• 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

• 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)

year 1
NESCent History year 2 year 3 year 4 year 5
You are here
First scientists arrive
Revised
NESCent plan

Interaction among Directors
Participation by faculty and students
Institutional support
Administrative processes

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 Board
Meets once a year. Provides general advice about
Center operation. Additional consultation as necessary through email and phone conversations.
Scientific Advisory Board
Meets twice a year. Primary role is review of proposals.
Also provides general advice regarding scientific activities.
Operations Committee
Directors plus at large members from each of the
Triangle Universities and one postdoc. Meets ~ monthly to discuss Center activities.

• 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

NESCent Staff Chart
Todd Vision,
Associate Director
Informatics
Hilmar Lapp
Assistant Director
Informatics
Jon Auman
Systems Admin
TBD
Dryad Database programmer
Xianhua Liu
Web/GUI
Project manager
Vladimir Gapeyev
Database programmer
Jim Balhoff
Research software
Developer
Cartik Kothari
Database Research
Brian Wiegmann,
Associate Director EOG
Jory Weintraub
Science Education
Manager
Kristin Jenkins
Science
Communication
Manager
Kathleen Smith,
Center Director
Joel Kingsolver,
Associate Director
Science & Synthesis
Ryan Scherle
Data repository architect
Jack D’Ardenne
Multimedia specialist
Dave Clements
GMOD
TBD
Assistant Director
Science
Karen Henry,
Assistant Director
Administration
Barbara Mitchell
Office manager
Financial analyst
Danielle Wilson
Logistics Manager
Candace Brown
Staff Assistant
Student workers and temporary employees
TBD
Accounting
Technician

900
800
700
600
500
400
300
200
100
0
Science
Informatics
Education
Advisory
Hosted
Yr 1 Visitors
Yr 2 Visitors Yr 3 Visitors Yr 4 Visitors

> 2300 visitors to the Center
> 120 meetings
> 1700 scientists in funded activities
> 700 visitors/year on average

NESCent 5 year budget
Administrative
Salary
Rent & renovation
General office
~$1,163,000
~$1,242,000
~ $350,000
Overhead
~$2.5
Science
~$5.6 million
Postdocs
Sabbatical scholars
Meeting support
Center operations
~$2.8
EOG
~$1.5
Informatics
~$2.8
Salary & consulting
Major equipment
Metadata
Center
~$2,374,000
$298,000
$151,000
~$2,147,000
~$620,000
~$2,481,000

Funding beyond the core grant
Duke 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

• 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

• 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

(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)

Core Funding
Catalysis Meetings
Working Groups
Postdoctoral Fellows
Sabbatical Scholars
Short-term Visitors
Other funding
Triangle Working Groups
Triangle Scholars
Hosted Meetings

Project type
Catalysis Meetings
Working Groups
Postdoctoral Fellows
Sabbatical Scholars
Triangle Working Groups
Triangle Scholars
Short-term Visitors
# of Projects
14
26
23
15
2
10
8

• 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

(each proposal into 2 subjects)
Level of Organization
Molecular
Molecular
Organism
Organism
Organism
Organism
Population
Population
Population
Population
Phylogeny
Phylogeny
Phylogeny
Education
Subject Area
Genomics/proteomics
Molecular evolution
Development
Physiology/Functional Morphology
Behavior/Neurobiology
Medicine
Evolutionary Ecology/Population Biology
Evolutionary Genetics
Phylogeography/Speciation
Conservation
Comparative Biology
Systematics/Phylogenetics
Paleontology
Education

Primary or secondary subject:
Genomics/Proteomics
Molecular evolution
Development
Physiology/Functional Morphology
Behavior/Neurobiology
Medicine
Evolutionary Ecology/Population Biology
Evolutionary Genetics
Phylogeography/Speciation
Conservation
Comparative Biology
Systematics/Phylogenetics
Paleontology
Education
All awards
19
10
2
20
15
10
6
10
13
7
3
8
12
21

Molecular
Organism
Population
Phylogeny
Molecular Organism Population Phylogeny
4 5
2
8
9
10
8
10
10
9

Integrating Science, Informatics & Education
Science
Informatics
Education
Science Informatics Education
55 12
6
3
0
3

Products
Postdoc Sabbat
Scholar
Working
Group
Catalysis
Meeting
Other Total
Publications
Grants/ proposals
Software
Collaborations
11
(6)
3
(2)
8
14
33
(4)
3
1
5
18
(11)
3
(1)
3
(1)
4
2
(2)
2
(7)
0
6
6
(4)
2
(4)
9
10
70
(27)
13
(14)
21
(1)
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

• 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?

• 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

• 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 Gapayev Database development
• Special projects
 Jim Balhoff
 David Clements
 Cartik Kothari
 Ryan Scherle
Application development
User support for genome databases
Data modeling and ontology specialist
Digital data repository architect

• Advisory boards
• Workshops
• Sponsored science program
• Whitepapers
• Partnerships (eg INTEROP)
• Peer review of major initiatives

• 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

 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

• 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-source software development
ATV NCL NESCent HyPhy PAUP* CIPRES GARLI TreeBase
Bio::CDAT Biojava BioSQL JEBL Bioruby BioPerl Biopython
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

• 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…

• 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

American Society of Naturalists
American Naturalist
Ecological Society of America
Ecology, Ecological Applications, Ecological Monographs
European Society for Evolutionary Biology
Journal of Evolutionary Biology
Society for Integrative and Comparative Biology
Integrative and Comparative Biology
Society for Molecular Biology and Evolution
Molecular Biology and Evolution
Society for the Study of Evolution
Evolution
Society for Systematic Biology
Systematic Biology
Commercial journals
Evolutionary Applications
Molecular Ecology
Molecular Phylogenetics and Evolution

• 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

• 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

• Training the next generation of synthetic researchers
• Promoting effective K-16 education
• Developing resources for biology educators
• Disseminating NESCent sponsored science

• Kristin Jenkins
• Jory Weintraub
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• science careers
• evo pedagogy
• science communication
• outreach to minority scientists and educators

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• 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

• 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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• 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

• 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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• 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.

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

• Journal Articles
• Press releases
• NESCent Newsletter
• NESCent Website
• Posters
• NC Museum of Natural Sciences/
Science Cafe

• 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

• 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