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Greetings from the iPlant Collaborative! If you've been wondering what iPlant has been up to since hosting over 300 plant and computer scientists, researchers, and educators at Grand Challenge Workshops last fall, we invite you to read on for more details.
iPlant Moving Forward on Grand Challenge Collaborations
The iPlant Collaborative's independently-chosen Board of Directors met in mid-March to review six Grand Challenge Collaboration requests. The Board's recommendations are now being translated into an implementation plan for Grand Challenge Collaboration Projects.
iPlant's high-level plan is to build a single plant science cyberinfrastructure designed to address unique Grand Challenge problems in plant science. Evolutionary relationships between plants were identified as a central theme to which physiological and molecular traits, as well as ecological relationships, could be linked. This would enable plant science researchers to address Grand Challenge problems by bridging the existing gap between genotypic information (genome sequence, genes, and chromosomal markers) and phenotypic information (traits and physiology) in the context of evolutionary and ecological relationships. This is a huge effort that will require extensive collaboration between experts in many disparate fields.
To achieve this high-level vision, iPlant will first focus its efforts on creating cyberinfrastructure to support tools to identify and display the evolutionary relationships between the half million green plant species. The proposal made by the Plant Phylogenetics group1was recommended as a first iPlant Collaborative Project to provide the evolutionary-relationships platform. As a first step, a Grand Challenge Team will be formed, comprising members of the Phylogenetics Grand Challenge Proposal Team along with other research community members with high interest in the project, available time to devote to the collaborative effort, and plant science or computational science expertise, and iPlant staff. Dr. Michael Sanderson will lead this multi-institutional Grand Challenge project and serve as the local contact with iPlant staff at the University of Arizona. Other Phylogenetics Grand Challenge Team leads include Michael Donoghue (Yale University), Pam Soltis and Doug Soltis (University of Florida), Alexis Stamatakis (Technische Universität München),Val Tannen (University of Pennsylvania)and Todd Vision (University of North Carolina).
The objectives of this initial iPlant Grand Challenge Collaborative Project are to generate cyberinfrastructure to facilitate creation of large phylogenetic trees of green plant species, visualize these phylogenetic trees, and begin to plan the linkage of various data types to specific species in these phylogenetic trees. Members of the plant science and computational sciences research communities will be recruited to serve as collaborative members of the Phylogenetics Grand Challenge Team. Once this Phylogenetics Team has coalesced, it will then meet to begin designing the detailed project plan to deliver the Phylogenetics cyberinfrastructure.
Following initiation of the Phylogenetics cyberinfrastructure project, a second iPlant effort will be planned to help increase the understanding of how genotypes influence phenotypes. Several of the Grand Challenge proposals submitted to iPlant described the need to integrate various data types, create interoperable data analysis tools, and drive standards on interoperability. The Board of Directors recognized understanding "Genotype-to-Phenotype" relationships as a recurring theme in several of the proposals that could help drive the design of a broadly useful cyberinfrastructure for the research communities. The proposal on the Phenology of Flowering1 was considered representative of the cyberinfrastructure needed to address many major issues in plant biology (climate change, development, growth efficiency, adaptation to the environment, etc.). The Board of Directors recommended engagement of community members through this proposing team as a route to creating cyberinfrastructure that supports large-scale data analysis and bridges the Genotype-to-Phenotype gap within the context of evolutionary relationships (as described for the Phylogenetics cyberinfrastructure efforts above). Interested members of the community will be encouraged to work with the Genotype-to-Phenotype Team in designing the project plan to ensure effective coordination with later Grand Challenge projects.
Finally, the Board of Directors also recommended that iPlant management consider reorganizing to streamline decision-making and align iPlant research efforts to the cyberinfrastructure development goals. The Board commended the iPlant team on achieving the first year goals of the project -to stimulate community participation and bring together various research group experts to propose Grand Challenge projects. With iPlant now transitioning to the design and creation of specific cyberinfrastructure components, the management was reorganized to reflect this change in emphasis. Rich Jorgensen will remain iPlant's PI and Dan Stanzione will become the sole co-PI of iPlant. The four previous co-PIs have graciously stepped-down from their co-PI roles to become Senior Project Personnel. Dan, currently Head of HPC at Arizona State University, will move to University of Texas at Austin in June to become Deputy Director of the Texas Advanced Computing Center. In his new role with iPlant, Dan will spend at least 35% of his time overseeing the cyberinfrastructure design and development aspects of the iPlant Grand Challenge projects. This reorganization of iPlant management reflects the enhanced focus on cyberinfrastructure development and enables further connection between iPlant and members of the cyberinfrastructure community.
1See Grand Challenge Collaborative Project Proposals posted on the iPlant Collaborative website,http://www.iplantcollaborative.org
Teaching Teachers to "Think Computationally"
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Agent-based model of the reaction between hydrogen and iodine developed using the AgentSheets application. This model will be used to teach concepts relating to chemical kinetics and equilibrium to high school students.
Photo credit: C. Kinney
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As the amount of data and the use of computers in the biological sciences explodes, researchers and educators must now "think computationally,"that is, incorporate computation at all levels of practice and teaching. To address this need, a new computational biology course offered this spring at Arizona State University (ASU) has attracted six secondary school teachers eager to prepare their students to face this level of rigor. The course, which meets both in the classroom and online, trains secondary instructors to develop curricula that will enable high school students - the next generation of scientists - to master the computational thinking required for the study of modern biology.
According to Professor and iPlant Collaborative's co-PI Dan Stanzione, the goal of the course is to understand "the appropriate role of computing in modeling, simulation, and data analysis [that is] essential to the practice of modern biology." Co-teaching the course with Stanzione are Jeff Krause from Shodor, and Scott Menor, assistant research scientist at ASU. The course is jointly sponsored by the iPlant Collaborative, ASU, University of Arizona, along with Shodor, TGen, and ASU's Fulton High Performance Computing Initiative (HPCI).
Deadline Approaching for iPlant Action Teams (iPATs) Program
To help the iPlant Collaborative identify successful innovative approaches and common vocabulary that will be useful in educating the next generation of plant and computer scientists in computational thinking, iPlant seeks participants for the iPlant Action Teams (iPATs) program (http://www.iplantcollaborative.org/communities/researchers/ipat-program).
An iPAT is a two-person team, comprising a computational faculty member and a plant biology faculty member, who will solve a mini-project in plant computational biology. The goal of the iPAT program is to develop models for successful and productive collaborations and the common vocabulary that facilitates such collaborations. A panel of iPlant core staff will select several iPAT teams, then visit each team at their home university to consult on and ensure software development support for solving their mini-project. Each team will then be responsible for locating and supporting a new mini-project team, in an each-one-teach-one model.
If you'd like to participate in an iPAT or would like more information, click on the link above or contact Ann Stapleton at
stapletona@uncw.edu by the preferred application deadline of April 10, 2009.
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Upcoming iPlant Activities and Events
Computational Biology for Biology Educators Workshop
University of California at Merced, CA, June 7 - 13, 2009. This 7-day workshop introduces college faculty to a variety of resources to help students acquire the computational thinking, modeling, and quantitative analysis skills that are now essential to the practice of modern biology. Hands-on sessions with software for building and running dynamic models, finding sequence motifs, inferring phylogeny, and predicting structure will be coupled with pedagogy and examples of integration into the biology classroom. The workshop is a partnership among the iPlant Collaborative, Shodor, Supercomputing and The University of California, Merced. For more information and to register online for the workshop, click here.
For questions, contact Martha Narro, narro@iplantcollaborative.org .
iPlant Summer Teacher Research Fellowships '09
For a second year, iPlant Education, Outreach, and Training (EOT)invited high school teachers from Arizona and around the country to apply for Summer Teacher Research Fellowships. iPlant Teacher Fellows participate in cutting-edge plant science research with a computational focus at University of Arizona and attend weekly seminars on computational thinking. Teachers then draw from these experiences to develop lessons and modules to take back to their classrooms. A graduate fellow also offers continuing support during the school year. Beginning next fall, some teachers will also be facilitating teacher workshops to disseminate content developed during the fellowship.Although the application deadline for Summer Teacher Research Fellowships '09 has passed, contact iPlant's K-12 Administrator, Lisa Howells (lhowells@iplantcollaborative.org), for more information or to be included in future notifications about this program.
The iPlant Collaborative Workshop on "Genomics in Education: Gene Annotation and Comparison
Washington University, St. Louis, MO, June 16 - 19, 2009. The workshop will focus on gene annotation and comparison in educational settings. This invitational workshop is full. The workshop program will be posted on the iPlant website soon.
Upcoming Conferences Where You Can Find the iPlant Collaborative
National Council of Teachers of Math
April 22-25, 2009, Washington, D.C. (L. Howells)
European Life Sciences Infrastructure for Biological Information (ELIXIR)
May 19-20, 2009, Copenhagen, Denmark (S. Goff)
BeeSpace Annual Workshop
May 22-23, 2009, University of Illinois, Urbana-Champaign (R. Jorgensen and S. Ram)
Society for Molecular Biology and Evolution
June 3 - 7, 2009, Iowa City, IA, "Database Tools for Evolutionary Genomics Workshop" (S. McKay)
Evolution 2009
June 12 - 16, 2009, Moscow, ID (S. McKay)
Computer Science Teachers Association
June 27, 2009, Washington, D.C. (L. Howells)
National Education Computing Conference
June 28 - July 1, 2009, Washington, D.C. (L. Howells)
Generic Model Organism Database Summer School
July 13 - 16, 2009, NESCent, Durham, NC (S. McKay)
Get "Linked in" to the iPlant Collaborative
We invite you to join the professional networking group that iPlant has created on Linked in: http://www.linkedin.com/groups?gid=1887479. We will use this group to announce upcoming iPlant events, conduct community discussions, and provide a forum for the community to share discoveries, resources, and ideas as we move forward together to build cyberinfrastructure to help solve Grand Challenge questions.
We value your feedback. To subscribe, leave a comment, or suggest a topic for The iPlant Leaflet,click here.
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