Ensembl Developers MeetingEnsembl Developers Meeting

September 2008September 2008

XosXosé Mª Fernándezé Mª FernándezEuropean Bioinformatics InstituteEuropean Bioinformatics Institute

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

Evacuation procedure

Fire Assembly point(under EBI oak tree)

Fire Assembly point(under EBI oak tree)

You are hereYou are here

ToiletsToilets

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• 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 OutlineMeeting Outline

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• Gene build Bronwen Aken & Jan-Hinnerk Vogel

• Ensembl Core Ian Longden• Ensembl Compara Javier Herrero• Ensembl funcgen Nathan Johnson

Hands onHands on

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Ensembl - ProjectEnsembl - 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)

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Ensembl - ProjectEnsembl - 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)

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Ensembl - ProjectEnsembl - 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)

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EnsemblEnsembl v50v50

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The family is growing!The family is growing!

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Ensembl - ProjectEnsembl - 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)

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IntegrationIntegration

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Release processRelease process

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Ensembl - ProjectEnsembl - 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.orghttp://www.ensembl.org • Open distribution of the analysis the community• Development of open, collaborative software (databases and

APIs)

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Ensembl - ProjectEnsembl - 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)

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Ensembl - ProjectEnsembl - 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)

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Ensembl’s roadmapEnsembl’s roadmap

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It ain’t a simple thingIt ain’t a simple thing

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Putting the blocks togetherPutting the blocks together

Gene buildRelease coordinationSoftware TeamCompara TeamVariation TeamWeb team

Gene buildRelease coordinationSoftware TeamCompara TeamVariation TeamWeb team

Gene buildRelease coordinationSoftware TeamCompara TeamVariation TeamWeb team

Gene buildRelease coordinationSoftware TeamCompara TeamVariation TeamWeb team

Gene buildRelease coordinationSoftware TeamCompara TeamVariation TeamWeb team

Gene buildRelease coordinationSoftware TeamCompara TeamVariation TeamWeb team

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Ensembl – release cycleEnsembl – release cycle

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• Hardware upgrade– Performance improvement

• New look & feel– Design changes

– Control panel across all pages

• Hidden goodies: Store your own data

http://beta.ensembl.orghttp://beta.ensembl.org

Ensembl from insideEnsembl from inside

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Bronwen & JanBronwen & Jan• Running the Ensembl

gene build pipeline

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JavierJavier• Multiple Alignments with Pecan • Constrained elements• Conservation scores

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NathanNathan• Functional Genomics

Annotation pipeline

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IanIan• Mapping xrefs

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AnneAnne• Web update

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PerlApplications Compara

Pipeline

ensj Java*

martj Java

martp Perl

EnsemblPipeline

EnsemblWeb Site

Apollo

JavaApplications

Variation

Compara

BioMart

User API Layer Database

Core

Core

BioDas Perl

ProServerDazzleLDAS

Variation

FunctgenFunctGen

API NetworkAPI Network

BioConductor

biomaRt

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Wrap upWrap 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…

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Ensembl TeamEnsembl TeamJuly 2006July 2006

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Ensembl TeamEnsembl Team

September 2008September 2008

Ensembl Paul Flicek (EBI), Steve Searle (Sanger Institute)

Vertebrate Genomics Mario Caccamo, Laura Clark, Jonathan Hinton, Zam Iqbal, Vasudev Kumanduri, Ilkka Lappalainen

SoftwareGlenn Proctor, Syed Haider, Andrew Jenkinson, Andreas Kähäri, Stephen Keenan, Rhoda Kinsella, Eugene Kulesha, Ian Longden, Daniel Rios

Comparative Genomics Javier Herrero, Kathryn Beal, Benoît Ballester, Stephen Fitzgerald, Leo Gordon, Albert Vilella

Functional Genomics Nathan Johnson, Stefan Gräf, Steven Wilder

Variation Fiona Cunningham, Yuan Chen

Analysis and Annotation Bronwen Aken, Julio Banet, Susan Fairley, Jan-Hinnerck Vogel, Simon White, Amonida Zadissa

Web Team James Smith, Eugene Bragin, Anne Parker, Bethan Pritchard, Steve Trevanion (VEGA)

Zebrafish Kerstin Howe, Britt Reimholz, James Torrance

VectorBase Dan Lawson, Martin Hammond, Karyn Megy

Outreach Xosé M Fernández, Bert Overduin, Michael Schuster (QC), Giulietta Spudich

Systems & Support Guy Coates, Tim Cutts, Shelley Goddard

Research Ian Dunham, Damian Keefe, Alison Meynert, Dace Ruklisa, Guy Slater, Daniel Zerbino

Ensembl Strategy Ewan Birney, Richard Durbin, Tim Hubbard