Newsletter Vol. 1 No. 2 October, 2007
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Banner Photo Credits (left to right): John Clamp, Zoothamnium niveum; Owen McMillan, Heliconius ; Sally Otto, Sula nebouxii; Amy Zanne, fern.
NESCent has just completed its third year of existence, and it has been a very productive and exciting year. We have hosted over 800 scientists in the past year, participating in a wide variety of meetings, working groups, and courses. NESCent supported scientists have produced over 67 published papers, and our activities have resulted in a large number of new collaborations, grants and initiatives. Many of our past and upcoming activities are detailed in this, our second newsletter.
Deadlines for proposals for our next set of funded activities will be December 1. These include proposals for postdoctoral fellowships, sabbatical scholars, working groups and catalysis meetings. Here I’d like to briefly highlight two programs.
The first program is our targeted sabbatical program. In this program, unlike the regular sabbatical program, where we pay up to half an academic year salary, we will provide full funding for a year’s sabbatical. We are targeting two groups this year. This first is faculty from minority serving institutions. We encourage faculty from these institutions to apply for sabbaticals, which may be a combination of work at NESCent as well as work in collaboration with faculty at one of our associated Universities. A second targeted sabbatical is for distinguished senior scientists who would like to prepare their long-term data collections for preservation and for transformation into a community resource, with the assistance of NESCent's informatics staff. For more information on either program visit our website.
We would also like to encourage people to apply for short term visits to NESCent. The next deadline for these applications is January 1. Short term visits may be for a period of 2 weeks to several months, and we particularly encourage collaborative proposals. More information on this program may be found on our website.
Finally, we welcome Dr. David Swofford, who has jointed NESCent as a Senior Scientist. David's time will be split between NESCent and Duke's Institute of Genome Sciences and Policy. As a NESCent Senior Scientist, he will continue his outstanding work in developing the theory and practical applications of computational approaches to phylogenetic questions, and will collaborate with other scholars on projects that leverage this expertise. More information about David Swoffordis available here.
Awards from the June 15 call for proposals have been made and NESCent is pleased to announce four new working groups and a Sabbatical Scholar. For more information on these and other awards at NESCent, go to Supported Projects.
As a follow-up to the NESCent catalysis meeting on “Evolution in Contemporary Human Populations”, Diddahally Govindaraju, Andrew Clark, Trudy Mackay and Stephen Stearns will be leading the working group “Measuring evolutionary change in modern human populations”. The group will be applying evolutionary analysis tools to the Framingham Heart Study to explore microevolution in this population.
Michael Schwartz and Fred Allendorf will be leading a working group co-sponsored by NESCent and NCEAS on “Genetic Monitoring: Development of tools for conservation and management”. This working group will focus on developing guidelines for and exploring the potential uses of genetic monitoring in conservation.
Samantha Forde and Ivana Gudelj will be leading “Mathematical models, microbes & evolutionary diversification” a working group which will address one of the 125 questions identified by Science – specifically: What determines species diversity?
Kenneth Kozak, Catherine Graham, and Carsten Rahbek will be leading the working group “Montane diversity in space and time” in studying evolutionary factors in biological diversity in montane regions.
George Gilchrist, from the College of William and Mary, will be a Sabbatical Scholar at NESCent starting in Fall 2008. Dr. Gilchrist will be working on the “Evolution of Performance Curves in Seasonal Environments” looking at the effects of changing temperature and photoperiods on population sizes.
The next Call for Proposals is December 1, 2007 and includes Post-doctoral Fellows, Sabbatical Scholars, Working Groups, and Catalysis Meetings. Proposals for the Short-term Visitors Program are due January 1, 2008. For more information, visit the Call for Proposals page.
Slides and handouts from a tutorial presented at the 2007 ISMB meeting by Jason Stajich and Albert Vilella are available on the hackathon wiki site. The tutorial arose from the December 2006 Hackathon at NESCent.
A day-long workshop on “Evolutionary Biology and Ontologies” will be held in Minneapolis, Minnesota on June 20th 2008, in conjunction with the Evolution 2008 conference .The goals of the workshop are to:
- Introduce what ontologies are, how they are built, what makes them useful, and how they can be used to facilitate interdisciplinary collaboration;
- Highlight ways in which ontologies are being used to address problems of interest to evolutionary biologists (e.g. Mabee et al. 2007, Maglia et al. 2007, Midford 2004, Ramirez et al. 2007) and
- Allow for discussion of future research directions among the workshop participants.
Workshop organizers include Paula Mabee (University of South Dakota), Barry Smith (National Center for Biomedical Ontologies and the University at Buffalo), Todd Vision (NESCent and UNC Chapel Hill), and Monte Westerfield (Zebrafish Information Network and the University of Oregon). Confirmed speakers include Melissa Haendel (ZFIN and the University of Oregon), Suzanna Lewis (NCBO and UC Berkeley), Anne Maglia (University of Missouri, Rolla), Chris Mungall (NCBO and the Howard Hughes Medical Institute), and Martin Ramirez (Museo Argentino de Ciencias Naturales). The workshop is sponsored by NESCent and the NCBO through a National Science Foundation grant to Mabee, Vision, and Westerfield (DBI-0641025). For more information click here.
Registration will be open to attendees of the Evolution 2008 conference at no additional cost. Mark your calendars now!
Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M (2007) Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology and Evolution 22, 345-50.
Maglia AM, Leopold JL, Pugener, LA, Gauch S (2007) An anatomical ontology for amphibians. Pacific Symposium on Biocomputing 12: 367-378.
Midford PE (2004) Ontologies for behavior. Bioinformatics 20, 3700-1.
Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J, Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC (2007) Text linking of digital images to phylogenetic data matrices using a morphological ontology. Systematic Biology 56, 283-94.
NESCent will be hosting a hackathon focused on the integration of comparative phylogenetic methods within the R statistical package from December 10th to 14th, 2007.
Comparative phylogenetic methods provide a rich and powerful way to understand the evolution of organismal traits, and the R statistical analysis package has emerged as a popular platform for implementation of these methods (e.g. Paradis 2006). The many individual software development efforts in R and the growing number of users present an opportunity to address the common challenges of data exchange, interoperability, and usability. A hackathon is an event at which a group of programmers who otherwise do not have the opportunity to interact on a routine basis meet to collaboratively develop working code that is of utility to the community as a whole. This hackathon will bring together different groups that have been developing comparative phylogenetic methods in R, or who would like to integrate their methods into, or interface a tool with, the R platform. The organizers are soliciting applications from individuals (including students and postdocs) who would are interested in participating. Travel, accommodation, meal expenses, etc., will be paid by NESCent. For more information, including application details, please visit the hackathon wiki.
Steven Kembel (UC Berkeley), Hilmar Lapp (NESCent), Brian O’Meara (NESCent), Samantha Price (NESCent), Todd Vision (NESCent), and Amy Zanne (NESCent).
Paradis, E (2006) Analysis of Phylogenetics and Evolution with R. Springer.
NESCent served as a mentoring organization in the 2007 Google Summer of Code. In this program, students receive a stipend from Google to spend a summer contributing to any of over 100 distributed open-source programming projects under the mentorship of an experienced programmer. Google sponsored eleven students to work with NESCent and a community of mentors drawn from throughout the evolutionary bioinformatics community. After months of interacting remotely, mentors and students finally met face-to-face at NESCent in mid-August for a highly enjoyable end-of-summer get-together. As the profiles of each project demonstrate, the students put their summers to very good use!
Lars Barquist – Ajax interface for the XRate command-line tool
Mentor: Ian Holmes
This project was aimed at making UNIX bioinformatics applications both more powerful and user-friendly through the development of interactive web interfaces. Using the perl programming language and the dojo dynamic HTML toolkit for client-server communication, we were able to create pages incorporating the functionality of the xrate phylo-grammar interpreter as well as several data visualization tools. In addition we are producing tutorials and documentation on the process of creating these interfaces. It is hoped that these applications will not only be useful in their own right, but serve as examples for bringing command line tools to the internet and a wider audience.
Jason Caravas - Phylogenetic XML <--> Object serialization
Mentor: Rutger Vos
A variety of file formats exist for the purpose of storing information on phylogenetic relationships. Few of these file formats offer a comprehensivescope,beingspecialized to represent only a few of the many types of available data. Fewer still have the ability to adapt to the growing demands researchers are placing upon them as phylogenetic analyses become more complex. We are developing an XML file format called Nexml to meet current demands, emphasizing extensibility and compactness in the design. To accompany the new format, Perl tools for Nexml parsing and serialization have been developed for the Bio::Phylo module.
Mentors: Hilmar Lapp (primary), Weigang Qiu, Bill Piel, Mike Muratet (secondary)
Despite comprising up to 90% of eukaryotic genomes, transposable elements (TEs) remain one of the least understood forms of biological organization. A barrier to current studies of TEs is the lack of a consistent taxonomic classification scheme as well as the lack of a comprehensive study of the evolutionary history of TEs across host genomes. My summer of code project seeks to assist in the study of the evolutionary history of TEs by developing a database system that can be used to store the taxonomic classifications and multiple evolutionary trees that will result from a major cross species study of TE evolution.
Klaas Hartman - Biodiversity Conservation Algorithms and GUI
Mentors: Tobias Thierer (primary), Rutger Vos (secondary)
Conservation organisations are often faced with the problem of having many species that could benefit from conservation but limited funding to allocate to the conservation of these species. This project provides several methods for finding the 'optimal' allocation of a limited budget to individual species such that the future biodiversity is maximised. Biodiversity is measured using phylogenetic diversity which is the length of the phylogenetic tree connecting the species that survive. This project also provides a graphical interface that can be used to easily access these algorithms. Hopefully this will help bridge the gap between the mathematical results/algorithms and conservation managers.
Gregory Jordan – Phyloinformatics Web Tools: PhyloSOAP and PhyloWidget
Mentors: Bill Piel (primary), Hilmar Lapp (secondary)
For my project, I am creating PhyloWidget, a web-based tool for creating, viewing, and editing phylogenetic trees, and PhyloSOAP, a service that makes it easy for scientists to store and retrieve their trees from an online database. Together, these tools will allow researchers to easily create their own repositories of phylogenetic information.
Bohyun Lee – APIs for BioJava
Mentors: Richard Holland
My GSoC project for this summer is to build APIs for BioJava, especially building methods for phylogeny reconstruction. I started with extending previous BioJava methods for NexusTreesBlock (AddTree, GetTree method in TreesBlock.java), and I implemented a new method (GetTreeAsJGraphT in TreesBlock.java) to converting NexusTree object to JGraphT object. Then, I developed some of the basic methods for phylogeny inference like UPGMA and Neighbor-Joining. Also, I am still working on developing the wrapper class for Maximum Parsimony/Maximum Likelihood methods in PHYLIP package. I hope my project to be a significant step for BioJava in terms of its co-operation with JGraphT and PHYLIP.
Mentor: Suzanna Lewis
My project is the oddly named xrateparser. It does not do any actual parsing, but instead simply harnesses xrate for tree generation. My project is a web application which uses Perl scripts to generate either .png or .svg images of trees to be displayed on a webpage. These trees are generated from either raw .tre files (Newick format) or by using special .stk files which are processed by xrate to generate trees.
Michael Nowak – Estimation of divergence time priors from fossil occurrence data
Mentor: Derrick Zwickl
Paleobiologists and molecular biologists and have been asking the same question for many years: How long ago did a group of species share a common ancestor? While paleobiologists employ statistical analyses of the fossil occurrences through time, molecular biologists use “molecular clock” analyses that rely on only a few key fossils for calibration. To date, no method exists for the implementation of fossil occurrence data in molecular clock analyses. In response to this need, we have developed a free software tool that utilizes fossil occurrence data to construct informative priors for implementation in existing Bayesian molecular divergence time software.
Hisanaga Mark Okada – Phylogenetic and Haplotype Displays for GBrowse
Mentor: Lincoln Stein
I have had the privilege of working on the Generic Genome Browser under the mentorship of Lincoln Stein of Cold Spring Harbor Laboratories. The Genome Browser is a powerful tool used to view the multiple levels of detail of an organism's genomic data. The first phase of the project was to aid Lincoln's restructuring of the browser to allow these multiple 'tracks' of data to be rendered asynchronously on different servers to distribute the data processing. The second phase was to create a data track that can display DNA alignment data for multiple target species.
David Suárez Pascal – Multi-language bindings to the C++ NEXUS Class Library
Mentor: Mark Holder
NEXUS is a digital format for phylogenetic data that allows encoding of useful information such as taxa names, trees and characters. With a modular and extensible design, this format provides a common language for bioinformatic tools, enabling easy communication between different applications. The main purpose of this project is to spread the application of the NEXUS format by extending an existing computer library to the scripting languages Perl, Python and Ruby. Given the preeminent role scripting languages have acquired in bioinformatics application development, we think this is an important contribution.
Yi-Hsin Erica Tsai - PhyloGeoViz, a phylogeography visualization tool
Mentor: David Kidd
Ever wanted to plot pie charts on a map? Then PhyloGeoViz is for you. Oftentimes phylogeographic analysis (or the study of a species' migration and population genetic history) starts with just such a simple visualization technique. However, the tools available to draw these figures are inefficient and difficult to use. This project strove to create an easy to use, web-based, pie chart plotter that interfaces with Google Maps and Google Earth. This product can be used not only by evolutionary biologists, but by anyone who has need for geographically placed pie charts.
For links to documentation for each project, and to obtain the software that was produced, please see the Phyloinformatics Summer of Code wiki site. NESCent would like to thank the many individuals who contributed ideas, time and technical expertise to this successful experiment.
Students and mentors from the Google Summer of Code meeting at NESCent.
To promote interest in evolutionary biology research among underrepresented students, NESCent is organizing several activities at the Society for the Advancement of Chicanos and Native Americans in Science (SACNAS) annual conference, in Kansas City, Missouri, October 11-13, 2007. Among the activities are a behind the scenes field trip to the Kansas Natural History Museum, a screening of “A Flock of Dodos” and a panel discussion on “Exploring Careers in Evolution and Ecology”. The goal of these activities is to excite and educate underrepresented students about the fields of evolution and ecology, make them aware of some of the “hot topics” in these fields, and inform them of career opportunities in these fields. These activities are being co-sponsored by the National Center for Ecological Synthesis (NCEAS), the Ecological Society of America (ESA), the Society for the Study of Evolution (SSE) and the American Institute of Biological Sciences (AIBS), with generous financial support from Springer.
The American Institute of Biological Sciences (AIBS) and NESCent co-sponsor an annual evolution symposium at the National Association of Biology Teachers conference. This year’s topic focuses on evolution and human health. Understanding how we have been shaped by evolution can help us understand the modern human condition. Evolutionary biology is making important contributions in the field of human health through studies of the human genome, physiology, lifestyle and interaction with the environment. This symposium focuses on the emerging field of evolutionary medicine which brings together comparative genomics, epidemiology, anthropology and other fields to synthesize a comprehensive view of human health. Symposium speakers will describe how this new work is leading to many exciting medical applications. The symposium speakers will also discuss ethical issues and more general implications of evolutionary research in society.
This year’s symposium will be December 1, in Atlanta. NESCent develops an educational resource CD to accompany the symposium, which will be available on our web site after the symposium. Hard copies are available upon request.
Participants in the Evolution Curriculum for Elementary School Workshop.
Sabbatical Scholar Joe Fail, from Johnson C. Smith University, has developed a comprehensive biology curriculum for elementary grades with a heavy emphasis on evolution. Drawing on his 16 years of teaching experience, Dr. Fail has developed a holistic style which uses “story telling” as a framework for building scientific knowledge. Previously Dr. Fail developed a similar curriculum for ecology. The curriculum starts with chemistry and builds up through biological structure and function, through genetics, evolution and ecology. This program was piloted with a group of 5th graders in Chapel Hill, NC, and 15 North Carolina elementary school teachers participated in a week-long workshop this summer. Dr. Fail hopes to publish his curriculum; meanwhile the materials are available by contacting Joe Fail.
Have you developed a great new lab protocol, program or other educational tool other educators might find useful? Are you looking for collaborators for a broader impact activity? Disseminate your materials and find collaborators at local or national educator’s conferences.
Most states have a science teacher’s association and these conferences can be great places to locate collaborators for broader impact activities. There are several national education conferences you might consider including Society for College Science Teachers (SCST), the Association of College and University Biology Educators (ACUBE), the National Science Teachers Association (NSTA), and the National Association of Biology Teachers (NABT). These conferences move around the country, so take advantage of a nearby event. Check websites for dates and locations. Be aware that presentation abstracts are due very early – a year in advance for NSTA!
Booth presentation at NABT by NESCent staff.