The iPlant Leaflet 09-04

Salutations from the iPlant Collaborative! This issue highlights the Gene Annotation Workshop held in St. Louis this summer, the progress of the inaugural iPlant Action Team (iPAT), and welcomes new members of iPlant's Board of Directors. Please watch your inbox for our next newsletter later this Fall, which will focus on the Genotype-to-Phenotype Grand Challenge Team project and will showcase some new Fall "color" for iPlant!

Workshop Report: iPlant's "Genomics in Education: Gene Annotation and Comparison"

By Martha Narro, iPlant Director of Education, Outreach, and Training, narro@iplantcollaborative.org

Conceived and lead by Dave Micklos with community members Sue Wessler, Sarah Elgin, and Steve Slater, iPlant's "Genomics in Education: Gene Annotation and Comparison" workshop brought together 44 participants from genomics research-education and bioinformatics and computer science to discuss integrating computational tools and thinking into college courses.

The workshop, held at Washington University in St. Louis, MO on June 16th - 19th, was designed to build community consensus about targets for future software development and best practices needed to make gene annotation and comparison broadly useful in undergraduate biology education. (Click here to see the workshop's agenda). There were workshop sessions on bioinformatics and visualization tools, integrating bioinformatics with bench science, integrating research experiences into courses, unmet needs in computational infrastructure, the role of gene annotation/comparison in iPlant Grand Challenge projects, and strategies for future collaboration.

The workshop provided a wealth of information and opportunities to refine iPlant's Genomics in Education project. The gene annotation and comparison workflow plan was revised to provide more support for comparative genomic analyses and added support for short-read DNA analysis from next generation sequencing and gene expression data. Additionally, workshop discussions generated a set of education projects to serve as initial test cases for the analysis tools. These projects focus on chloroplast evolution, maize genomics and genetics, and phenology of a common plant.

At the workshop, links between the Genomics in Education effort and iPlant's Grand Challenge projects became clear. Specifically, student sequencing and annotation of chloroplast rbcL genes was identified as an experimental focus that would benefit the iPToL Grand Challenge project, and a citizen science project to connect phenological data on flowering time to genetics data may support the Genotype-to-Phenotype Grand Challenge project.

Created By: Uwe Hilgert, Cornel Ghiban, Scott Cain, Zhenyuan Lu, Dave Micklos (CSHL)

As iPlant's EOT Director, I was pleased that the workshop stimulated thought and discussion far beyond Genomics Education. The tremendous synergy between education and research was evident in many of the presentations, a testament to the faculty who teach research-focused courses and to the Howard Hughes Medical Institute, which has had the foresight to champion and support such educational endeavors. One exciting and completely unexpected outcome was that the presentations and discussions helped Steve Welch (lead on the Genotype-to-Phenotype Grand Challenge project) to realize how important it was for iPlant's cyberinfrastructure to focus on enabling users to visualize information and relationships among data.

For a detailed listing of the iPlant Gene Annotation and Comparison Workflow click here for project objectives and here for potential projects.

iPAT to Focus on Genomics Data Analysis Tools

By Ann Stapleton, iPlant Faculty Advisor, stapletona@iplantcollaborative.org

The inaugural iPlant Action Team (iPAT), Min He and Judith Brusslan of California State University-Long Beach (CSULB), have joined forces to complete an intensive collaborative project in tool development for genomics data analysis. He, a computer scientist, and Brusslan, a plant biologist, are interested in developing tools for analysis of genomic data, and in teaching at the junction of these disciplines. Ann Stapleton of the iPlant Collaborative visited He and Brusslan to provide an initial day-long consultation to help them develop a common vocabulary and a project plan. The project plan allows He and Brusslan to further develop their computational savvy and biological knowledge, with test data analyses and refinement of R/BioConductor tools for genomic data. The team's computational tools are projected to become part of the Discovery Environment that iPlant will develop for the Genotype-to-Phenotype Grand Challenge.

Brusslan and He's iPAT collaboration has had the intended 'ripple effect', with their future plans including team-teaching a bioinformatics class as CSULB and facilitating formation of a new iPAT at CSULB or nearby, as part of the "each one, teach one" philosophy behind the iPAT program.

For more information about how you can participate in iPlant's Action Team program, contact Ann Stapleton at stapletona@iplantcollaborative.org or Tina Lee at: tinal@iplantcollaborative.org

Welcome New iPlant Board of Directors Members!

By Vicki Bryan, Special Assistant to the Director, vbryan@iplantcollaborative.org

iPlant works closely with its community-representative Board of Directors (BoD) on major decisions for the allocation of iPlant resources to specific Grand Challenge Projects. A "bootstrapping" process, in which a Nominating Committee (assembled by the PI with NSF oversight), is used to select the Board of Directors. One-third of the Board will be 'refreshed' every year (beginning summer, 2009) and replaced by individuals selected by the Nominating Committee (click here for a list of Nominating Committee members). Listed below are iPlant's current Board members and their respective areas of expertise.

Computational and Mathematical Biology; Bioinformatics

• Reka Albert, Pennsylvania State University
  

• Rodrigo Gutierrez, Pontificia Universidad Catolica de Chile
  

• Richard Jefferson

• David Rand, Warwick Systems Biology & Mathematics Institute
  

Computing Infrastructure

• Amy Apon, University of Arkansas

• Tom Finholt, University of Michigan

• Al Hevner, University of South Florida

• Gwen Jacobs, Montana State University - Chair

• Kenneth Klingenstein, University of Colorado, Boulder/EDUCAUSE

• Ralph Roskies, University of Pittsburgh

Board Member, Amy Apon

Board Member, Loren Rieseberg

Ecology, Evolutionary, and Organismal Biology

• Vivian Irish, Yale University

• Russell K. Monson, University of Colorado, Boulder

• Muriel E. Poston, Skidmore College

• Loren Rieseberg, University of British Columbia

• Daniel Zamir, The Hebrew University of Jerusalem

Molecular, Cellular and Developmental Biology

• Jim Birchler, University of Missouri, Columbia

• Stacey Harmer, University of California, Davis

• Marta Laskowski, Oberlin College

• Rob Last, Michigan State University - Associate Chair

• Hei Leung, International Rice Research Institute (IRRI)

• Jean-Philippe Vielle-Calzada, National Laboratory of Genomics for Biodiversity (Langebio)

Education, Outreach and Training

• Susan Singer, Carleton College - Chair, Education, Outreach and Training Advisory Committee

NABT Booth Space Available

The iPlant Collaborative will host a booth at the National Association of Biology Teachers (NABT) Conference, Denver, CO, Nov. 11 - 14, 2009. We have space for a limited number of additional Plant Biology Educators to share the iPlant booth, at no cost, to distribute materials and meet with people. Priority will be given to educators who work with iPlant Grand Challenge team members or who have attended iPlant workshops. For details, please contact iPlant's K-12 Administrator, Lisa Howells,lhowells@iplantcollaborative.org

Studying iPlant: The Role of An Outside Evaluator

By Barbara Heath, Principal, East Main Educational Consulting, bheath@emeconline.com

East Main Educational Consulting (EMEC) has been contracted as the external evaluation team responsible for conducting formative and summative evaluation activities for the iPlant Collaborative project. The evaluation team, led by Dr. Barbara Heath, has been working closely with project members since the pre-proposal stage. EMEC's role is to (1) track the progress of the project in relation to its stated goals and objectives through various data collection avenues, and (2) provide feedback and recommendations to iPlant's executive team. Our data collection and tracking methodologies include surveys, interviews, and document review, which we summarize in phone calls, interim memos, post-survey reports, and annual formative reports. The information we provide is occasionally disseminated through the iPlant Collaborative website and in the future, through The Leaflet newsletter.

To understand the development of the iPlant Collaborative and the community that forms around it, we launched a community-oriented survey (July 2009) in collaboration with Dr. Susan Brown, who leads iPlant's social science research efforts. We would like to thank those who already responded and invite anyone who has not done so to take a few minutes to contribute to the evaluation of the iPlant Collaborative. Please click here to take the survey.

In addition to tracking the iPlant community formation, EMEC also studies how the project is being managed and implemented. Data from multiple sources is analyzed and used to determine project successes and shortfalls. This is done by comparing project progress to stated goals and outcomes. In June 2009, we deployed an internal Social Network Analysis survey in collaboration with Dr. Brown to gauge the depth of interaction among the internal iPlant Collaborative project staff and faculty. Interviews are scheduled periodically with faculty and staff, as well as with the Board of Directors, to get first-hand accounts from those actively involved in iPlant. Also, review of project documents, e.g., email, meeting minutes, reports, and presentations, helps us track progress of the project and provides a full-project perspective.

EMEC will continue to evaluate the iPlant project, which will provide the project team with information to disseminate to the community. We look forward to learning more about the development of the interdisciplinary community we refer to as iPlant and hope to become collaborators with you, the community, as well.

Please visit http://survey.emeconline.com/survey3/TakeSurvey.aspx?SurveyID=86KI572 to take the online survey.

NSF Genome Research Awardees Meeting
Washington, D.C. (tentative) September 10th - 11th, 2009. Rich Jorgensen (PI) and Dan Stanzione (Co-PI) to present iPlant's Vision for Cyberinfrastructure for the Plant Sciences (note: this meeting is typically by invitation only to awardees).

Grace Hopper Conference: Celebrating Women in Computing
Tucson, AZ; Sept. 30, 2009. Martha Narro to present at the General Poster Session: Computing Opportunities in Plant Science.

Internet 2 Member Meeting
San Antonio, TX, October 5 - 8, 2009. Gwen Jacobs, Chair, iPlant Board
of Directors, to present in Plenary Session.

9th International Plant Molecular Biology Congress
St. Louis, MO, October 25th - 30th, 2009. Steve Goff to present on iPlant's Grand Challenge Projects.

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.

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