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Published on APAC National Grid (http://grid.apac.edu.au)

Molecular Docking

Molecular Docking

Project Leader: Raj Buyya, University of Melbourne

Description

The aims of this project are to provide the biotechnology sector in Australia with ready access to technologies that enable them to perform drug-lead exploration in an efficient and inexpensive manner using grid computing-based cyberinfrastructure.  It provides secure web-based access to docking applications and a wide variety of chemical databases, as well as tools to assist in the analysis and archival of the screening results. As docking each molecule in the target chemical database is both a compute and data intensive task, The Australian BioGrid provides an affordable and efficient solution for biologists to accelerate the screening of chemical databases, utilising large-scale, distributed computing systems. 

The project leverages a number of collaborative efforts and developments.  WEHI has developed molecular docking software framework in collaboration with a number of colleagues in Australia.  The Gridbus Project at the University of Melbourne has developed the Gridbus Brokering framework that supports distributed data-intensive applications.  This BioGrid project has developed a BioGrid Web Portal for customised chemical database screening and a Web-based interface for automated analysis, visualisation and storage of virtual screening results.  The portal is being installed for operation on the National Grid and utilises the Gridbus Broker for managing parallel execution of molecular docking operations on local and national computing resources.

The project was started in January 2005.

Achievements

1H2005
  • Developed system requirements and design document.
  • Created initial prototype to help elicit requirements for the system.
  • First iteration of BioGrid portal completed, using GridSphere portlets and successful integration of Gridbus Broker technology.
  • Obtained initial feedback from WEHI and will work towards incorporating this feedback into the portal.
  • Enhanced Gridbus Broker to be compatible with current APAC infrastructure and to better support deployment within a web portal environment.
  • Improved Gridbus Broker performance to ensure better memory usage and fault tolerance.
2H2005
  • Completed second iteration of BioGrid portal:
  • Closer integration with Gridsphere Grid Portlet’s modules.
  • Improved user interface design and added functionality.
  • Improved scalability as result of extensive system testing.
  • Improved Grid execution components (grid experiment/job management).
  • Presented paper detailing our Grid portal’s design as well as providing experimentation results at APAC ’05.
  • First version of BioGrid has been implemented and enhanced version has been demonstrated widely to various researchers and end-users.  It was also demonstrated at APAC’05 conference and e-Science 2005 conference.
  • Established collaboration with EU CoreGrid Project, which a network of excellence in Grid computing.
  • The Gridbus Broker has been made to work with the current configuration of the APAC GRID resources and operate despite the firewall restrictions.  The broker is able to submit jobs to the queuing systems on both brecca-2.vpac.org and lc1.apac.edu.au via Globus.  We expect that further changes will be required to support the evolving National GRID infrastructure.
  • Studied new architecture for APAC Grid infrastructure and accordingly we have restructured our development activities.  Working on supporting SRB based access to data sets.
  • Further improved Gridbus Broker performance to ensure better memory usage and fault tolerance.

Plan for 2006

The first half of 2006 will focus on deploying the system onto the APAC Grid and allowing it to be trialled by initially interested biologists for real molecular docking experimentation, incorporating feedback provided.  The second half of the year will look towards growing the user base and enhancing the system by developing more efficient algorithms, support for workflows, and integrating the portal with other Grid systems including the APAC VO system and GridBank.  At the end of 2006 the molecular docking portal will be fully functional and run on the APAC Grid, as well as on other Grid resources, with substantial user community support.

Milestones for 2006

1H2006
  • Solicit requests of interest from molecular docking user community through existing collaborators and key researchers in the field.  Currently interacting with Dr. Kim Branson (who just moved to Stanford University) and Australian collaborators to develop a software roll out plan and use cases.
  • Introduce GSI based distributed data management using GridFTP and SRB.
  • Update web-based Interface to Biogrid and include online tutorials for new users.
  • Deploy BioGrid system on APAC Grid and open access to BioGrid to initial users.
  • Collect user feedback and extend system to meet additional requirements
  • Extending portal and the broker to operate with the new Gateway-based grid resources
2H2006
  • Prepare a user-manual for BioGrid.
  • Prepare a paper on the work for publication in conference/journal.
  • Deploy the software widely and continue to grow user community.
  • Continue to incorporate user feedback.
  • Extend the software to confirm to new standards that emerge in Grid and Web services community (create docking grid service to run on ngportal).
  • Integration with Grid Accounting system (GridBank).
  • Integrate with APAC Grid virtual organisation infrastructure and extend the notion of virtual organisation, if necessary, to meet advanced needs of BioGrid.
  • Develop and implement advanced algorithms that optimise resource allocation.
  • Prepare a journal paper based on new and innovative advances made to the portal and application execution environment within APAC National Grid.
  • Extend the Grid Scheduler to Support Advanced Workflow for BioGrid.
  • Demonstrate BioGrid at SC 2006 Conference in Florida, USA.
  • Ensure software is generallised and share with other communities.
  • Integrate broker with APAC Software Information Registry Service (when available) to support dynamic discovery of Grid resources supporting “docking” services
  • Leverage existing tools and develop a GUI environment assisting users in docking experiment input data preparation life cycle

Participating Organisations

Resources for 2006

Source URL:
http://grid.apac.edu.au/OurUsers/MolecularDocking