A problem solving environment for bioinformatics on grid

Abstract

Recently, bioinformatics field meets exponential growth of data and increasing problem complexity. The result is inevitable need of comprehensive solution that enables flexible coordination of combined bioinformatics analysis and high-throughput and high-performance computing together. In this thesis, we suggest a new approach that solves the current and upcoming problems in the field of bioinformatics analysis. We have developed an integrated system, BioGrid Problem Solving Environment (BioGridPSE) that harbors bioinformatics tools enabled on grid environment and their integrated solutions under workflow management. This system includes grid resource and job management tools generated from Condor system that can be applicable to the other grid middleware such as Globus. Most important feature of this system is on the interfacing tools that make the developer or user build the integrated tools from basic tools. The integration of various tools and grid resources are possible by the comprehensive workflow design. In this thesis, we report also the usability of this new system on high-throughput computation, flexible combination of computational tools, user customized interface generation and programmable data parsing. The efficiency and usability of this system have been tested with real-world bioinformatics problems such as genome sequence analysis and a comparative genome analysis.