OBIYagns: a grid-based biochemical simulator with a parameter estimator |
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Authors: | Kimura Shuhei Kawasaki Takuji Hatakeyama Mariko Naka Takashi Konishi Fumikazu Konagaya Akihiko |
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Institution: | Bioinformatics Group, RIKEN Genomic Sciences Center, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. |
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Abstract: | SUMMARY: 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. |
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