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The Modern Synthesis

The Modern Synthesis. Systematics. Paleontology. Population genetics. Botany and Zoology. Post-modern. Modern. Address grand challenge questions in evolutionary biology Focus on areas ripe for conceptual synthesis Allow the wealth of existing data to be fully utilized

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The Modern Synthesis

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  1. The Modern Synthesis Systematics Paleontology Population genetics Botany and Zoology

  2. Post-modern Modern

  3. Address grand challenge questions in evolutionary biology • Focus on areas ripe for conceptual synthesis • Allow the wealth of existing data to be fully utilized • Facilitate collaboration among disciplines and institutions • Support scholars pursuing synthetic research

  4. Sponsored science at NESCent • Visiting postdoctoral and sabbatical scholars • Catalysis meetings (~30 participants; highly interdisciplinary, to spawn collaborations) • Working groups (~15 participants, more focused topic, multiple meetings, specific outcomes)

  5. Education & Outreach • Staff • Kristin Jenkins • Jory Weintraub • Disseminate NESCent science • Promote evolution education at institutions serving under-represented groups • Organize annual symposium for National Association of Biology Teachers (with AIBS) • Support NESCent postdoc professional development • Consult on broader impacts

  6. Business & Logistics • Staff • Karen Henry, Assistant Director for Administration • Jeff Sturkey, Logistics Manager • Barbara Mitchell, Business Manager • Marcia Painter, Administrative Assistant

  7. Informatics @ NESCent Mission • Support for sponsored science • “Cyberinfrastructure” to enable evolutionary synthesis • Data sharing/exchange and database technology • Software development • Training, dissemination and user support Resources • IT and bioinformatics staff (currently hiring!) • Hardware for HPC, software development, web/db services • Logistical and technical support for collaborative development projects

  8. Thinking about a proposal?Here’s what to expect • We can • Provide infrastructure for collaborative projects • Prototype databases, software, etc. meant for public dissemination • Partner with you on external grants to go beyond the prototype stage • We can’t • Provide long-term maintenance for public resources (except through SDSC Data Central) • Adopt all possible technologies • Substitute for data experts or database curators

  9. Major initiatives • Where do they come from? • Working groups and center visitors • Whitepapers - come to us with your dreams! • Advisory groups • Leverage a vast array of existing resources • Open source software initiatives • Expertise and energy within the evolution community (and beyond) • This is your center - use us!

  10. Evolutionary model organisms

  11. Evolutionary model system databases Interface of genomics and evolutionary biology • Genome models are venturing into phylogenetics and population genetics • Evolutionary biologists are acquiring genomic information for their own model systems How many times must we invent the same genome database? • Expensive • Distracting • Not easy to do, but easy to do poorly

  12. Tailoring GMOD to evolutionary model systems • Extension of schema and visualization tools for genetic and phenotypic variation, geographic information and phylogenetics • Providing user support

  13. Brokering between natural phenotypic diversity and model organism genetics Working group led by Paula Mabee (U. South Dakota) & Monte Westerfield (U. of Oregon)

  14. Phenotypic reasoning • What zebrafish mutants differ from the wild type the same way that this apomorphy distinguishes this clade? • Are characters that are phylogenetically correlated also genetically correlated in zebrafish mutants?

  15. What is an ontology? • A way for a community to agree upon the meanings of terms and relations in order to reliably share knowledge about a specific domain • Automated processes that share this knowledge representation can perform simple reasoning

  16. Elements of an ontology • Types: Collections of objects that share common attributes • Attributes: properties that objects can have and share • Instances: Specific objects that manifest a type • Relations: ways that objects can be related to one another

  17. Gene Ontology from yeastgenome.org

  18. Representing phenotypes • Entity-Qua[l|nt]ity (EQ) syntax • Entities come from an organism-specific anatomy ontology (AO) • Several are being developed for genomic model organisms • Qualities come from the Phenotype Attributes and Trait Ontology (PATO)

  19. Use of PATO from arabidopsis.info

  20. Use your center • Upcoming calls for proposals • Postdoc/sabbaticals - December • Working groups/catalysis meetings - Dec & June • Submit a whitepaper (whenever) • Consider us for collaborative projects • Contact us: • Todd Vision (Assoc. Director): tjv@bio.unc.edu • Hilmar Lapp (Asst. Director): hlapp@duke.edu

  21. Globally Unique Identifiers (GUIDs) • With • Taxonomic Data Working Group (TDWG) • Global Biodiversity Information Facility (GBIF) • The aim: to have a persistent, unique, resolvable identifier for a biological resource that can be distinguished from its location on the web • Museum specimens • Taxonomic concepts • Publication (e.g. DOI) • Adopting Life Science Identifiers (LSIDs)

  22. Software initiatives • Sponsoring working groups and hackathons in phyloinformatics and population genetics • Training • Summer course in evolutionary informatics

  23. Outline • The importance of informatics to evolutionary synthesis • What kinds of informatics support NESCent set up to do (and not to do) • Leveraging open source software initiatives and training the future community of evolutionary informaticists • The role of databases and our efforts to tailor GMOD to evolutionary model organisms • Some semantic web technologies (e.g. ontologies) that every evolutionary biologist should care about • The cypriniformes phenotype comparison engine as an example that ties these themes together

  24. DRIADE Stakeholders Wkshp5 Dec 2006

  25. Published data today

  26. Where we’d like to be tomorrow

  27. Digital Repository for Information and Data in Evolution (DRIADE)

  28. Proposed role for DRIADE Specialized data repositories (eg Genbank, Morphbank, PaleoDB Treebase) Societies Journals Digital Data Repository Editors Publishers Reviewers Researchers

  29. Data registries and repositories

  30. Role of metadata • Two central questions • What metadata to keep? • How to get the metadata that’s needed? • Partnership with the <MRC> • Director: Jane Greenberg

  31. Many other decisions to be made • Technical • What software solutions to adopt? • Centralized or distributed physical storage? • How to interface with journals and specialized databases? • Social • Is deposition mandatory? • Are there additional incentives? • Intellectual Property • Are there any limits on data use? • Business • How to ensure long-term financial stewardship? • How much to invest in metadata curation?

  32. Other disciplinary data repositories and data integration projects • caBio (Cancer Biology) • Conservation Commons (Conservation Biology) • GEON (Geology) • ICPSR (Inter-university Consortium for Political and Social Research) • Marine Metadata Initiative • Virtual Observatory (Astronomy) • World Data Center System (Geography)

  33. A reality-based approach

  34. DRIADE: Near-term plans • Requirements gathering and evaluation phase • Technical consultations • Workshop for information science experts in March 2007 • To learn from the experiences of other disciplines • Stakeholder consultations • Major design meeting in May 2007 • Implementation • Phase I: Stopgap solution? • Phase 2: for which external funding will be required • Feasible milestones?

  35. Schedule 9:00-10:00 - Background Hilmar Lapp - Objectives and requirements gathering Jane Greenberg & Co. - Issues regarding metadata Ahrash Bissell - OpenContext 10:00 - Brainstorming session What use cases do we imagine? What are the requirements and priorities? How to continue gathering requirements? What experts and stakeholders to include? 12:00 Lunch

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