Parasitology Grid
Project Leader: Michael Mee, University of Technology, Sydney
Description
The primary goal of the work is to develop a framework to enable the sharing and remote processing of biological data for the ARC Network for Parasitology. This program commenced July 2005 as part of the creation of a new support unit at UTS. Due to the late start of the project, a higher rate of effort has been put into the project.
This project of work was developed at UTS during the second half of 2005. The particular aims are as follows:
- Set up a grid-accessible storage repository at ac3/UTS to store biological data for the Parasitology Network.
- Develop standardised bioinformatics workflows and interfaces to the APAC grid by adapting tools developed in the European myGrid program (in particular Taverna).
- Assist in the installation of bioinformatics programs and in the integration of biological databases onto the ac3 cluster.
Additionally, in conjunction with the APAC Information Infrastructure Program:
- Assist in the development of infrastructure to support access to public biological data stored on the Bio-mirror server.
- Assist in the development of intelligent update procedures for the publicly available databases.
Achievements
| 2005 |
- Creation of Computational Research Support Unit.
- Preliminary discussion held at Bioinformatics Application Support Project Workshop (at Murdoch University).
- Preliminary discussions with members of IT Subcommittee of ARC Network for Parasitology (Prof. Ross Coppel [Monash] and Dr Sabina Belli [UTS]).
- Development of project proposal.
- Initial requirements analysis for Parasitology Network portal.
- Demonstration of workflow to automate queries against public web portals containing parasitology data.
- Specification and ordering of test server hardware based on APAC gateway machine specifications (UTS funded).
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| 1H2006 |
- Installed test server at UTS including required software such as SRB, globus, environment modules, bioinformatics software, Trac/subversion for project management.
- Set up of website framework for the Parasitology network and bulletin board to allow for collaboration. The website is based on wiki format so the members can maintain site.
- Assessment of Taverna workbench as platform for workflow development and execution.
- Created parasitology specific Taverna modules to access public data portals and for use in the running of a specific workflow from the desktop. There has been some difficulty in getting feedback and requirements from the Parasitology network.
- Developed and ran course for biologists/bioinformaticians in the use of Taverna.
- Installed GUS/WDK to test its suitability as a framework for holding Parasitology data and creating tools to access the data.
- Developed procedures to install bioinformatics tools on ac3 cluster to satisfy the associated grid framework requirements. The initial application installed was the NCBI toolkit (blast) as this is a prerequisite for later a milestone.
- Initial development of web portal (http://crsu.science.uts.edu.au/reblast) to perform automated regular sequence searches to report new matches in public databases.
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Milestones for 2006
- Continued development of ‘reblast’ web portal.
- Create standardised database of test parasite data – awaiting data.
- Creation and deployment of portal for data access, searching, and post-processing.
- Ability to run bioinformatic programs at ac3 from desktop.
Participating Organisations
- University of Technology Sydney
- ac3
- ARC Network for Parasitology
Resources for 2006
- Total resources available to the project for 2006 are 1.49 efts (UTS 1.49)
- APAC is providing funds to support 0.67 efts (UTS 0.67).
