2. 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

3. 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)

4. NESCent History year 1 year 2 year 3year 4 December 2004 December 2005 December 2006 December 2007 December 2008 year 5 First scientists arrive Revised NESCent plan You are here

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

6. 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.

7. 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.

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 Outstanding staff

9. 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 Lapp Assistant Director Informatics Jon Auman Systems Admin TBD Dryad Database programmer Xianhua Liu Web/GUI Project manager Jim Balhoff Research software Developer Jory Weintraub Science Education Manager Kristin Jenkins Science Communication Manager Barbara Mitchell Office manager Financial analyst Danielle Wilson Logistics Manager Candace Brown Staff Assistant Student workers and temporary employees Vladimir Gapeyev Database programmer Cartik Kothari Database Research Ryan Scherle Data repository architect Dave Clements GMOD Jack D’Ardenne Multimedia specialist TBD Accounting Technician TBD Assistant Director Science NESCent Staff Chart

10. Visitors to NESCent

11. Visitors to NESCent years 1-4 > 2300 visitors to the Center > 120 meetings > 1700 scientists in funded activities > 700 visitors/year on average

12. 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

13. 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)

14. 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

15. 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

16. 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

17. 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)

18. Main Science Activities Core FundingOther funding Catalysis MeetingsTriangle Working Groups Working GroupsTriangle Scholars Postdoctoral FellowsHosted Meetings Sabbatical Scholars Short-term Visitors

19. Science Projects (yrs 1-4) Project type# of Projects Catalysis Meetings14 Working Groups26 Postdoctoral Fellows23 Sabbatical Scholars15 Triangle Working Groups2 Triangle Scholars10 Short-term Visitors8

20. 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

21. Science participants at NESCent through Feb 08

22. Level of OrganizationSubject Area MolecularGenomics/proteomics MolecularMolecular evolution OrganismDevelopment OrganismPhysiology/Functional Morphology OrganismBehavior/Neurobiology OrganismMedicine PopulationEvolutionary Ecology/Population Biology PopulationEvolutionary Genetics PopulationPhylogeography/Speciation PopulationConservation PhylogenyComparative Biology PhylogenySystematics/Phylogenetics PhylogenyPaleontology Education Classification of proposals (each proposal into 2 subjects)

23. Science awards (yrs 1-4) Primary or secondary subject:All awards Genomics/Proteomics10 Molecular evolution13 Development8 Physiology/Functional Morphology12 Behavior/Neurobiology7 Medicine3 Evolutionary Ecology/Population Biology21 Evolutionary Genetics19 Phylogeography/Speciation10 Conservation2 Comparative Biology20 Systematics/Phylogenetics15 Paleontology10 Education6

24. Cross-disciplinarity of Science awards (yrs 1-4) MolecularOrganismPopulationPhylogeny Molecular 4588 Organism 2910 Population 10 Phylogeny 9

25. Science Awards: Integrating Science, Informatics & Education ScienceInformaticsEducation Science55123 Informatics60 Education3

26. Productivity of science projects through Feb 2008 ProductsPostdocSabbat Scholar Working Group Catalysis Meeting OtherTotal Publications11 (6) 33 (4) 18 (11) 2 (2) 6 (4) 70 (27) Grants/ proposals 3 (2) 33 (1) 2 (7) 2 (4) 13 (14) Software813 (1) 0921 (1) Collaborations145461039

27. 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

28. 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

29. 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

30. 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)

31. 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

33. 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

34. 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

35. 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?

36. 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

37. 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

38. An informatics team with diverse expertise Leadership  Hilmar LappAssistant Director of Informatics Systems and in-house support  Jack D’Ardennes Desktop and multimedia support  Jon AumanSystems administration Applications development for sponsored science  Xianhua LiuWeb development  Vladimir GapayevDatabase development Special projects  Jim BalhoffApplication development  David ClementsUser support for genome databases  Cartik KothariData modeling and ontology specialist  Ryan ScherleDigital data repository architect

39. Obtaining community input into strategy and goals Advisory boards Workshops Sponsored science program Whitepapers Partnerships (eg INTEROP) Peer review of major initiatives

40. 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

41. 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

42. 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

43. Promoting open-source software development TreeBase PAUP* CIPRES HyPhy ATV GARLI NESCent NCL JEBL Biojava Biopython Bioruby BioSQL Bio::CDAT BioPerl Phyloinformatics hackathon (2006), organizers: Mark Holder, Hilmar Lapp, Aaron Mackey, Arlin Stoltzfus, Todd Vision, Rutger Vos

44. r-phylo.org Comparative methods in R hackathon (2007), Organizers: Steven Kembel, Hilmar Lapp, Brian O’Meara, Sam Price, Todd Vision, Amy Zanne

45. Cyberinfrastructure priorities: gmod.org

46. 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…

47. 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

48. Cyberinfrastructure priorities: data sharing A digital repository for published data in evolution, ecology and related fields

49. 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

50. 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

51. 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

52. 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

53. 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

54. NESCent: Education and Outreach Kristin Jenkins Jory Weintraub science careers evo pedagogy science communication outreach to minority scientists and educators

55. Postdoctoral Training: Collaborative Research and Professional Development

56. 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

57. Affecting Evolutionary Education from 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)

58. 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

59. “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

60. 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.

61. 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

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

63. 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

64. 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