G Shell (gsh): Flexible and Extensible Environment for Genome Information Analysis

Akira Suyama[1,2]
Hiroaki Kaku[2]

[1]Institute of Physics, College of Arts and Sciences, The University of Tokyo
[2]Department of Bio-Engineering, Nagaoka University of Technology


G Shell (gsh: Genomic Shell) is a flexible and extensible environment for genomic information analysis, adopting one of basic ideas of the UNIX environment, "Software Tools". It is constructed with a client/server model, and runs on UNIX with the X Window system. Standard input/output, pipeline, and redirection features supported by the gsh server allow complex analysis commands made up of many simple analysis tools to be executed rapidly because those features provide high-speed data transmission between tools without the interprocess communication facility. In addition, utilities to maintain server-supported tools allow a user to reconstruct his own environment with both flexibility and rapidity easily.