nescent’s mission support and enable synthetic research in evolutionary biology develop &...
TRANSCRIPT
NESCent’s mission • Support and enable synthetic research in
evolutionary biology• Develop & disseminate new tools for
evolutionary informatics • Take the lead in promoting a culture of
data sharing• Increase the public understanding of
science• Broaden the demographics of evolutionary
biology
Overview of presentation
• Brief overview of NESCent – organization and current status (Kathleen)
• Synthetic science at NESCent (Joel) • Creating and supporting a culture of
sharing and collaboration (Todd)• Increasing the understanding of science
in the K-16, public and evolutionary biology communities (Brian)
• Goals for the Community summit (Kathleen)
NESCent History
year 1 year 2 year 3 year 4
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08
year 5
First scientists arrive
Revised NESCent plan
You are here
Institutional collaboration
Interaction among Directors
Participation by faculty and students
Institutional support
Administrative processes
NESCent’s branches function as a synergistic whole
Directors act as a team. Scientific, informatics and educational activities are inextricably intertwined and many of our efforts can’t be easily separated.
NESCent continually receives community input
Senior Advisory BoardMeets once a year. Provides general advice about Center operation. Additional consultation as necessary through email and phone conversations.
Scientific Advisory BoardMeets twice a year. Primary role is review of proposals. Also provides general advice regarding scientific activities.
Operations CommitteeDirectors plus at large members from each of the Triangle Universities and one postdoc. Meets ~ monthly to discuss Center activities.
The NESCent in-house community
• 12-15 postdoctoral fellows 2-3 year terms
• 2-5 sabbatical scholars Targeted & traditional
• Senior scientists Triangle sabbatical scholars & visitors Short term visitors, visiting scholars &
resident scientists
• Outstanding staff
Kathleen Smith, Center Director
Todd Vision, Associate Director
Informatics
Brian Wiegmann,Associate Director EOG
Joel Kingsolver, Associate Director
Science & Synthesis
Karen Henry, Assistant Director
Administration
Hilmar LappAssistant Director
Informatics
Jon AumanSystems Admin
TBDDryad Database
programmer
Xianhua LiuWeb/GUI
Project manager
Jim BalhoffResearch software
Developer
Jory WeintraubScience Education
Manager
Kristin JenkinsScience
CommunicationManager
Barbara MitchellOffice manager
Financial analyst
Danielle WilsonLogistics Manager
Candace BrownStaff Assistant
Student workersand temporary
employees
Vladimir GapeyevDatabase
programmer Cartik KothariDatabase Research
Ryan ScherleData repository
architect
Dave ClementsGMOD
Jack D’ArdenneMultimedia specialist
TBD Accounting Technician
TBD Assistant Director
Science
NESCent Staff Chart
Visitors to NESCent
Visitors to NESCent years 1-4
> 2300 visitors to the Center
> 120 meetings
> 1700 scientists in funded activities
> 700 visitors/year on average
Science ~$5.6 million
Informatics ~$2.8
EOG~$1.5
Center operations ~$2.8
Overhead ~$2.5
NESCent 5 year budget
Postdocs ~$2,147,000
Sabbatical scholars
~$620,000
Meeting support
~$2,481,000
Salary & consulting
~$2,374,000
Major equipment
$298,000
Metadata Center
$151,000
Administrative Salary
~$1,163,000
Rent & renovation
~$1,242,000
General office
~ $350,000
Funding beyond the core grantDuke University ~ $186,000 per year
External grants:
• NSF: Linking Evolution to Genomics Using Phenotype Ontologies (P. Mabee, M. Westerfield) • NESCent Total Direct: $853,338 (subcontract through UNC-CH) (June 2007- May 2010)
• NIH: Enhancement of the GBrowse Genome Annotation Browser (I. Holmes, L. Stein)• NESCent Total Direct: $242,565 (subcontract through UNC-CH) (April 2007 – March 2010)
• NIH: Development of the www.EcoliCommunity.org Information Resource (Jim Hu)• NESCent Total Direct: $30,550 (subcontract through UNC-CH) (June 2007 – May 2009)
• NSF: Digital Repository for Preservation and Sharing of Data in Evolutionary Biology• NESCent Total Direct $1,907,531 (September 2008 – September 2012)
• NSF: INTEROP: International Virtual Data Center for the Biodiversity and Environmental (W. Michener)
• NESCent Total Direct: $39,535 (subcontract) (January 2008 – December 2010)
• NSF: CCLI: Show me the evolution!• NESCent total direct costs $117,976 (January 2009 – December 2010) (with UC Berkeley,
Understanding Evolution)
• NSF: DatanetONE (William Mitchener) Under review• NESCent total direct costs $390,490 (subcontract) (October 2008 – September 2013)
Funded external award total: $3,191,495.00 (direct costs only)
NESCent partners with a variety of organizations
NESCent has partnered with over 50 organizations nationally and internationally.
•Co-sponsorship & hosting of meetings and projects•Co-sponsorship of courses•Collaboration on important initiatives
Includes a multitude of informatics, educational and scientific organizations.
•Dryad•Phenoscape•NABT
Important means to leverage NESCent’s reach beyond what can be accomplished by the core Center grant
NESCent’s mission • Support and enable synthetic research in
evolutionary biology• Develop & disseminate new tools for
evolutionary informatics • Take the lead in promoting a culture of
data sharing• Increase the public understanding of
science• Broaden the demographics of evolutionary
biology
Synthetic Science at NESCent
• Brings together diverse scientists to create new approaches to important questions
• Provides a stimulating environment for theoretical breakthroughs
• Stimulates new synthetic analyses• Promotes new initiatives for synthesis
Adding value to biological data
Science Board members (Summer 2008)
• Stanley Blum (Cal Academy)
• Troy Day (Queens)• Lisa Donovan (Georgia)• Fred Gould (NC State)• Catherine Graham (SUNY-
SB)• Elizabeth Hadly (Stanford)• Hopi Hoekstra (Harvard)• Junhyong Kim (Penn)• Joe Neigel (Louisiana)
• Maria Orive (Kansas)• Patrick Phillips (Oregon)• William Piel (Yale)• Bruce Rannala (UC-Davis)• Todd Streelman (Georgia
Tech)• Paul Turner (Yale)• Peter Wagner (Smithsonian)• Cheryl Wilga (Rhode Island)• Tony Zera (Nebraska)
Main Science Activities
Core Funding Other fundingCatalysis Meetings Triangle Working Groups
Working Groups Triangle Scholars
Postdoctoral Fellows Hosted Meetings
Sabbatical Scholars
Short-term Visitors
Science Projects (yrs 1-4)Project type # of Projects
Catalysis Meetings 14
Working Groups 26
Postdoctoral Fellows 23
Sabbatical Scholars 15
Triangle Working Groups 2
Triangle Scholars 10
Short-term Visitors 8
The NESCent in-house community
• 12-15 postdoctoral fellows 2-3 year terms
• 2-5 sabbatical scholars Targeted Traditional
• Senior scientists Triangle sabbatical scholars & visitors Short term visitors Visiting scholars Resident scientists
Science participants at NESCent through Feb 08
Level of Organization Subject Area
Molecular Genomics/proteomics
Molecular Molecular evolution
Organism Development
Organism Physiology/Functional Morphology
Organism Behavior/Neurobiology
Organism Medicine
Population Evolutionary Ecology/Population Biology
Population Evolutionary Genetics
Population Phylogeography/Speciation
Population Conservation
Phylogeny Comparative Biology
Phylogeny Systematics/Phylogenetics
Phylogeny Paleontology
Education Education
Classification of proposals(each proposal into 2 subjects)
Science awards (yrs 1-4) Primary or secondary subject: All awards
Genomics/Proteomics 10
Molecular evolution 13
Development 8
Physiology/Functional Morphology 12
Behavior/Neurobiology 7
Medicine 3
Evolutionary Ecology/Population Biology 21
Evolutionary Genetics 19
Phylogeography/Speciation 10
Conservation 2
Comparative Biology 20
Systematics/Phylogenetics 15
Paleontology 10
Education 6
Cross-disciplinarity of Science awards (yrs 1-4)
Molecular
Organism
Population
Phylogeny
Molecular 4 5 8 8
Organism 2 9 10
Population 10 10
Phylogeny 9
Science Awards:Integrating Science, Informatics &
Education
ScienceInformati
csEducatio
n
Science 55 12 3
Informatics 6 0
Education 3
Productivity of science projects through Feb 2008
Products Postdoc
SabbatSchola
r
Working
Group
Catalysis
Meeting
Other Total
Publications 11(6)
33(4)
18(11)
2(2)
6(4)
70(27)
Grants/proposals
3(2)
3 3(1)
2(7)
2(4)
13(14)
Software 8 1 3(1)
0 9 21(1)
Collaborations
14 5 4 6 10 39
NESCent brings together diverse scientists to create new conceptual
and analytical approaches• Catalysis meeting: Evolution in contemporary human populations
(Stearns and Govindaraju) Focus: Human genetic variation and its epidemiological &
evolutionary consequences Researchers and educators from evolution, medicine, human
genetics and public health• Outcomes
Working group: measuring evolutionary change in human populations using cohort data (Framingham Heart Study)• Clark, Govindaraju, Mackay, Stearns
Collaboration: Documenting evolutionary change in indigenous populations using biomedical data• Hurtado and Ellison
NABT Symposium 2007: Evolution and Medicine
The life cycle of synthesis
Linking evolution to genomics using phenotype ontologies
• Catalysis meeting -> WG -> NSF grant Paula Mabee, Monte Westerfield Zebrafish genetic mutants <-> natural phenotypic diversity in the Cypriniformes
• Collaboration among Cypriniformes Tree of Life morphologists NESCent informatics ZFIN (zebrafish genomics database) National Center for Biomedical Ontologies DeepFin
Understanding plant biodiversity:Linking phylogeny, ecology & global
change• Working Group: Phytogeography
of the northern hemisphere (Donoghue and Manos) Combining phylogenetic,
fossil, character and distribution data
Standardized analyses: pathways and timing of movement and divergence
Testing models of niche conservatism and environmental change
PNAS 2008;105:11549-11555
NESCent provides a stimulating environment for theoretical
breakthroughs • Sabbatical scholar Sally Otto• Projects
Evolution of sex and recombination Ecological interactions in evolutionary
models• Outcomes
Completed book: A Biologist’s guide to mathematical modeling (Otto and Day)
Publications: Genetics, Cell, TREE, Proc of the Royal Society, PLoS Genetics, Am Nat
New Projects• Recombination in Yeast (with Zeyl)• Ecological interactions and non-random mating (with
Servedio [Triangle Scholar], Nuismer)
NESCent stimulates new synthetic analyses of important evolutionary
questions• Postdoctoral fellow Samantha Price
Cetartiodactyl evolution: the transition from land to sea
Integrating fossils and molecular phylogenies in character evolution
• Postdoctoral fellow David Kidd Phylogenetic Information Science: linking
phylogenies and earth history GeoPhyloBuilder 1.0
• Collaboration: Visualizing Artiodactyla evolution in space and time
What is Synthesis? A NESCent community project
• What is synthesis? Reading group discussions The Synth-a-thon: July 2008
• A Practice Guide to Evolutionary Synthesis David Kidd, Ganesh Ganapathy, Einat Hazkani-Covo, Kristin Jenkins,
Hilmar Lapp, Lauren McCall, Sam Price, Ryan Scherle, Brian Sidlauskas, Paula Spaeth
Intended for PLoS Biology
NESCent Science: Successes
• Enabling new collaborations and explorations• Establishing a diverse and productive portfolio
of scientific projects• Engaging multiple science communities in
evolutionary biology• Integrating science and informatics in
evolutionary synthesis• Maintaining a strong in-house scientific
community, including postdoc training
NESCent Science: Challenges
• Ensuring consistent productivity of different projects
• Assessing the impacts of collaboration (e.g. catalysis meetings)
• Increasing the involvement of graduate students and postdocs
• Expanding evolutionary synthesis: applied evolution; social sciences
• Extending the scale of synthesis: how do we hit grand slams?
NESCent Informatics
• Developing and supporting tools to discover, organize, and share data and knowledge, in partnership with the evolutionary biology community relevant and successful efforts in related fields
• Promoting a community of open, collaborative software development
• Facilitating remote scientific collaboration
Initial informatics objectives
• Obtain community input into strategy and goals
• Bring diverse expertise on-staff and on-site• Provide high-end IT infrastructure to
sponsored scientists• Promote open and collaborative software
development• Offer informatics training opportunities• Acquire external funding for several new
cyberinfrastructure priorities
An informatics team with diverse expertise• Leadership
Hilmar Lapp Assistant Director of Informatics
• Systems and in-house support Jack D’Ardennes Desktop and multimedia support Jon Auman Systems administration
• Applications development for sponsored science Xianhua Liu Web development Vladimir GapayevDatabase development
• Special projects Jim Balhoff Application development David Clements User support for genome databases Cartik Kothari Data modeling and ontology
specialist Ryan Scherle Digital data repository architect
Obtaining community input into strategy and
goals• Advisory boards • Workshops• Sponsored science program• Whitepapers• Partnerships (eg INTEROP)• Peer review of major initiatives
Criteria for setting priorities
• The strength of commitment among the evolutionary biology community
• The anticipated impact on facilitating evolutionary synthesis
• The disciplinary diversity of the scientific communities that are affected
• Feasibility and cost-effectiveness• The strength of the match to the informatics
capabilities of the center• The extent to which the success of the initiative
would depend on the participation of the center
Informatics support for sponsored science
Turnkey• Electronic collaboration• Software development/production environment• High performance computing• Assessment of informatics needs/goals during the
review process
Customized• Allocation of programmer effort to specific high
impact projects• Assessed as part of the proposal review process
Primate Life History Working Group
• Joint w/ NCEAS, PIs: Karen Strier, Susan Alberts• “What are the roles of phylogeny, ecology, environment,
and behavior in shaping patterns of mortality, fertility and aging in primates?” Synthesis of data from long-term field studies of wild
populations of multiple primate species• Customized solution
A database hosted by NESCent A web interface for remote data entry, download, and
browsing Data coding standards with corresponding XML
schema Scripts for bulk data upload from spreadsheets Access security
Image: Michael Boardman © 2002
Promoting open-sourcesoftware development
TreeBaseTreeBasePAUP*PAUP* CIPRESCIPRESHyPhyHyPhyATVATV GARLIGARLINESCentNESCentNCLNCL
JEBLJEBLBiojavaBiojava BiopythonBiopythonBiorubyBiorubyBioSQLBioSQLBio::CDATBio::CDAT BioPerlBioPerl
Phyloinformatics hackathon (2006), organizers: Mark Holder, Hilmar Lapp, Aaron Mackey, Arlin Stoltzfus, Todd Vision, Rutger Vos
r-phylo.org
Comparative methods in R hackathon (2007), Organizers: Steven Kembel, Hilmar Lapp, Brian O’Meara, Sam Price, Todd Vision, Amy Zanne
Cyberinfrastructure priorities: gmod.org
Training
• Annual phyloinformatics summer course 14 co-instructors in 2008 Modules in Java, Perl, R special applications:
Mesquite, Hyphy, Diverse students
• GMOD Summer School• Google Summer of
Code• Others…
Cyberinfrastructure priorities: Ontologies to compute over
phenotypes• Catalysis meeting -> WG -> NSF grant
WG PIs: Paula Mabee, Monte Westerfield Zebrafish genetic mutants <-> natural phenotypic diversity in the
Cypriniformes
• “Linking evolution to genomics using phenotype ontologies” Partnership with ZFIN, NCBO, DeepFin Standards development (OBO/NeXML) Workshops at Evolution, SICB
Cyberinfrastructure priorities: data sharing
A digital repository for published data in evolution, ecology and related fields
• A digital data repository for published data in evolution, ecology, and related fields
• Funded by recent NSF BDI award (4yr, $2.18M)• Partners
NESCent, Metadata Research Center, NCSU Digital Library Program, TreeBASE, LTER
• Goals One-stop data deposition at publication Universal data IDs tied to publications Sophisticated search and retrieval services Management by multiple journals and societies
http://datadryad.org
American Society of NaturalistsAmerican Naturalist
Ecological Society of AmericaEcology, Ecological Applications, Ecological Monographs
European Society for Evolutionary BiologyJournal of Evolutionary Biology
Society for Integrative and Comparative BiologyIntegrative and Comparative Biology
Society for Molecular Biology and EvolutionMolecular Biology and Evolution
Society for the Study of Evolution EvolutionSociety for Systematic Biology
Systematic BiologyCommercial journals
Evolutionary ApplicationsMolecular EcologyMolecular Phylogenetics and Evolution
NESCent Informatics: Successes
• A generally high level of IT support for sponsored scientists
• A variety of useful software products From sponsored science, hackathons, training
activities, cyberinfrastructure initiatives
• Tapped into an impressive community of collaborative software developers Hackathon participants, GSoC mentors, etc.
• Cyberinfrastructure initiatives Succeeded in acquiring external funds Developed productive partnerships
• A vibrant and varied training program
NESCent Informatics: Challenges
• Effectively supporting the number and diversity of sponsored science projects
• Long-term maintenance and hosting of databases• Acquiring resources for later-stage software
development Testing, hardening, usability, documentation, user support
• Improving the availability of standards for evolutionary data
• Improving diversity among informatics participants Virtualizing activities such as hackathons
Education: The evolutionary biology community, K-16 & the public
• Training the next generation of synthetic researchers
• Promoting effective K-16 education• Developing resources for biology
educators• Disseminating NESCent sponsored
science
NESCent: Education and Outreach
• Kristin Jenkins• Jory Weintraub
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• science careers• evo pedagogy• science
communication• outreach to
minority scientists and educators
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Postdoctoral Training: Collaborative Research and Professional
Development
Postdoctoral Training: Collaborative Research and Professional
Development• Enabling interdisciplinary interactions through working groups, seminars,
committee involvement, outreach
• Developing professional careers (teaching, interviewing, publishing, funding )
• Communicating science (brown bag lunches, professional meetings, mentoring)
• Teaching Opportunities in the local community and beyond
NEScent sponsored Summer Courses
Guest Lectures
Bodega Bay Phylogenetics Workshop
Affecting Evolutionary Educationfrom K to 16
• SELECTION Working Group (John Jungck)
• Evolution Across the Curriculum Working Group (Uno and Scotchmoor)
• TREE (Tree Reasoning in Evolutionary Education) Working Group (Sam Donovan)
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NABT Evolution Symposium
• Work w/AIBS to plan, organize, facilitate day-long symposium• 2006 “Macroevolution”
2007 “Evolution: Human Health and Populations”2008 “Illuminating Biology Through Evolution”
• Develop, produce, distribute instructional CD-ROM on topic• Videotape symposium for web broadcast• Evaluation
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“Evolution in the News” Podcasts
• Partnership with UC Berkeley “Understanding Evolution” NCSU graduate student, Elsa Youngsteadt,
science journalism internship from SCIENCE UNC students produced Evolution in the
News podcasts from current literature as class assignment
• spawned a collaborative NSF Course, Curriculum, and Laboratory Improvement (CCLI) project
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CCLI PHASE 1 “Show Me the Evolution”
• newly funded! - $150,000 to Kathleen Smith and Kristin Jenkins; 2 years
• implements the ‘Evolution in the News’ program, a collaboration of UC Berkeley Museum of Paleontology ‘s Understanding Evolution (UE) and NESCent
• assess, and then improve, the educational value of the Evolution in the News program, develop more targeted dissemination strategies, and develop pedagogical recommendations for classroom integration.
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Outreach to Underrepresented Groups -Diversifying Evolution
This is a core priority of Center-wide activities
• Targeted sabbaticals
• Recruitment and scholarships in our informatics courses to students from underserved groups
• Network with faculty at local MSI
• Undergraduate Diversity at Evolution-- a collaboration with Scott Edwards and Richard Kliman, an NSF-funded program to provide targeted scholarships to the Evolution Meetings
Communicating NESCent Science
• Journal Articles • Press releases• NESCent Newsletter• NESCent Website• Posters• NC Museum of Natural
Sciences/ Science Cafe
NESCent EOG- Projecting Ahead
• expanding collaboration with Understanding Evolution (Berkeley), CCLI Phase II...‘The Evolution Undergraduate Lounge’
• continuing interactions with AIBS, professional societies, NAS, AAAS
• extending “Diversifying Evolution” initiatives
• connecting with educators through assessment, workshops, and feedback
Extending our Reach
• expanding opportunities for the current and next generation of evolutionary biologists
• capturing the energy of evolutionary synthesis to improve public understanding of science and promote biology education