Chemistry Portal
Project Leader: Andrey Bliznyuk, ANU
Description
This project is developing a grid access point for the APAC computational molecular science community that will remove much of the overhead from using advanced computing systems. The portal includes a uniform web-based interface to support input file preparation, remote job submission and monitoring (with optimisation of runtime parameters such as memory and disk usage), and post-processing analysis and visualisation.
Two major new features should make the interface unique among other products:
- the ability to exchange data between different computational chemistry applications
- the ‘shelf’ concept to allow users to perform a unified set of operations on a set of molecules.
Achievements
| 2004 |
- Completed review of functionality of existing computational chemistry interfaces.
- Completed review of the existing grid-based environment and identification of suitable software for National Facility.
- Completed survey of key APAC computational chemistry users and their requirements.
- Established a dedicated Linux web server at ANU.
- As the result of the review of existing software and survey of the key national facility users, the main features of the future user interface were established. Two major new features should make the interface unique among other products: 1) the ability to exchange data between different computational chemistry applications; 2) the ‘shelf’ concept to allow users to perform a unified set of operations on a set of molecules.
- Middleware technology for portal implementation was determined:
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| 1H2005 |
- On the basis of a review of chemistry-related user interfaces and talks with computational chemistry users, a new plan for the grid user interface was developed.
- A first stage portal for Amber and Gaussian has been implemented and tested, including file upload, job submission and retrieval. Prediction of the resources required for Amber jobs is included; prediction for Gaussian has been deferred to the next period.
- A protocol for interaction between java applets and Gridsphere portlets was developed and tested.
- An initial version of the molecular viewer and editor has been created.
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| 2H2005 |
- Steering Committee meeting discussed the review of Chemistry Portal and updated plan for its development was formulated and distributed between interested parties.
- Continued development of portals for Gaussian, Amber, Gamess and Gromacs; some delays are experienced due to switch from java awt to java swing.
- Added many new features to the molecular viewer and editor.
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Plan for 2006
Main structure of the chemistry portal and its features have already been established as the result of consulting with computational chemistry community. Now the remaining development of the software includes further testing and refinement of the “shelves” interface that allow users to work simultaneously with several molecules at one time and extending the portal for additional computational chemistry programs. To this end, the aim is to present a complete unified user-interface to the following programs: Gaussian, Amber, Gamess, Gromacs, Mopac and Molpro. Additional enhancements include further improvements to the molecular editor and the development of a chemistry-related database interface. The release of the full portal functionality is tied to the service delivery of an operational grid gateway service.
Milestones for 2006
| July |
- Molecular Editor
- Add hydrogens automatically
- Add solvent molecules
- Shelves
- Jobs submission and monitoring and output files receiving
- Gamess portlet
- Gromacs portlet
- File conversions for new portlets
- Interacting with grid directly from local computers as opposite to GridSphere
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| December |
- Molecular Editor
- Draw molecule
- Optimize geometry to transform imperfect drawings to 3D structure
- Advance search in database of molecules
- Mopac portlet
- Molpro portlet
- Post process analysis
- Use of job broker services, if available on the National Grid
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Participating Organistions
- University of Sydney
- Australian National University
- Swinburne University
