1. EBI is an Outstation of the European Molecular Biology Laboratory. Bert Overduin Daniel Rios Stephen Fitzgerald Edinburgh, 24 & 25 February 2009 Ensembl Developers Workshop

2. Workshop schedule Tue 24 February 2009 IntroductionBert Overduin Core APIBert Overduin Variation APIDaniel Rios Wed 25 February 2009 Variation APIDaniel Rios Compara APIStephen Fitzgerald

3. Ensembl - Goal Provide automatic annotation of genomes Integrate this annotation with other biological data Make all these data available to all

4. Ensembl - Organisation Joint project between the European Bioinformatics Institute (EMBL-EBI) and the Wellcome Trust Sanger Institute (WTSI) Started in 1999 for the Human Genome Project Funded primarily by the Wellcome Trust, with additional funding by EMBL, the EU, NHGRI, NIH-NIAID, MRC and BBSRC Team of ca. 50 people, led by Ewan Birney (EBI) and Tim Hubbard (Sanger)

5. Wellcome Trust Genome Campus Hinxton, Cambridge © John Freebrey (www.thedigitaldarkcloth.com)

6. Ensembl - Species 45 chordates, ranging from human to ‘primitive’ chordates 3 key eukaryote model organisms: fruitfly (Drosophila melanogaster) nematode (Caenorhabditis elegans) yeast (Saccharomyces cerevisiae) 2 insect pathogen vectors: malaria mosquito (Anopheles gambiae) yellow fever / dengue mosquito (Aedes aegypti)

7. Ensembl - Data Genomic sequence Gene/transcript/protein models External references Mapped cDNAs, proteins, micro array probes, BAC clones, cytogenetic bands, markers, repeats etc. Comparative data: orthologs and paralogs, protein families, whole genome alignments, syntenic regions Variation data: SNPs Regulatory data: “best guess” set of regulatory elements

8. Ensembl - Databases MySQL Species-specific databases: core: genomic sequences and most annotation variation:genetic variation funcgen:regulatory elements Cross-species database: compara:all comparative data

10. Ensembl - Access to data Release web site http://www.ensembl.orghttp://www.ensembl.org Pre-Release http://pre.ensembl.orghttp://pre.ensembl.org Archive http://archive.ensembl.orghttp://archive.ensembl.org BioMart http://www.ensembl.org/biomart/martviewhttp://www.ensembl.org/biomart/martview http://www.biomart.org/biomart/martview FTP site ftp://ftp.ensembl.orgftp://ftp.ensembl.org Amazon Web Services http://aws.amazon.com/publicdatasetshttp://aws.amazon.com/publicdatasets MySQL interface ensembldb.ensembl.org Perl API http://www.ensembl.org/info/data/api.htmlhttp://www.ensembl.org/info/data/api.html

11. Application Programming Interface “An Application Programming Interface (API) is a set of definitions of the ways in which one piece of computer software communicates with another. It is a method of achieving abstraction, usually (but not necessarily) between lower-level and higher-level software. One of the primary purposes of an API is to provide a set of commonly-used functions (…). Programmers can then take advantage of the API by making use of its functionality, saving them the task of programming everything from scratch.”