The iPlant Collaborative iPToL Data Assembly Workshop November 21 st, 2009 Steve Goff, Sonya Lowry, Martha Narro, Dan Stanzione University of Arizona, Texas Advanced Computing Center

What is the iPlant Collaborative?? iPlant’s nature: enables new conceptual advances through integrative, computational thinking an organization that enables new conceptual advances through integrative, computational thinking an organization that is by, for, and of the community a service-oriented project, not a research project (creates CI in support of plant science research; but does not perform research outside of prototyping & testing) iPlant’s mission: address an evolving array of plant science grand challenge questionsaddress an evolving array of plant science grand challenge questions to enable the research community to identify the in plant sciences, then to develop & pursue needed CI solutions to enable the research community to identify the major problems in plant sciences, then to develop & pursue needed CI solutions

What is the process for identifying GC questions? Encourage and assist the community in organizing grand challenge workshops, forming grand challenge teams and developing grand challenge ‘white papers’ (‘proposals’) Community-representative Board of Directors (drawn from community nominations) evaluates ‘proposals’ and teams and makes recommendations for priorities iPlant leadership team decides whether & how to implement the Board’s recommendations and assists GC team leads in assessing needs, specifying requirements and designing ‘Discovery Environments’ to serve the team’s and the broader community’s needs

Biological questions will drive cyberinfrastructure design Phylogenetic relationships among species – Building large phylogenetic trees (species and gene) – Understanding Green Plant species relationships – Understanding gene family evolution – Addressing taxonomic problems and concepts – Facilitating understanding of evolution – form & function – Facilitating understanding of evolutionary processes Phenotype-Genotype relationships Slide # 4

Biological questions will drive cyberinfrastructure design Phylogenetic relationships among species Phenotype-Genotype relationships – Sharing, accessing, and integrating datasets – Analysis and extraction of information and patterns (automated phenotyping, imaging, etc) – Identifying complex relationships; networks & systems – Assigning functions to genes, networks & systems – Integration of phenological & ecological data with networks and systems of genes, proteins, etc. – Understanding responses to environmental changes & stresses (including climate) - natural and ‘ag’ ecosystems Slide # 5

The iPlant Collaborative Internal Advisory Board Science Opportunities Teams Administrative Support Team Education, Outreach, and Training Team Cyberinfrastructure Development Team Executive Team National Science Foundation Board of Directors Community Grand Challenge Teams

Executive Team Co-Director Steve Goff Co-Director Dan Stanzione Cyberinfrastructure Development Team Project Managers Karla Gendler Michael Gonzales Lead Developer Sonya Lowry Semantic Web Architect Damian Gessler CI Team Phylogenetics Engagement Team Lead Sheldon Mckay Gen2Phen Engagement Team Lead Matt Vaughn CI Advisory Team Greg Andrews Sudha Ram Nirav Merchant Lincoln Stein Doreen Ware IT/ I nfrastructure Edwin Skidmore Developers, Systems Staff, Research Scientists at ASU, CSHL, UA, UT

Scope: What iPlant won’t do iPlant is not a funding agency – A large grant shouldn’t become a bunch of small grants iPlant will not fund data generation iPlant will (probably) not fund – Whose funding is ending iPlant will not replace all online databases iPlant will not *impose* community standards

Scope: What iPlant *will* do Provide storage, computation, hosting, & programmer effort to support GC projects Work with community to support & develop standards Provide forums to discuss the role and design of CI in plant science Help organize the community to collect data Provide appropriate funding for time spent helping us design and test the CI

GC Projects to Date 2 Grand Challenges 11 Working Groups Participation from ~45 scientists from ~25 institutions beyone the iPlant original team

iPToL Final Deliverable – A web (interface) environment allowing the scientific community to create, access, share, annotate, and visualize phylogenetic tree(s) of varying size and complexity. Included in this environment are the software tools, as well as the infrastructure to host, process, analyze, and store this information. 6 working groups

iPToL Working Groups Data Assembly – Assembling the data to produce the 500k taxa tree Big Trees – Providing the methods (and the tree) to produce a 500K taxa tree Trait Evolution – Providing methods to relate phylogenetic trees to the evolution of specific traits Tree Reconciliation – Developing tools for inferring gene family histories in the context of species trees Data Integration – Combining data from different sources to initially meet the needs of the iPToL working groups Tree Visualization – Developing tools to visualize large trees and annotations

iPToL WG Membership Big Trees Alexandros Stamatakis (lead) Wayne Pfeiffer Stephen Smith Fernando Izquierdo Data Assembly Doug Soltis (lead) Pam Soltis (lead) Michael Donoghue (lead) Casey Dunn Gordon Burleigh Trait Evolution Brian O’Meara (lead) Joe Felsentein Rod Page David Ackerly Jeremy Beaulieu Tree Reconciliation Todd Vision (lead) Dannie Durand Cecile Ane Benjamin Vernot Data Integration Val Tannen (lead) Bill Piel Tree Visualization Michael Sanderson (lead) Karen Cranston iPlant Engagement Team Sheldon McKay (lead) Karla Gendler (PM) Liya Wang Jerry Lu Scott Menor Adam Kubach

iPG2P Final deliverable: – Procedure allowing an investigator to begin with trait of interest in species possessing limited genetic resources and progress toward ability to predict trait scores for known genotypes in given, non-constant environments Identifying cross-cutting biological use cases to be addressed by working groups – Ex: develop informatics tools to reveal regulatory networks underlying photosynthetic differentiation in C3 and C4 plants 5 working groups

iPG2P Working Groups NextGen Sequencing – Establishing an informatics pipeline that will allow the plant community to process NextGen sequence data Statistical Inference – Developing a platform using advanced computational approaches to statistically link genotype to phenotype Modeling Tools – Developing a framework to support tools for the construction, simulation and analysis of computational models of plant function at various scales of resolution and fidelity Visual Analytics – Generating, adapting, and integrating visualization tools capable of displaying diverse types of data from laboratory, field, in silico analyses and simulations Data Integration – Investigating and applying methods for describing and unifying data sets into virtual systems that support iPG2P activities

iPG2P WG Membership NextGen Sequencing Tom Brutnell (lead) Steve Rounsley (co-lead) Ed Buckler Justin Borevitz Todd Mockler Pat Schnable Michelle Morgante Bob Schmitz Michael Gonzales Zhenyuan (Jerry) Lu Liya Wang Statistical Inference Dan Kliebenstein (lead) Ed Buckler (co-lead) Barb Stranger Chris Myers Scott Menor Liya Wang Modeling Tools Chris Myers (lead) Jeff White (co-lead) Melanie Correll Pankaj Jaiswal Johanna Schmitt Stephen Welch Xinguang Zhu Liya Wang Adam Kubach Visual Analytics Ruth Grene (lead) Greg Abram (co-lead) Nicholas Provart Eric Lyons Lenwood Heath Richard Bruskiewich Bjoern Usadel Adam Kubach Data Integration Doreen Ware (lead) Chris Jordan (co-lead) Eva Huala Justin Borevitz George Copeland Pankaj Jaiswal Ruth Grene Lukas Mueller Carolyn Lawrence Doina Caragea Jim Jones Weijia Xu Scott Menor Zhenyuan (Jerry) Lu iPlant Engagement Team Matt Vaughn (lead) Karla Gendler (PM) Liya Wang Jerry Lu Scott Menor Adam Kubach Michael Gonzales Weijia Xu Chris Jordan Greg Abram

Additional Efforts (in progress or consideration) Image Analysis Platform – Edgar Spalding, BS Manjunath, Kris Kvilekval, Justin Borovitz, Steve Welch, Ed Buckler Semantic Web – Damian Gessler APWeb2 – Taxonomic Intelligence –

Why Evolution of Plants is more Exciting than Evoultuion of Humans Slide # 18 versus

Discussion