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OBIYagns: a grid-based biochemical simulator with a parameter estimator.

Shuhei Kimura·Takuji Kawasaki·Mariko Hatakeyama·Takashi Naka·Fumikazu Konishi·Akihiko Konagaya
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Abstract

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.

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AlgorithmsBiochemistryCell Physiological PhenomenaComputer GraphicsComputer SimulationGene Expression RegulationModels, BiologicalSignal TransductionSoftwareUser-Computer InterfaceJournal Article

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Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, Akihiko Konagaya. 2004-02-12. OBIYagns: a grid-based biochemical simulator with a parameter estimator.. https://doi.org/10.1093/bioinformatics%2Fbth122

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