Upload
jesse-hendrix
View
15
Download
1
Tags:
Embed Size (px)
DESCRIPTION
Growing the Tree of Life at SDSC: Kick-Off Meeting. Mark A. Miller San Diego Supercomputer Center. OTHER SDSC/MULTI-SITE PROJECTS in BIOLOGY Alliance for Cell Signaling Encyclopedia of Life Joint Center for Structural Genomics Protein Data Bank Protein Kinase Resource - PowerPoint PPT Presentation
Citation preview
11 1
Growing the Tree of Life at SDSC:Kick-Off Meeting
Mark A. Miller
San Diego Supercomputer Center
OTHER SDSC/MULTI-SITE PROJECTS in BIOLOGY
• Alliance for Cell Signaling
• Encyclopedia of Life
• Joint Center for Structural Genomics
• Protein Data Bank
• Protein Kinase Resource
• Lipid Maps (Lipid Metabolomics)
Informatics Center
VirtualCollectionsVirtual
CollectionsVirtual
Collections
Integrated Views
Integrated Views
Linux ClustersLocal
ResourcesLocal
Resources
Scientific Community
SMPs
Discovery Portal
Computational Resources
Domain ScientistsDomain Scientists
Disciplinary Interfaces• Molecular Biology• Structural Biology• Algorithm developers
Disciplinary Interfaces• Molecular Biology• Structural Biology• Algorithm developers
FederatedData
Collections
FederatedData
Collections
View Providers
View Providers
Tool Providers
Tool Providers
“The GRID”“The GRID”
TOL Project functions:
• Algorithm development• Model development• Methodologies for model evaluation• Database methodologies• Software development• Scalability/High end computing• Integration technology• Education/outreach
Role of SDSC:
• Unite the users with resources to do their science.• Create standards for the resource in partnership w/community.• Design a reference architecture that supports interoperability, evolvability, and extensibility.• Provide a common point of contact for project members and the community.• Create a resource that gives persistence to the work created under this funding.
For each project function we must ask:
• What are the overall goals?
• What resources do we have presently?
• Where is IT support limited?
• What are the requirements for delivering on goals?
• How can we formalize communication?
Of the project management we must ask:
How shall we prioritize the allocation of resources to goals?• How much effort to stabilize/wrap legacy SW (and which SW)?• What are trade offs of architectural specifications (SW and HW)?• What are the computational requirements (grid vs local) ?• What functions do we need to provide immediately?• What is the right mix of short term/long term investment?
Synergies: Features under development in other SDSC Projects
• HEC (DataStar: IBM power4; 7 tf/ 235 GB memory; SunFire 12K)
• Web/grid services (Blue Titan)
• Workflows (Ptolemy II; Scitegic)
• e-Notebook (partnership with Kinematik; internal efforts)
• Molecular visualization tools (mbt.sdsc.edu)
• Biological data federation (IBM DL federation;
http://quatermass.sdsc.edu:8080/federation/index.html )
Where do we start?
• Create infrastructure that supports communication.http://landscape.sdsc.edu:8080/PHYLO/
• Create a specifications document/project plan for each
functional area.
• Map the specifications to existing resources; strategize
around weaknesses.
• Propose one or more architectures that map to the groups
needs.
Proposed timelineNovember 2003 Inception:
• possible architectures described. • requirements for systems identified• project planning and staffing, • Life Cycle Objectives documentation with at least one feasible system architecture.
February 2004 Elaboration:• System Software Architecture Description created.• Life Cycle Architecture review and commitment.
October 2004 Construction• Major coding of product occurs, • culminating in the delivery of "alpha" capability to the user together with documentation.
SDSC Tree of Life Team
Mark Miller – Management/Logistics/Strategy
David Stockwell – Data Base/Architecture
Alex Borchers – Architecture/Data delivery tools/ User requirements
Dana Jermanis – Graphic Art/Web Master
1212 12
Metadata sharing
Virtual community messaging
TOL NotebookTOL Notebook
SOAP Queries
Database
SOAP Server
XML/RDF store
BLAST DataKeyword data
Stored queries
Annotations
Session info
Scheduler
BLASTKeyword queries
Invoke
Encyclopedia of Life