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Population Biology at VectorBase

Population Biology at VectorBase. Seth Redmond, Bob MacCallum Imperial College, Christophides group Emmanuel Dialynas , Pantelis Topalis IMBB, Louis group. Genomic variation. VB is generally very genome- centred :. Individual genotypes.

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Population Biology at VectorBase

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  1. Population Biology at VectorBase Seth Redmond, Bob MacCallum Imperial College, Christophides group Emmanuel Dialynas, PantelisTopalis IMBB, Louis group

  2. Genomic variation VB is generally very genome-centred:

  3. Individual genotypes Neafsey, et al. Science, 2010. 330(6003): p. 51 Sample information is minimal at best

  4. Population Genomics @ VB UCLA / UC Davis ~9k samples: • species • mol/chr form • karyotype • Not extensible • Schema closely linked to data • Relatively little genomics data • ~6 SNPs, some microsattelite data

  5. Separation of genomic & phenotypic sets

  6. Integration forced by large-scale genotyping

  7. GMOD natdiv consortium:

  8. GMOD Natural Diversity module • Lightweight schema • All objects defined by ontologies • General • SO / GO / PATO • Spp. specific • IDOMAL / MIRO • Flexible • can handle all data from consortium • Vector spp. & butterflies • Rice & peaches

  9. VB Population Biology Browser (beta) http://funcgen.vectorbase.org/PopulationBETA/ • Still under active development • Currently > 15k samples from 1600 field collections UC-Davis data IR-base data Neafseyet al. SNP-chip data

  10. Sample

  11. Assay

  12. Project

  13. Visualisations

  14. server-side processing: DB serves data Server processes data& formats for browser Closed data layer server JSON NatDivDB

  15. client-side processing Server outputs basic data Open text format (json) Browser processes data Open data layer: json JSON NatDivDB

  16. Custom display: same data JSON NatDivDB

  17. Same display: custom data JSON JSON JSON PlasmoDB ? NatDivDB

  18. VB + plasmoDB http://funcgen.vectorbase.org/PopulationBETA/xquery/plasmodb/ VB + geonames http://funcgen.vectorbase.org/PopulationBETA/xquery/geoplaces/ VB + google http://funcgen.vectorbase.org/PopulationBETA/xquery/starbucks Examples:

  19. Submitting data: Bob MacCallum PantelisTopalis Emmanuel Dialynas • Data submission pipeline • Uses standard tools: • Phenote / ISA-tab (Sim to array express MAGE-tab) • documentation available at: http://funcgen.vectorbase.org/PopulationBETA/submission/

  20. Acknowledgements Imperial: Christophides / Kafatos lab George Christophides IMBB: PantelisTopalis Emmanuel Dialynas GMOD Natdiv consortium: NaamaMenda Sook Jung Dave Clements Scott Cain Maren Friesen Nescent

  21. Browser / display methods • Submitter can chose from a number of displays • Bar / dot graphs + maps (more to come…) http://funcgen.vectorbase.org/popgenDev/project/~id=34 http://funcgen.vectorbase.org/popgenDev/project/~id=37 http://funcgen.vectorbase.org/popgenDev/project/~id=141

  22. GMODEvo-Hackathon • Nescent, Nov 2010 • Gather together interested parties to write tools needed for gmod

  23. Forthcoming: • SNP chip: • geographic range analysis • MS hybridization/ecological zone analysis • ONNV / P.falciparum infections • insecticide resistance mapping • HT-Sequencing • Infravec • MalariaGEN– population sampling • TransMalariaBloc– P.falciparum field infections

  24. A problem of definition… • Field samplings • Which location? what method? • Species identification • What method? • Phenotyping assay • What were you assaying? how? In what context? • Genotyping • Which gene/feature is associated

  25. Genetic Variation in VectorBase

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