SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks

摘要: The size and complexity of published biochemical network reconstructions are steadily increasing, expanding the potential scale derived computational models. However, construction large models is a laborious error-prone task. Automated methods have simplified reconstruction process, but building kinetic for these systems still manually intensive Appropriate equations, based upon reaction rate laws, must be constructed parameterized each reaction. complex test-and-evaluation cycles that can involved during model would thus benefit from automated law assignment. We present high-throughput algorithm to automatically suggest create suitable laws type according several criteria. criteria choices made by influenced in order assign desired This implemented software package SBMLsqueezer 2. In addition, this program contains an integrated connection kinetics database SABIO-RK obtain experimentally-derived when desired. described approach fills heretofore absent niche workflows large-scale construction. applications has already been demonstrated useful scalable. platform independent used as stand-alone package, plugin, or through web interface, enabling flexible solutions use-case scenarios.