The iPlant Collaborative - New Phytologist · The iPlant Collaborative: ... computer, information...
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The iPlant Collaborative: A Cyberinfrastructure-Centered Community of Plant and Computing Scientists Steve Goff University of Arizona New Phytologist Symposium Sept 18, 2008 www.iplantcollaborative.org
Transcript of The iPlant Collaborative - New Phytologist · The iPlant Collaborative: ... computer, information...
The iPlant Collaborative: A Cyberinfrastructure-Centered
Community of Plant and Computing Scientists
Steve GoffUniversity of ArizonaNew Phytologist SymposiumSept 18, 2008
www.iplantcollaborative.org
The Origin: NSF’s Plant Science Cyberinfrastructure
Collaborative (PSCIC) Program
PSCIC Goals: “to create a new type of organization - a cyberinfrastructure collaborative for plant science” “to enable new conceptual advances through integrative, computational thinking”
“to address an evolving array of grand challenge questions in plant science: the driving force and organizing principles for the collaborative”
www.iplantcollaborative.org
What is Cyberinfrastructure?
Infrastructure for a knowledge economy
Infrastructure - roads, power grids, telephone systems, bridges, rail lines, etc., required for an industrial economy
Cyberinfrastructure - infrastructure based upon distributed computer, information and communication technology, required for a knowledge economy
• Also called “e-Science”
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Cyberinfrastructure ComponentsDistributed computingMultiple teraflop computing systemsMultiple petabyte data storesHighly distributed small processorsVery high capacity networksFlexible data integration and analysis software
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CI is a Challenge for BiologyData in many distributed databasesNeed to analyze data independent of db’sIncompatibility of database schemasVariable quality of dataTrend toward collaborative networksMany different locations generating dataMany different formats of similar dataInteroperability, Usability, Sustainability
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Scientific Cyberinfrastructure ExamplesGEON – Distributed Geoscience Cyberinfrastructure (http://www.geongrid.org/)
National Virtual Observatory – Astronomy (http://www.us-vo.org/)
NEES – Network for Earthquake Engineering & Simulation (http://www.nsf.gov/news/special_reports/nees/about.jsp)
Cactus – Astrophysics (http://www.cactuscode.org)
nanoHub? – Nanotechnology (http://www.nanohub.org/)
Biological Cyberinfrastructure in DevelopmentBeeSpace – Integrative Biology (http://www.beespace.uiuc.edu/)
NESCent – National Evolutionary Synthesis Center (http://www.nescent.org/index.php)
NCEAS – National Center for Ecological Analysis & Synthesis (http://www.nceas.ucsb.edu/)
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Single national collaborative funded by NSF (Emerging Frontiers): $50M for 5 years, with opportunity to renew for additional 5 years
•Led by University of Arizona (BIO5 Institute)•Partners:
•Cold Spring Harbor Laboratories•Arizona State University•Purdue University•University of North Carolina, Wilmington
•Community-appointed Board of Directors•Chair: Robert Last, Michigan State University
The iPlant Collaborative
Grand Challenge Identification ProcessBuilt on Successful Models & Existing Tools
(e.g., NCEAS, NESCent)
Phase I: Community Selects Board of Directors Phase II: Kick-off ConferencePhase III: Grand Challenge WorkshopsPhase IV: Grand Challenge Teams Form
GC Projects Proposed; Prioritized by BoD
Phase V: iPC & GC Teams Develop Discovery Environments in Collaboration
Com
mun
ityE
ducation, Training,and O
utreach
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Grand ChallengeTeams & Projects
DiscoveryEnvironments
CyberinfrastructureSolutions
NewKnowledge
Community-Driven Workshops
New Questions
The Grand Challenge
Cycle
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GC Identification ProcessProgress to Date
Board of Directors Selected by the Nominating Committee, Jan - Feb, 2008
Rob Last (Michigan State) - Chair of BoDKick-off Conference Held April 7-9 at CSHL
200 Participants from Plant & Computing SciencesNine Grand Challenge Workshops Proposed
BoD recommended 4-6 workshops July 9Five Workshops Scheduled for Fall, 2008Dir., Cyberinfrastructure Development hired (Rick Blevins)
Com
mun
ityE
ducation, Training,and O
utreach
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Phase III: Focused Grand Challenge Symposia (~40 participants each)
Self-forming groups propose GC symposia on specific GC areasRetreat-like workshops at Biosphere 2 or Banbury Conf CtrBoD evaluates, prioritizes and recommends Organizers summarize outcomes
Grand challenges describedResearch/data requirementsCISE requirements
May lead to Grand Challenge Team/Discovery Environment proposal(s)
2008 Grand Challenge Workshops
Sep 30 - Oct 3“Mechanistic Basis of Plant Adaptation”
• David Salt (Purdue), William Beavis, Justin Borevitz, Edward Buckler, Susan McCouch, John Willis
Sep 30 - Oct 3“Impacts of Climate Change on Plant Productivity: Prediction of Phenotype from Genotype; Data Integration Across Scales”
• Ruth Grene (Virginia Tech), Melanie Correll, T.M Murali, Stephen Welch, Jeffery White, & Pamela Ronald
2008 Grand Challenge WorkshopsNov 7-10
“Developing common models for molecular mechanisms, crop physiology, and ecological studies: rhythms, stress challenges and growth opportunities”
• Stacey Harmer (UC Davis), Katherine Denby, David Wild, Cynthia Weinig
Nov 19-23“Assembling the Tree of Life to Enable the Plant Sciences”
• Michael Donoghue (Yale), Mike Sanderson, Pam Soltis, Doug Soltis, Val Tannen, & Todd Vision
2008 Grand Challenge WorkshopsDec 15-18
“Computational Morphodynamics of Plants”• Eric Mjolsness (UC Irvine), Elliot Meyerowitz, Philip Benfey,
Edgar Spalding, B.S. Manjunath, Christophe Godin
To be held at Biosphere 2, Oracle, Arizona~40 participants, plus iPC, BoD, NSF observersRemote participation; local wireless internetContact organizers or Steve GoffDetails at www.iplantcollaborative.org
Grand Challenge Project Proposals
Workshop not required
RFP to be available mid-September
Target date: February 1, 2009
Board will meet early March, 2009, to recommend GC projects for Discovery Environment development
Proto-Grand Challenge Projects
The Board of Directors also recommended that iPC staff engage two teams prior to workshops based on their apparent maturity and readiness
However, no commitment to full projects: project proposals still required
• Computational Morphodynamics of Plants
• Assembling the Tree of Life to Enable the Plant Sciences
Discovery EnvironmentsOnline environments for sharing ideas, data, algorithms and models (“Web 2.0”)
Allow researchers to develop protocols, perform analyses, discuss results, publish findings and reach out to students and the lay community
Designed with, and in service to, GC teamsPrimary characteristics
Mashups enable distributed, integrative research Editability gives communities ownership of contentOpen Source infrastructure widens the community & provides sustainability
How DEs are CreatedDesigned by iPC staff to meet the needs of community Grand Challenge Teams.
Prototypes by Integrated Solutions Team • Professional software developers, faculty, postdocs & students
Production quality software by Core Infrastructure Team
DEs are open source Engage outside software development communityDEs live on indefinitely
Progressive Decentralization
Centralized core services will gradually become distributed - and eventually, will be fully absorbed by the community
The iPC will encompass the broadest possible community
Open source philosophy
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Community Building: Inherent to iPC Design and Processes
Grand Challenge prioritiesDriven by the Research Community
Grand Challenge TeamsSelf-forming from the community
Discovery Environments: designed to involve a broad community
Researchers from many disciplinesUniversity & college studentsK-12 Citizen science
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SummaryPlant Science is rapidly evolvingData generated faster than exponentialComputational thinking & tools are criticalCyberinfrastructure enables these toolsCollaborations & teamwork are essentialMany external drivers demand action now
Population change & Westernization of diets & lifestylesAvailability & sustainability of agricultural landsWater & fertilizer availability, costs, & consequencesClimate change & environmental factors
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AcknowledgementsUniversity of ArizonaRich JorgensenMartha NarroRick BlevinsSudha RamGreg AndrewsSue BrownVicki ChandlerNirav MerchantSteve RounsleyKobus BarnardTravis HuxmanJohn HartmanRamin Yadegari
Cold Spring Harbor LaboratoryLincoln SteinMatt VaughnDoreen WareDave MicklosRob MartienssenArizona State UniversityDan StanzionePurdue University Rebecca DoergeUniversity of North Carolina-WilmingtonAnn StapletonEast Main Educational ConsultingBarbara Heath
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Contact [email protected] for more information
