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