafishKerstin Howe, Britt Reimholz, James Torrance VectorBaseDan Lawson, Martin Hammond, Karyn Megy OutreachXosé M Fernández, Bert Overduin, Michael Schuster (QC), Giulietta Spudich Systems & SupportGuy Coates, Tim Cutts, Shelley Goddard ResearchIan Dunham, Damian Keefe, Alison Meynert, Dace Ruklisa, Guy Slater, Daniel Zerbino Ensembl StrategyEwan Birney, Richard Durbin, Tim Hubbard