NESCENT_IJSCM day 1

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  • Rich Kay, Hylander, Andrea Taylor, Christine Wall,
  • Rich Kay, Hylander, Andrea Taylor, Christine Wall,
  • An important role is development of software solutions to support sponsored science projects. A sampling of those projects: Top, an interactive database of maximum bodysizes throughout geological time, in support of a working group. Middle, a database that allows members of a primate life history working group to integrate long-term field observation from studies of primates in the wild – data that has never before been sharable or shared. Bottom, a visualization tool that allows users to overlay a phylogenetic topology onto a landscape within standard geographic information system software.
  • A major informatics initiative has been the Dryad data repository, a general-purpose archive for data supporting peer-reviewed articles in basic and applied biosciences. It is used by leading journals in the field (such as Evolution, Journal of Evolutionary Biology, Molecular Ecology).Dryad, together with policies from funding agencies and journals that require or encourage increased archiving of published data, provides a way to make data to be available not just for validation, but also for new method development, meta-analysis, and other types of synthetic science; and give researchers credit for their data as a first-class scholarly product.The image at right shows how the data submission process is coupled with article submission. At the end of the process, the article his published with a data citation, and the data link back to the original article.

Transcript

  • 1. TransformShareConnect NESCent The National Evolutionary Synthesis Center ADDRESSING FUNDAMENTAL CHALLENGES IN EVOLUTIONARY SCIENCE
  • 2. TransformShareConnect NESCent is presently funded by the NSF NESCent is a collaborative partnership between • Duke University • The University of North Carolina at Chapel Hill • North Carolina State University
  • 3. TransformShareConnect NESCent in Durham, North Carolina
  • 4. TransformShareConnect How does one define a synthesis center? Our Mission • NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. • NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries.
  • 5. TransformShareConnect Sidlauskas et al (2009). Linking Big: the Continuing Promise of Evolutionary Synthesis. Evolution Volume 64, Issue 4, pages 871-880. What is Synthesis?
  • 6. TransformShareConnect What is the value of a synthesis center? • As a synthesis center, NESCent’s role is to Connect, Share, Transform
  • 7. TransformShareConnect How do we build a successful research incubator? • Goal: Foster and enable novel and transformative research so that the chances for successful funding increases • Structure: – Interdisciplinary, self-identified teams – A neutral, physical space – A resident community – Freedom from distractions – Data reuse, not data generation – Core informatics support
  • 8. TransformShareConnect NESCent as a Synthesis Center • As a synthesis center, NESCent’s role is to Connect, Share, Transform
  • 9. TransformShareConnect NESCent as a Synthesis Center • As a synthesis center, NESCent’s role is to Connect, Share, Transform • NESCent is an Incubator for new scientific research – Provision of informatics resources – Provision of administrative and logistic support – Triage of high-risk science
  • 10. TransformShareConnect NESCent as a Synthesis Center • As a synthesis center, NESCent’s role is to Connect, Share, Transform • NESCent is an Incubator for new scientific research – Provision of informatics resources – Provision of administrative and logistic support – Triage of high-risk science • NESCent promotes the establishment and development of Communities of Practice and Grassroots Resource Solutions – groups of individuals working in similar areas or on similar problems, and sharing similar requirements and constraints
  • 11. TransformShareConnect Education & Outreach • Working Groups Approaches: Core Science Programs
  • 12. TransformShareConnect Education & Outreach • Working Groups • Catalysis Meetings Approaches: Core Science Programs
  • 13. TransformShareConnect Education & Outreach • Working Groups • Catalysis Meetings • Sabbatical Scholars Approaches: Core Science Programs
  • 14. TransformShareConnect Education & Outreach • Working Groups • Catalysis Meetings • Sabbatical Scholars • Postdoctoral Scholars Approaches: Core Science Programs
  • 15. TransformShareConnect Education & Outreach • Working Groups • Catalysis Meetings • Sabbatical Scholars • Postdoctoral Scholars • Short Term Visitors Approaches: Core Science Programs
  • 16. TransformShareConnect Education & Outreach • Working Groups • Catalysis Meetings • Sabbatical Scholars • Postdoctoral Scholars • Short Term Visitors • Graduate Fellowships Approaches: Core Science Programs
  • 17. TransformShareConnectPrimate Life Histories Karen Strier (Univ. Wisconsin), Susan Alberts (Duke), 2007-2008
  • 18. TransformShareConnectPrimate Life Histories Develop “… a collaborative, shared database allowing analyses of irreplaceable life history data on wild primates.” Karen Strier (Univ. Wisconsin), Susan Alberts (Duke), 2007-2008
  • 19. TransformShareConnectPrimate Life Histories Develop “… a collaborative, shared database allowing analyses of irreplaceable life history data on wild primates.” Karen Strier (Univ. Wisconsin), Susan Alberts (Duke), 2007-2008
  • 20. TransformShareConnectPrimate Life Histories Karen Strier (Univ. Wisconsin), Susan Alberts (Duke), 2007-2008
  • 21. TransformShareConnectPrimate Life Histories Karen Strier (Univ. Wisconsin), Susan Alberts (Duke), 2007-2008
  • 22. TransformShareConnect • Examples of activities: Evolutionary Medicine Initiative
  • 23. TransformShareConnect • Examples of activities: – A “mini-camp” on evolutionary biology for medical practitioners, at NESCent Evolutionary Medicine Initiative
  • 24. TransformShareConnect • Examples of activities: – A “mini-camp” on evolutionary biology for medical practitioners, at NESCent – A CME summer course at Mt. Desert Island, sponsored by NESCent Evolutionary Medicine Initiative
  • 25. TransformShareConnect • Examples of activities: – A “mini-camp” on evolutionary biology for medical practitioners, at NESCent – A CME summer course at Mt. Desert Island, sponsored by NESCent – An Evolutionary Medicine symposium at Evolution 2011. Evolutionary Medicine Initiative
  • 26. TransformShareConnect • Examples of activities: – A “mini-camp” on evolutionary biology for medical practitioners, at NESCent – A CME summer course at Mt. Desert Island, sponsored by NESCent – An Evolutionary Medicine symposium at Evolution 2011. • Working Groups on Curriculum Development for pre- med and med students Evolutionary Medicine Initiative
  • 27. TransformShareConnect • The Perils of Being Bipedal: an Evolutionary Perspective on Human Muscoloskeletal Disorders. Evolutionary Medicine Initiative Bruce Latimer (CW Reserve) and Linda Spurlock (Kent State) Walking on extended hind limbs is the hallmark adaptation characterizing our species but it makes us vulnerable to a wide range of serious joint and soft tissue problems …chronically sprained ankles, hernias, osteoporotic fractures of the hip, spine, and forearm, obstetric problems, knee problems, foot disorders, fatigue fractures. Goal: develop and implement a model curriculum for medical students, create a reference website, and publish an edited volume.
  • 28. TransformShareConnect • Genetics and Genealogy: Teaching Evolution and Human Diversity to Middle School Students K-12 Evolution Education Initiative Nina Jablonski (Penn State), Mark Shriver, Catherine Bliss, Eric Plutzer Goal: develop a summer‐camp curriculum for middle school students entitled, “The Peopling of the World and Me!” • Use personal history and genealogy to introduce the principles of inheritance, modern genetics, and the evolutionary process. • “This is a more exciting and memorable way of teaching these concepts than is the study of peas or fruitflies.”
  • 29. TransformShareConnect The Social Challenge: Engineering Grassroots Resource Solutions • Why Grassroots Solutions? – Needs-based. Community-driven identification of requirements ensures, at the outset, that there is a real need for the tools and resources that are being developed. • Advantages: – Buy-in. By working with people who contribute to the construction of resources, and who have a vested interest in their deployment, we overcome the social barriers to the adoption of technological resources that often plagues top-down development. – Built-in test cases. The scientists who participate in the development of the resources will include people who want to use the prototypes in their own research. Hence, we have a ready-made pool of alpha- and beta-testers in each project. – Re-use. The information technologists and computational biologists who work with many development teams have a high-level understanding of the resources that each group uses, as well as the potential to re-use resources. – Sustainability. By including postdoctoral scholars and graduate students in this process, the resources that are developed take on a life of their own beyond the term of the project. This is because these emerging scientists are likely to continue to use and develop these resources.
  • 30. TransformShareConnect Approaches: Custom tools for sponsored scientists Physiological data of mammalian feeding (FEED: https://www.nescent.org/wg_feeding) Integrating ontologies for genes, phenotypes, and evolution (PHENOSCAPE: http://phenoscape.org)
  • 31. • Data archived during publication • Easy submission process • Available to peer reviewers • Persistent link from paper to data • Supports data citation (data DOIs) • Open and explicit terms of reuse • Option to embargo • Deep data indexing and searching • Updatable datafiles • File format migration & preservation • Governed and sustained by journals http://datadryad.org National Evolutionary Synthesis Center
  • 32. TransformShareConnectApproaches: Education and Outreach Serving… •Education Community •Science Community •General Public •Underrepresented Minorities •International Science Community
  • 33. TransformShareConnectThe Darwin Day Roadshow • NESCent scientists and education/outreach staff visit schools (K-16) and communities to talk about evolutionary science and science careers • Targets smaller, more rural communities • 2011 – Iowa, Montana, Nebraska, Virginia • 2012 – Over 100 applications from 27 states
  • 34. TransformShareConnectThe NESCent AcademyNESCent Academy • Evolutionary Quantitative Genetics • Next-gen Sequencing: data acquisition, comparative genomics, design and analysis for population genetics, systematics and development • Anatomy ontologies in evolutionary biology and genetics 2012 @NESCent academy.nescent.org 2011 • 2 courses @NESCent • 4 co-sponsored off-site courses • Travel awards for 22 participants from under-represented minorities
  • 35. TransformShareConnectMinority Outreach NESCent postdoc Juan Santos works with elementary school students as part of SALSA! NESCent postdoc Carlos Botero mentors undergraduate students at the SACNAS conference LOCAL PROGRAMS SALSA! (Seeing and Learning Science Afterschool) NATIONAL PROGRAMS SACNAS (Society for the Advancement of Chicanos and Native Americans in Science)
  • 36. TransformShareConnectNESCent Ambassadors Program • International Outreach – NESCent scientists/informatics/education staff work with local scientists and educators in developing nations • To date: Ecuador/Galapagos, Indonesia, Madagascar • Upcoming: Caribbean, Kenya, Galapagos, Panama Dr. Carlos Valle (USFQ) discussing finch evolution with natural history guides on San Cristobal NESCent postdoc Peter Unmack works with Indonesian students on the island of Bali
  • 37. 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 Total No. No. of Participants 8 159 292 557 378 512 439 785 653 622 4356 No. of Software/Datasets 1 21 25 16 8 14 34 2 121 No. of Publications 1 2 24 68 65 90 79 89 113 40 571 No. of News Coverage 4 5 45 43 65 100 25 287 No. of Catalysis Meetings 4 6 3 4 5 5 7 0 34 No. of Active Working Groups 2 9 15 17 20 22 21 15 12 55 No. of New Postdoctoral Fellows 5 7 4 3 8 4 6 4 4 46 No. of Active Sabbatical Scholars 4 5 1 5 3 5 5 5 5 38 No. of Courses 5 11 6 7 4 6 4 43 No. of Course Participants 78 84 142 57 123 169 97 750