Newsletter Vol. 2 No. 1 May, 2008

 

In this issue:

A Message from the Director

Science and Synthesis

New Awards

Call for Proposals

Darwin Day Symposium 2008

Informatics

R Hackathon 

Upcoming workshops

  • GMOD Workshop
  • Evolutionary Biology and Ontologies Workshop
  • Phyloinformatics Summer Course
  • Google Summer of Code

Dryad

Employment and Internship Opportunities

Education and Outreach

Educational Resources from the 2007 NABT Evolution Symposium 

Darwin Day Symposium 2008

Evolution in the News with UE

Tools for Teaching Evolution Workshop

Summer Workshop for Elementary School Teachers

Increasing Undergraduate Diversity at the Evolution Meetings

 

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Banner Photo Credits (left to right): John Clamp, Zoothamnium niveum; Owen McMillan, Heliconius ; Sally Otto, Sula nebouxii; Amy Zanne, fern.

 

A Message from the Director

Kathleen Smith

Kathleen SmithIt's been awhile since our last newsletter and you'll see that a lot has been going on here at NESCent in the last six months. In this newsletter we announce our latest round of awards, and a number of summer courses through the IT group, including our second year with the Google Summer of Code and the NESCent Computational Phyloinformatics course.

I'd like particularly to point out our next deadline for funding, June 15. At this time we'll accept proposals for sabbatical scholars, working groups and catalysis meetings. The next deadline for postdoctoral fellows is December 1.

I'd also like to extend an invitation to all attending the Evolution 2008 meeting in Minneapolis, June 19-24, to take the opportunity to speak to NESCent Directors about activities at the Center and funding opportunities. We will be sponsoring a breakfast on Sunday June 22 that is free and open to all, and provides a good opportunity for informal chats. Details may be found in the Evolution program, on our website (as the date approaches) or at our booth. We'd also encourage you to stop by the booth to get further updates on our activities or to talk to NESCent Directors, informatics or education and outreach staff. In the meantime, we encourage you to check our website for information about current events at NESCent or to learn more about applying for funding.

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Science and Synthesis

New Awards

Awards from the December 1, 2007 call for proposals have been made and NESCent is pleased to announce four Sabbatical Scholars, six Post-doctoral Fellows, two Short-term Visitors, two new working groups and two catalysis meetings. For more information on these and other awards at NESCent, go to Supported Projects.

Sabbatical Scholars

Michael Antolin - Sabbatical book project: Genetics of small populations

Christian D'Orgeix - Evolution courses, mountaintop lizards and a view toward future research

Elizabeth Lacey - Temperature and the evolution of floral design

Robert Pennock - Darwinian design: From artificial life to evolving intelligencepeople talking

Post-doctoral Fellows

Josh Auld - Evaluating the effects of inbreeding on dispersal

Carlos Botero - Evolution of conventional signals: From individuals to populations and back

Alison Boyer - A synthetic database of avian biodiversity on Pacific Islands

Marc Lajeunesse - Meta-analysis and the comparative phylogenetic method

Trina Roberts - Sticky tips and misplaced roots: Is there a bias in intraspecific phylogenetics?

Stephen Smith - Integrating species distribution modeling and phylogenetics

Short-term Visitors

Oliver Eulenstein - Gene tree parsimony for genome-scale studies

David Houle - Measurement theory and evolutionary ratesmeeting pic

 

Working Groups

Floral assembly: Quantifying the composition of a complex adaptive structure.

PIs Charles Fenster, Scott Armbruster, Pamela Diggle

Building tools for emerging model systems in Development, Evolution, and Ecology

PIs Scott Hodges, Elena Kramer, Hopi Hoekstra

Catalysis Meetings

What role, if any, does heritable epigenetic variation play in phenotypic evolution?

PIs Christina Richards, Oliver Bossdorf, Massimo Pigliucci

Perspectives on the origin and conservation of biodiversity in Patagonia.

PIs Jack Sites, Daniel Faith

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Call for Proposals

The submission deadline for the next call for proposals is June 15, 2008.  Proposals for working groups, catalysis meetings and both traditional and targeted sabbaticals will be accepted.  In addition, applications for the Short-term visitors program will be evaluated July 1, September 1, and December 1, 2008. 

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Darwin Day

 

 

 

 

Darwin Day Symposium 2008

NESCent celebrated Darwin’s birthday early this year with a symposium on “Origins and Early Evolution of Life” on March 8th.  The symposium was open to the public and held at the Sigma Xi headquarters in Research Triangle Park.  NESCent was pleased to welcome Carol Cleland, Mark Bedau, Abigail Allwood, Janet Siefert, Andrew Roger, and Laura Landweber as the symposium speakers.  Topics included defining life, detecting traces of early life, the process of generating synthetic life, unusual metabolic processes and conditions on early earth, strange genomes, and the current status of the eukaryotic tree of life. The speakers gave general presentations on their research at the day-long symposium, and then joined NESCent post-docs and faculty the following day for a round-table discussion of some of the thornier issues in this area of research. Presentations from the symposium will be available on the NESCent website in the near future. 

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Informatics

Comparative Methods in R Hackathon 

r logoThe R statistics package has emerged as a popular platform for implementation of comparative phylogenetic methods. To encourage the open development of software for this growing area of evolutionary data analysis, NESCent hosted a Hackathon in December 2007 that brought together nearly 30 experts in R programming and users of comparative methods.  The immediate outcome of the meeting has been development of better software tools for studying diversification rates, estimating divergence times, and modeling the evolution of continuous phylogenetic characters, as well as improved online documentation, shared libraries for basic phylogenetic data manipulation, and interoperability between R and the Mesquite package.  The meeting also spurred the creation of a new special interest group (SIG) mailing list (called R-SIG-phylo) open to anyone interested in discussing the application of comparative phylogenetic methods within R.  In addition, based on suggestions from hackathon participants a community web-site and wiki was launched and seeded with the how-to documentation that resulted from the hackathon. The site is hosted by NESCent, but anyone can edit or add content by simply creating an account.  For more information, see the hackathon wiki.

A publication describing the previous year's Phyloinformatics Hackathon has recently been published in the journal Evolutionary Bioinformatics.

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Upcoming workshops

GMOD WorkshopGMOD logo

The first annual GMOD Workshop will be held July 11-13, 2008 at NESCent, in Durham, North Carolina. GMOD is a collection of interoperable open source software tools that are used in diverse contexts, ranging from genome annotation projects within individual labs to major model organism databases.

The course will provide an overview of GMOD and cover these popular components in detail:
* Chado - a modular and extensible database schema
* Apollo - genome annotation editor
* GBrowse - genome viewer
* CMap - comparative map viewer
* Community Annotation System - A bundle of GMOD's most popular components in a single system

This is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components. There will also be a concurrent 1 day session aimed at principal investigators that will give decision makers an overview of what GMOD can do, how the project operates, and what level of resources are needed to get a GMOD installation up and running.

The National Evolutionary Synthesis Center has joined the GMOD project with the goal of lowering the barrier to entry for research communities focused on emerging model organisms. The GMOD Summer School is a part of this effort. NESCent is also extending GMOD tools, particularly Chado, to better support comparative and evolutionary data.

 

Evolutionary Biology

Evolutionary Biology and Ontologies Workshop

This workshop will be held June 20, at the Evolution 2008 Meeting in Minneapolis, MN.  The course is organized by NESCent and the National Center for Biomedical Ontologies (NCBO).  The workshop will focus on the application of ontologies in evolutionary biology and related disciplines, with a particular emphasis on studies of the phenotype.

NESCent Computational Phyloinformatics Summer Course

July 24- August 4, NESCent, Durham, NC


For the second year in a row, NESCent will offer a summer short course in Computational Phyloinformatics. This 10-day course will focus on how to script large-scale and complex analyses, as well as how to write your own scripts and programs to address questions in phylogenomics. Thirty-five graduate students, post-docs, and researchers in biology have applied.  More information about the course is available here.

Google Summer of Code

NESCent is participating for the second year as a mentoring organization in the Google Summer of Code. Through this program, Google provides undergraduate, masters, and PhD students with a unique opportunity to obtain hands-on experience writing and extending open-source software under the mentorship of experienced developers from around the world.  NESCent will be working with five students and their mentors through the summer.  More information on the projects is available here

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Dryad dryad logo

The initial version of the Dryad data repository is now available for use. Dryad stores data underlying published

works in evolutionary biology and related fields. Dryad will preserve the data and provide citable identifiers, allowing future investigators to validate published findings, explore new analysis methodologies, and repurpose data for research questions unanticipated by the original authors.

Do you have an upcoming publication? If so, you can deposit the underlying data in Dryad, and cite the Dryad identifiers in the publication. Dryad will preserve your data, allowing others to access and cite it. Submission of data for previously published works is also encouraged. See the Dryad Deposition Policies for more information. 

Dryad is working with a number of partner journals. As development of Dryad progresses, the journals' manuscript submission process will be integrated with the Dryad data submission process to provide more direct access.

(Image courtesy of creativity+ on flickr.com)

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Employment and internship opportunities with NESCent Informatics

Interested in working with the NESCent Informatics group?  NESCent currently has an opening for a Bioinformatics Programmer with a specialization in databases and middleware. Learn more about this position, as well as summer and internship positions on the NESCent employment page.

 

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Education and Outreach

 

Educational Resources from the 2007 NABT Evolution Symposium

nabt cd

In our previous newsletter, we announced the 2007 NABT Evolution Symposium on “Evolution: Applications In Human Health and Populations”.  At the symposium, held December 1 in Atlanta, participants learned about recent developments in genomics and epidemiology.  They also learned about historical aspects of epidemiology, what modern biology has to say about race, and interesting applications of evolutionary theory in behavioral studies.  For those of you who were not able to attend, or who want to share these presentations with your students, the presentations are also posted on our website.

A CD of educational resources was also developed in support of this event and is posted on our website.  (Hard copies for individuals or workshops are available upon request.)  The CD contains background information on the symposium speakers, video interviews with research scientists interested in the application of evolutionary theory in human health, essays, and classroom activities.  In addition, there are links to resources from the National Institutes of Health including publications, curriculum materials, and internship opportunities. 

As with all our activities, we appreciate your feedback.  Please let us know if you found these products useful, or if you have suggestions for improvement, contact us at: eog@nescent.org.

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Darwin Day

Darwin Day Symposium 2008

The 2008 Darwin Day Symposium was recorded and the presentations will be posted on line later this Spring.  We hope you can use them in your classroom.  Abigail Allwood’s presentation is a fantastic and really interesting demonstration of the scientific process, and Andrew Roger’s talk on the eukaryotic tree of life is an engaging overview of the state of affairs in this field.  Carol Cleland, Janet Seifert and Marc Bedau’s talks are thought-provoking discussion starters on “life”.  And for emphasizing the purely puzzling nature of biology, try Laura Landweber’s presentation on Oxyticha trifallax, which chops its genome into pieces and then reconstructs it.

Other educational resources for the symposium are on the website and include recommended reading suggested by the speakers, as well as more general background articles and books.  There is a link to a free DVD from NASA on “Looking for Life”, links to computer simulations such as AVIDA, and classroom activities available from the National Academies of Science and NASA. 

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Evolution in the News with UE

shrewNESCent is pleased to announce a new partnership with Understanding Evolution.  Based at the University of California, Berkeley Museum of Paleontology, Understanding Evolution has a wide collection of resources for teaching evolution including a monthly “Evolution in the News” story.  NESCent’s Evolution in the News series will now be coordinated with Understanding Evolution’s stories.  NESCent is producing podcasts of interviews with scientists to compliment stories from Understanding Evolution.  The stories and podcasts may be reached from either the NESCent Education and Outreach site, or the Understanding Evolution site.  Check out the first in this series -  “The New Shrew That’s Not” – which includes a podcast interview with NESCent’s Director, Kathleen Smith, and NESCent post-doctoral fellow, Samantha Price.

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Education and Outreach Workshops

Tools for Teaching Evolution

SELECTION logo

John Jungck and Tony Weisstein are the organizers of the SELECTION working group at NESCent.  This group has brought together researchers and educators to develop educational materials using real data sets from evolutionary biologists.  These data sets can be analyzed in the classroom using the same tools that researchers use.  BioQUEST has developed modules, problem spaces, and tutorials to support educators in bringing these activities to the classroom.  A workshop will be offered May 29 at NESCent for educators interested in learning more about these tools.

NESCent Offers Summer Workshop for Elementary School Teachers

For the second year in a row, NESCent will be offering a week-long continuing education course for elementary school (4th through 6th grade) teachers entitled "Teaching An Elementary Story of Life: The Web of Biology, Ecology, and Evolution".  This course was developed and taught last summer by Dr. Joseph Fail, an Associate Professor of Biology at Johnson C. Smith University in Charlotte, NC, and former NESCent Sabbatical Scholar.  During his year-long sabbatical at NESCent, Dr. Fail developed curriculum to facilitate the teaching of biology, ecology and evolution as connected chapters of a story to be taught over a school year.  Due to the overwhelming success of his Summer 2007 continuing education teacher workshop, in which he introduced the curriculum to classroom teachers, he will be offering the workshop again this summer, from July 14th through 18th, at NESCent's facility in Durham.  For more information, click here.

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NESCent Minority Outreach

NESCent and Harvard Collaborate to Increase Undegraduate Diversity at SSE 2008
For the last five years, Dr. Scott Edwards (Harvard University evolutionary biologist and member of NESCent’s Senior Advisory Board) has worked to increase undergraduate diversity by sponsoring an NSF-funded travel award program to bring undergraduate students (with a particular emphasis on underrepresented groups) to the annual meeting of the Society for the Study of Evolution/Society of Systematic Biologists (SSE/SSB). Once there, the students attend scientific presentations, receive mentoring from evolutionary biologists, participate in career development workshops, present their own research in a special poster session and attend social functions. The goal is to excite undergraduates about performing research and pursuing graduate degrees and careers in evolutionary biology, and to increase diversity in the field. At this year’s SSE/SSB meeting, which will be held in Minneapolis, MN from June 20th to 24th, NESCent will be teaming up with Dr. Edwards by providing funds to increase the number of students that can attend. NESCent scientists and education/outreach staff will also participate by acting as mentors and organizing/delivering career development workshops for the undergraduates. For more information, including information on how to apply, click here.

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