EU US Plant Biotechnology

Transcription

1 EU US Plant Biotechnology Doreen Ware US EU Co-Chair USDA ARS EU US Task Force meeting June 22 th, 2012 Bremen Germany Recommendations from Plant Biotechnolgy 5-year strategy Also, continuous activities Hinxton 2009 Next generation bioinformatics education Cyberinfrastructure Data Integration: Standards, Ontologies, Tools Databases and Knowledgebases: on: Information/coordination of calls (Work Programmes 2012/2013) Exploration of virtual meeting approaches Exploitation of synergies with other working groups A unified platform for plant biology, stewardship

2 Mechanisms for implementation of action plan Positive framework for coordination in the area of bioinformatics: US IPlant Arabidopsis Research Coordination Network Other projects EC-US TF Workshops Courses EU transplant AllBio Phenotyping Infrastructures Other projects Plant Bioinformatics workshop 2012 Objective: Provide a brief update of the current resources, discuss current challenges and make recommendation of prioritize area of collaboration Plant Animal Genome meeting, January 13, Participants: Scientist and Observers from EC and US Presentations: IPlant Matt Vaughn, Transplant Paul Kersey, EPIC Robert Martienssen, Plant Ontology Pankaj Jaiswal, MaizeGDB Jack Gardiner, Sol Network Luka Mueller, TGAC Mario Caccamo, IAIC Ruth Bastow, Gramene & KBase Doreen Ware, Recommendations in the next year Two Coordinated workshops (WS) Three Sub-Working Groups (SWG) for future development

3 Workshops WS1: Genomes to germplasm: Collaborative proposals for development of infrastructure for archiving, exchange and analysis TransPlant coordinated activity WS2:Phenotypes: Collaborative proposals for development of infrastructure for laboratory and field based assays Gramene & iplant coordinated activity Sub-Working Groups (SWG) Working group leads US & EU. Responsibilities to establish working groups, virtual meetings, in person meeting, and recommendations/whitepaper for data integration and synthesis iplant support for web hosting and virtual meeting (July 2012) SWG1: Genetic Diversity (genotype/population) SWG2: Phenotypes (phenotype field and laboratory) SWG3: Community/Organmism/Clade resources (community portals, center of synthesis)

4 Summary of recent and forthcoming activities 2011 Mutual publication and promotion of relevant US/EU calls Submission of collaborative research proposals Holding regular video conferences on issues including the plant biotech and other Task Force Working Groups Support to collaborations: FR7 TransPlant 2012 Bioinformatic Resource meeting PAG Support to collaborators: NSF IOS Gramene Establishment of Sub-Working Groups Workshop: Genomes to Germplasm 2013 Workshop: Phenotypes Draft recommendations from SWG Collaborative proposals from Workshops Training course on standards and ontologies; possibly run in parallel with scientific meeting Gramene 2012 Ed Buckler, Susan McCouch, Pankaj Jaiswal,Doreen Ware

5 Gramene Pankaj Jaiswal, Crispin Taylor, Lincoln Stein, Paul Kersey, Helen Parkinson, Doreen Ware Aim 1. Establish reference data for plant genomes and comparative annotation. 1.1 Establish an integrated reference genome resource. 1.2 Visualization of Epigenomic, Genotypic, and Functionally Phenotypic Diversity. 1.3 Representation of the pan-genome. 1.4 Comparative genomics: analysis of plant genomes and visualization informed by evolutionary histories 1.5 Stewardship of the maize B73 genome and assembly for one update Aim 2. Establish integrated gene network analysis for plants 2.1 Functional annotation of core model organisms for reconstruction of metabolic and signaling pathway networks. 2.2 Meta data analysis and annotation of the gene expression datasets. Aim 3. Integrate new and existing visualization/analysis tools for exploring emerging genomic 3.1 Build a high-capacity data warehouse that promotes flexible implementation of software modules. 3.2 Improve visual interfaces and site navigability. 3.3 Improve community data access. Aim 4. Transform the community through communication and training opportunities 4.1 Gramene users (researchers and general public interested in plant biology). 4.2 Data annotation, exchange and format standardization workshops (collaborators and experts). 4.3 Collaboration with the American Society of Plant Biologists (ASPB) publishing group. 4.4 Annotation jamborees (young investigators and students). 4.5 Public Lecture series at Cold Spring Harbor Laboratory. 4.6 Summer internships for undergraduate students and faculty. iplant Collaborative

6 Brief History of iplant Funded by NSF February 1 st, 2008 Kickoff Conference at CSHL April 2008 Grand Challenge & CI Workshops Sept 2008 Jan 2009 GC White Paper Review & Recommendations Mar 2009 Project Kickoffs May 2009 & August 2009 Requirements gathering ongoing since May 2009 Start of software development Sep 2009 First prototypes delivered to public Apr 2010 IBP Collaboration Announcement Jan 2011 DE release with user-driven tool integration Jul 2011 DE Verdant Version released Jan 2012 ianimal portal clone & announcement Jan 2012 Life Science CI is: Leveraging existing compute & storage Hundreds of millions $ in NSF investment Focus on a CI platform not specific tools leveraging physical resources integrating tools integrating data Sustainable Species-independent Includes collaboration to bridge the gap

7 CI Philosophy iplant is designed to be consistent with the pillars of CIF21 High Performance Computing Data and Data Analysis Virtual Organization Learning and Workforce. 13 Major Ways to Access iplant iplant Data Storage: All data large and small The Discovery Environment: Integrated Web apps. MyPlant: Social Networking. DNASubway: Annotation and more Atmosphere: For virtual hosting of web apps, sites, databases. Standalone Apps: TNRS, TreeViewer, PhytoBisque, etc The API: For programmers embedding iplant CI capabilities Command line for experts (thru TeraGrid/XSEDE) 14

8 iplant Data Store This is Cloud Storage but it s not Amazon 16 Fast data transfers via parallel, non-tcp file transfer Move large (>2 GB) files with ease Multiple, consistent access modes iplant API iplant web apps Desktop mount (FUSE/DAV) Java applet (idrop) Command line Fine-grained ACL permissions Access and a storage allocation is automatic with your iplant account Sharing made simple

9 A rich web client Discovery Environment Provides a consistent interface to a range of bioinformatics tools Provides a portal to users not wishing to interact with lower level infrastructure An integrated, extensible system of applications and services Provides additional intelligence above low level APIs Provenance, Collaboration, etc. 17 Project Atmosphere API-compatible implementation of Amazon EC2/S3 interfaces Virtualize the execution environment for applications and services Up to 12 core / 48 GB instances Access to Cloud Storage + EBS Run servers, CloudBurst desktop use cases. Big data and the desktop are co-local again! 18 >60 hosted applications in Atmosphere today, including users from USDA, Forest Service, database providers, etc.

10 Postdocs: Barbara Banbury Jamie Estill Bindu Joseph Christos Noutsos Brad Ruhfel Stephen A. Smith Chunlao Tang Lin Wang Liya Wang Norman Wickett iplant Team Executive Team Steve Goff Dan Stanzione Students: Peter Bailey Jeremy Beaulieu Devi Bhattacharya Storme Briscoe Ya-Di Chen John Donoghue Steven Gregory Yekatarina Khartianova Monica Lent Amgad Madkour Aniruddha Marathe Kurt Michaels Dhanesh Prasad Andrew Predoehl Jose Salcedo Shalini Sasidharan Gregory Striemer Jason Vandeventer Kuan Yang Faculty Advisors & Collaborators: Ali Akoglu B.S. Manjunath Greg Andrews Nirav Merchant Kobus Barnard David Neale Sue Brown Brian O Meara Thomas Brutnell Sudha Ram Michael Donoghue David Salt Casey Dunn Mark Schildhauer Brian Enquist Doug Soltis Damian Gessler Pam Soltis Ruth Grene Edgar Spalding John Hartman Alexis Stamatakis Matthew Hudson Ann Stapleton Dan Kliebenstein Lincoln Stein Jim Leebens-Mack Val Tannen David Lowenthal Todd Vision Robert Martienssen Doreen Ware Steve Welch Mark Westneat Staff: Greg Abram Sonali Aditya Roger Barthelson Brad Boyle Todd Bryan Gordon Burleigh John Cazes Mike Conway Karen Cranston Rion Doodey Andy Edmonds Dmitry Fedorov Michael Gatto Utkarsh Gaur Cornel Ghiban Michael Gonzales Hariolf Häfele Matthew Hanlon Anthony Heath Barbara Heath Matthew Helmke Natalie Henriques Uwe Hilgert Nicole Hopkins Eun-Sook Jeong Logan Johnson Chris Jordan B.D. Kim Kathleen Kennedy Mohammed Khalfan Seung-jin Kim Lars Koersterk Sangeeta Kuchimanchi Kristian Kvilekval Aruna Lakshmanan Sue Lauter Tina Lee Andrew Lenards Zhenyuan Lu Eric Lyons Naim Matasci Sheldon McKay Robert McLay Angel Mercer Dave Micklos Nathan Miller Steve Mock Martha Narro Praveen Nuthulapati Shannon Oliver Shiran Pasternak William Peil Titus Purdin J.A. Raygoza Garay Dennis Roberts Jerry Schneider Bruce Schumaker Sriramu Singaram Edwin Skidmore Brandon Smith Mary Margaret Sprinkle Sriram Srinivasan Josh Stein Lisa Stillwell Kris Urie Peter Van Buren Hans Vasquez-Gross Matthew Vaughn Fusheng Wei Jason Williams John Wregglesworth Weijia Xu Jill Yarmchuk Design Principles Ad hoc, reconfigurable analysis workflows Community-led authorship of new components Re-use of existing codebases Computational scalability Enable sharing and collaboration Presentation of well-designed APIs Attractive visualization of results Facile data integration 8