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In order to explore some possible Systems Biology Knowledgebase implementations and architectures, as well as demonstrate and characterize the range of computational challenges facing systems biology projects, part of this Knowledgebase development effort will support pilot projects to address three goals:
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Develop benchmarks for existing computational biology and bioinformatics programs on existing architectures,
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Develop prototypic computational biology and bioinformatics programs on new architectures including cloud architectures, and
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Develop novel and integrative web platforms as possible solutions to bioinformatics problems in anticipation of and to inform a future Systems Biology Knowledgebase.
The projects will focus on prototype development of software on a variety of architectures including cloud computing, which involves open-source infrastructures that provide tools to allow users to deploy virtual machines similar to Amazon's EC2. Areas of interest include but are not limited to:
- Extend existing computational biology and bioinformatic methods and algorithms on novel computer architectures such as cloud architectures which could include the Magellan project, the Elastic Cloud Computing infrastructure (Amazon), or the Eucalyptus infrastructure at the University of California, San Diego.
- Benchmark computational biology and bioinformatic methods and algorithms on existing distributed or High Performance Computer architectures.
- Develop methods for maximizing bandwidth between disk and memory for bioinformatic challenges.
- Develop prototype integrative internet platforms for bioinformatic problems either on new architecture or existing architectures. These prototypes could include extensible object-relational systems, service-orientated architectures, semantic languages, and advances in deductive (logic) rule-based and inferred databases.
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