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Rafael C Jimenez DAS DAS Workshop 2012 February 27-29, 2012 Using DAS software, an introduction to some DAS implementations.

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Presentation on theme: "Rafael C Jimenez DAS DAS Workshop 2012 February 27-29, 2012 Using DAS software, an introduction to some DAS implementations."— Presentation transcript:

1 Rafael C Jimenez DAS DAS Workshop 2012 February 27-29, 2012 Using DAS software, an introduction to some DAS implementations

2 Split data and presentation Databases serving data as primitive datatypes defined by open standards Different front ends or components of front ends compete for users Data Representation

3 Tools for data handling Frameworks – MyDAS (Java) – Dazzle (Java) – Proserver (Perl) – LDAS (Perl) Application – EasyDAS (Proserver) Data Representation Libraries – JDAS (Java) – Dasobert (Java) – Bio::Das::Lite (Perl) – jsDAS (Javascript)

4 Applications Sources – Genome (gene, pseudogene, transcript, phenotype, SNP, CNV, probeset, QTL, …) UCSC ENSEMBL ArrayExpress … – Protein (domain, PTM, literature, expression, variants, … ) UniProt Pfam CBS … Data Representation Clients – Dalliance – IGV – Ensembl – Gbrowse – IGB – SPICE – Dasty – Jalview – PeppeR – DASher – EpiC – STRAP – EBI search

5 Ways to share in DAS Lots of annots with IT support Many annots without IT support Few annots easyDAS myDAS, proserver DAS WriteBack client

6 Clients

7 7 Protein sequence data Dasty

8 pFam Protein sequence data

9 DASher Protein sequence data

10 Spice Protein sequence data

11 Jalview Protein sequence data

12 STRAP Protein sequence data

13 Genome sequence data Ensembl

14 Genome sequence data Dalliance

15 Genome sequence data myKaryoview

16 Genome sequence data WormBase

17 Protein structure data Spice-Sisyphus

18 Sequence alignment data Pfam

19 Summaries Pfam

20 3D-EM Pepper

21 EMAP data EMAP: The Edinburgh Mouse Atlas Project Gene expression databases (EMAGE & GXD) DAS reference server EMAP - Ontology DAS annotation servers EMAGE GXD

22 Protein-protein interaction data iPfam

23 PSICQUIC Query Interactions PSICQUIC Registry PSI-MI MIQL Input Output PSICQUIC Service A PSICQUIC Service B PSICQUIC Service C User View Web Service System Data Provenance PSICQUIC for molecular interactions

24 Thanks! Questions? Acknowledgements


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