Interoperability of GADU in Using Heterogeneous Grid Resources for Bioinformatics Applications
- Resource Type
- Periodical
- Authors
- Sulakhe, D.; Rodriguez, A.; Wilde, M.; Foster, I.; Maltsev, N.
- Source
- IEEE Transactions on Information Technology in Biomedicine IEEE Trans. Inform. Technol. Biomed. Information Technology in Biomedicine, IEEE Transactions on. 12(2):241-246 Mar, 2008
- Subject
- Bioengineering
Computing and Processing
Bioinformatics
Grid computing
Genomics
Genetics
Large-scale systems
Data analysis
Databases
Data systems
Computer applications
Computer architecture
high-throughput computations
interoperability of grids
multiple grids
- Language
- ISSN
- 1089-7771
1558-0032
Bioinformatics tools used for efficient and computationally intensive analysis of genetic sequences require large-scale computational resources to accommodate the growing data. Grid computational resources such as the Open Science Grid and TeraGrid have proved useful for scientific discovery. The genome analysis and database update system (GADU) is a high-throughput computational system developed to automate the steps involved in accessing the Grid resources for running bioinformatics applications. This paper describes the requirements for building an automated scalable system such as GADU that can run jobs on different Grids. The paper describes the resource-independent configuration of GADU using the Pegasus-based virtual data system that makes high-throughput computational tools interoperable on heterogeneous Grid resources. The paper also highlights the features implemented to make GADU a gateway to computationally intensive bioinformatics applications on the Grid. The paper will not go into the details of problems involved or the lessons learned in using individual Grid resources as it has already been published in our paper on genome analysis research environment (GNARE) and will focus primarily on the architecture that makes GADU resource independent and interoperable across heterogeneous Grid resources.