We have developed the RIKEN AJAX browser computing (RABC) system. This system enables the simple realization of large scale Global Computing systems, like the SETI@home project, that take advantage of unused computing resources. Its greatest advantage is that an agent program, which has been traditionally required, does not need to be installed. Volunteers can participate by simply browsing to a Web page provided by the RABC system. This system allows greater CPU cycle resources to be acquired than traditional methods. We have evaluated a performance difference between JavaScript and legacy computer languages.

A method is described for enumerating the frequencies of DNA subsequences on a system comprising a host computer and a field programmable gate array (FPGA) board with one FPGA. Frequencies of subsequences with lengths of up to K0+ K1+ K2(24 in the current implementation) are enumerated in three phases. In these three phases, subsequences with lengths of up to K0, K0+ K1, and K0+ K1+ K2, respectively, are enumerated; these three phases are executed simultaneously on a pipelined circuit, resulting in high performance. The enumeration of frequent subsequences in databases, which are becoming larger and larger, will enable subsequences that are unique and/or repeatedly used in many parts of the sequences to be found.

We have developed an instant environment for protein sequence profile scanning application by re-mastering Knoppix distribution as high throughput computing edition. This is an integrated environment with bioinformatics applications, parallel file system and scheduler. The integrated environment allows biology researchers to perform scanning applications immediately on their computational pool without any system configuration changed.

UNLABELLED: OBIYagns (yet another gene network simulator) is a biochemical system simulator that comprises a multiple-user Web-based graphical interface, an ordinary differential equation solver and a parameter estimators distributed over an open bioinformatics grid (OBIGrid). This grid-based biochemical simulation system can achieve high performance and provide a secure simulation environment for estimating kinetic parameters in an acceptable time period. OBIYagns can be applied to larger system biology-oriented simulation projects. AVAILABILITY: OBIYagns example models, methods and user guide are available at https://access.obigrid.org/yagns/ SUPPLEMENTARY INFORMATION: Please refer to Bioinformatics online.