iPlant Collaborative Kickoff Conference, April 7-9, 2008 Meeting report, April 10, 2008 (2 p.m., CBCB conference room)

General information and important URLs iPlant Collaborative iplantcollaborative.org Community wiki page (meeting wiki) wiki.iplantcollaborative.org/farm/mtg042008/index.php/Main_Page Grand Challenge Workshop draft RFP ~/public/index.php/RFP_For_Grand_Challenge_Workshops My own meeting summary (this PowerPoint presentation) clfs.umd.edu/labs/mount/iPC-mtg08d.ppt clfs.umd.edu/labs/mount/iPC-mtg08d.ppt

Management Team (Rich Jorgensen, Greg Andrews, Sudha Ram, Lincoln Stein, Nirav Merchant) Community (everyone, plant scientists) Grand Challenge Teams (Plant Science Community) Integrated Solutions teams (iPC staff) Computational Infrastructure (iPC staff) Grand Challenges Foundational Tools Discovery environments Cyberinftrastructure Key Concepts

Process Workshop Proposal Workshop Grand Challenge Proposal Grand Challenge Project Permanent Cyber- infrastructure 5-6 workshops Sept to Dec projects more each year (6 mos.cycle)

The iPC grand challenge project will produce discovery environments that support grand challenges. Teams Grand Challenge Team Integrated Solutions Team Computational Infrastructure Team 1. GC has idea 2. I S team responds 3. I S team assigns liasons 4. prototype DE 5. production level discovery environment, cyberinfrastructure, “hardening”

A Grand Challenge is - compelling - tractable The Grand Challenge Team will work with the iPC to develop discovery environments, each of which will be a cyberinfrastructure within which the GC team and the community will address and solve the grand challenge. Grand Challenges and Discovery Environments

Examples of Grand Challenges: Genotype to phenotype Single cell to developed plant “How you get from a fertilized egg to a mature organism that is suitably responsive to its environment” Effect of global warming on plant diversity Getting K-12 students interested in plants Grand Challenges

- evaluates the Grand Challenge Proposals - represents the community Link to iPC Board of DirectorsiPC Board of Directors Board of Directors

The product of a Grand Challenge Project is a Discovery Environment - mashups enable distributed integrated work (example)example (discussion of the relevant coordinate system(s), such as nodes of the tree of life; geospatial; homolgous locations on a plant in 5 dimensions: x, y, z, developmental and “real” time). - editable (everyone has ownership) - aggressively open source Each GC team gets (from the integrated solutions team) - a public web site - wiki, mailing lists, discussion forum - web / video conferencing services Grand Challenge

The iPC grand challenge project will not get any money to produce new data. There will be no support for lab equipment or supplies, but there will be support for people working in labs. Foundational tools were much discussed. The project is very much about producing foundational tools, but there is no direct money for foundational tools, except for the first year (because of the startup gap). This is not for new data!

Because the first grand challenge proposals would not be funded until after the end of the first year, there is room for expedited review, by the Board of Directors, of grand challenges and foundational tools. Foundational tools funded in the first year should be: “Grand Challenge-agnostic” or “Grand Challenge-ecumenical” The key concern is that all tools be developed in response to grand challenge questions The gap

NSF has imposed a mandate that everything must be in the service of grand challenge questions. Question: If all projects are in response to grand challenge questions, which are biological, then is there any role for computational people (other than the iPC staff)? Answer: They would have to join Grand Challenge teams. (Lincoln: anyone can attend the weekly teleconference) (The GC Workshop mechanism could be used to fund workshops on topics other than grand challenges) What about computational people?

Francine Berman, Director, San Diego Supercomputer Center, Opportunities and Challenges in Cyberinfrastructure Development Atkins Report NSF advisory panel (“Report of the National Science Foundation Blue-Ribbon Advisory Panel on Cyberinfrastructure”)Report of the National Science Foundation Blue-Ribbon Advisory Panel on Cyberinfrastructure Cyberinfrastructure is an enabling environment that is application driven. In CI, usability trumps innovation (vs. CS, where innovation trumps usability) Everyone must agree on how success will be measured Discussion of permanent professional staff.

Lee Allison, State Geologist & Director, Arizona Geological Survey Building a Cyberinfrastructure Coalition – the Geoscience Information Network Example of GEONGEON - distributed - interoperable - ownership of data is maintained The product is protocols and standards, anyone can participate (model of the world wide web) He showed a great video on herding cats.video on herding cats

Elliott Meyerowitz, Biology, CalTech Defining solvable grand challenges in plant growth and development computational morphogenesis - image processing - develpmental models - mechanism Eric Mjolsness, Computer Science, UC Irvine Challenges in computational modeling of growth and development - causal models - reusable pieces of modeling Cellerator

John Willis, Duke University Grand Challenges in Ecology, Evolution, Biodiversity and Organismic Biology Plant Systems 2020 Working Report NRC “Achievement of the Natural Plant Genome Initiative and New Horizons in Plant Biology ‘Frontiers in Evolutionary Biology” 2005 report to NSF Genotype to phenotype (G2P) list of phenotypes: flower size, flowering, salt tolerance, etc…

Dennis Shasha, Computer Science, NYU Dealing with Scale in Visualization and Machine Learning Presented by Manpreeti Katari For each grand challenge: straw (-omics data) to gold (robust conclusions)

Education, Training and Outreach Suzanne Westbrook on Computational Thinking (following Jeanette Wing) David Miklos (Cold Spring Harbor DNA Learning Center) Cyberinfrastructure for EOT Susan Singer, Carlton College Integrating research with EOT “EOT will be part of every Grand Challenge.”

Richard Jefferson, CEO, CAMBIA BiOS InitiativeCAMBIA Vision and Strategy: Structuring grand challenges in plant science to help solve the grand challenges of society. An amusing philosophical talk. This project is about producing products and services, not the software itself. Don’t make the mistake of monetizing the software. Scientists do not solve problems, they answer questions, some of which are important for the solution to problems. If you like solving problems, getting into the patent field for the purpose of subverting it for the public good is a lot of fun.

Lincoln Stein Bioinformatics, Cold Spring Harbor Laboratory; iPlant’s Integrated Solutions Team and community Grand Challenge Teams: a collaboration to build prototype cyberinfrastructures (“Discovery Environments”) to solve the community's most compelling grand challenges.

Break-out groups on grand challenges What is a grand challenge: examples. Genotype to Phenotype How has the auxin signaling system evolved? How do plant hormones work?

Self-forming group (Wed. afternoon) Predicting the Plant A group met to discuss the possibility of grand challenge questions related to evolution, development and comparative genomics. After some wide-ranging discussion the group showed a surprising degree of consensus and excitement around the idea of using available data (primarily genomic and expression) to develop a framework that could be used to predict plant phenotypes (development and environmental responses and secondary metabolites) from raw high throughput genome sequence. Foundational tools would allow mapping orthologous genes and their expression patterns across defined nodes in the tree of plant life.

General information and important URLs iPlant Collaborative iplantcollaborative.org Community wiki page (meeting wiki) wiki.iplantcollaborative.org/farm/mtg042008/index.php/Main_Page Grand Challenge Workshop draft RFP ~/public/index.php/RFP_For_Grand_Challenge_Workshops My own meeting summary (this PowerPoint presentation) clfs.umd.edu/labs/mount/iPC-mtg08d.ppt clfs.umd.edu/labs/mount/iPC-mtg08d.ppt