Скачать презентацию The Modern Synthesis Systematics Paleontology Population genetics Botany Скачать презентацию The Modern Synthesis Systematics Paleontology Population genetics Botany

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

Modern Post-modern Modern Post-modern

 • Address grand challenge questions in evolutionary biology • Focus on areas ripe • 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

Sponsored science at NESCent • Visiting postdoctoral and sabbatical scholars • Catalysis meetings (~30 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)

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

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

Informatics @ NESCent Mission – Support for sponsored science – “Cyberinfrastructure” to enable evolutionary 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

Thinking about a proposal? Here’s what to expect • We can – Provide infrastructure 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

Major initiatives • Where do they come from? – Working groups and center visitors 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!

Evolutionary model organisms Evolutionary model organisms

Evolutionary model system databases Interface of genomics and evolutionary biology – Genome models are 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

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

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

Phenotypic reasoning • What zebrafish mutants differ from the wild type the same way 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?

What is an ontology? • A way for a community to agree upon the 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

Elements of an ontology • Types: Collections of objects that share common attributes • 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

Gene Ontology from yeastgenome. org Gene Ontology from yeastgenome. org

Representing phenotypes • Entity-Qua[l|nt]ity (EQ) syntax – Entities come from an organism-specific anatomy ontology 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)

Use of PATO from arabidopsis. info Use of PATO from arabidopsis. info

Use your center • Upcoming calls for proposals – Postdoc/sabbaticals - December – Working 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

Globally Unique Identifiers (GUIDs) • With – Taxonomic Data Working Group (TDWG) – Global 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)

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

Outline • The importance of informatics to evolutionary synthesis • What kinds of informatics 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

DRIADE Stakeholders Wkshp 5 Dec 2006 DRIADE Stakeholders Wkshp 5 Dec 2006

Published data today Published data today

Where we’d like to be tomorrow Where we’d like to be tomorrow

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

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

Data registries and repositories Data registries and repositories

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

Many other decisions to be made • Technical – What software solutions to adopt? 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?

Other disciplinary data repositories and data integration projects • ca. Bio (Cancer Biology) • Other disciplinary data repositories and data integration projects • ca. Bio (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)

A reality-based approach A reality-based approach

DRIADE: Near-term plans • Requirements gathering and evaluation phase – Technical consultations • Workshop 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?

Schedule 9: 00 -10: 00 - Background Hilmar Lapp - Objectives and requirements gathering Schedule 9: 00 -10: 00 - Background Hilmar Lapp - Objectives and requirements gathering Jane Greenberg & Co. - Issues regarding metadata Ahrash Bissell - Open. Context 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