Transcript 5dec05.tjv

The Modern Synthesis
Systematics
Paleontology
Population genetics
Botany and Zoology
Modern
Post-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
• Facilitate collaboration among
disciplines and institutions
• Support scholars pursuing
synthetic research
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 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 Sturkey, Logistics Manager
– Barbara Mitchell, Business Manager
– Marcia Painter, Administrative Assistant
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 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
– 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
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
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
•– 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 Mabee (U. South Dakota)
& Monte Westerfield (U. of Oregon)
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 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
• 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
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 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): [email protected]
– Hilmar Lapp (Asst. Director): [email protected]
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
• Training
– Summer course in evolutionary 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
Published data today
Where we’d like to be tomorrow
Digital Repository for
Information and Data in
Evolution (DRIADE)
Proposed role for DRIADE
Specialized data
repositories
(eg Genbank, Morphbank,
PaleoDB Treebase)
Societies
Editors
Publishers
Journals
Reviewers
Digital Data
Repository
Researchers
Data registries and
repositories
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
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
• 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)
A reality-based approach
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
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