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Bioinformatics Computing Portal @ ASCC BioPortal Hsin-Yen Chen & Chi-Wei Wang Academia Sinica Computing Centre Nov. 18~21, 2003 SC2003, Phoenix, USA

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Bioinformatics Computing PortalASCC BioPortalHsin-Yen Chen Chi-Wei WangAcademia Sinica Computing CentreNov. 1821 - PowerPoint PPT Presentation


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Bioinformatics Computing Portal @ ASCC BioPortal Hsin-Yen Chen & Chi-Wei Wang Academia Sinica Computing Centre Nov. 18~21, 2003 SC2003, Phoenix, USA . ASCC Bioinformatics IT Service/Support Team. Introduction (3). Network. High throughput architecture. Sequence analysis tools (CE 1).

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slide1

Bioinformatics Computing Portal

@

ASCC BioPortal

Hsin-Yen Chen & Chi-Wei Wang

Academia Sinica Computing Centre

Nov. 18~21, 2003

SC2003, Phoenix, USA

ASCC Bioinformatics IT Service/Support Team

introduction 3
Introduction (3)

Network

  • High throughput architecture

Sequence analysis tools (CE 1)

UI (Web server)

Virtual Organization

GRID technology

Database cluster (DBMS)

Structure biology tools (CE2)

grid web service solution
Grid + Web Service Solution
  • Grid is an (network) environment that provides uniform access and management to a large number of diverse and distributed resources
    • Grid is not batch schedulers, cluster managers, or storage systems that happen to be connected to the Internet
    • Grid incorporates Network Computing as its fundamental component
    • Grid may add new standards that extends the network protocol layers

Web Services is to hide the complexity and provide transparent access to the Grid services

    • Typical components are: WSDL, UDDI and SOAP
  • However, Grid is still largely a framework, explicit support to Bioinformatics and Contents needs to be worked out
conceptual bio grid application infrastructure
Conceptual Bio-Grid Application Infrastructure

Life Scientist Access

ACCESS GRID

Bio Portal Web

Life Science A

pplications

IBM WebSphere

, OGSA

Data Analysis/Visualization

Federated Database

Oracle, DB2, MySQL, Text file

IBM DiscoveryLink

Grid Middleware

Network/Computing Infrastructure

grid enabled bioportal@ascc
Grid Enabled [email protected]
  • Design Considerations
    • Allows for the end user to share the computing resources and complex databases under one system
    • The scale of computing resource can be re-sized as needed
    • The computing resource can be allocated dynamically
    • The complexities of computing resources allocation should be hidden by web interface
grid enabled bioportal@ascc6
Grid Enabled [email protected]
  • Implemention
    • A Web-based uniform entrance for providing bioinformatics computing service to biology researchers world-wide
    • The integration of heterogeneous computing platforms
    • The integration of federated bioinformatics data bases
    • A high throughput computing environment
  • Current Status
    • Open for On-line services since July 2003
    • Based on home grown grid emulated middleware
    • On-line applications including
      • Analysis Tools: NCBI BLAST (all types), CRASA, FASTA, OPASS, R (Microarray analysis), etc.
      • Databases: SMD
    • Web Site: http://bits.sinica.edu.tw

Sponsor: National Research Program for Genomic Medicine

future works
Future works
  • Expand application suites to fulfil the NRPGM need
  • Build necessary life science databases
  • Federated database implementation
    • Collaborate with IBM, Taiwan
  • Add more computing elements
  • Migrate to IBM WebSphere portal environment
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