This resource provides a set of of mechanistic models of functional components to use as building blocks to construct computational models of biological systems.
Models of biochemical systems—including signaling pathways, electrophysiological systems, and cellular metabolism—are built from models of individual components such as enzymes, transporters, and ion channels. This databank of open source of component models uses a consistent notation, obeying a common set of criteria, with clear documentation and links to the primary literature. Code modules for enzymes and transporters can be downloaded in CellML or MATLAB, for use with the BISEN package.
Enzyme Mechanisms for Biochemical Reactions
Fumarate reductase (Fumarase)
NAD-linked isocitrate dehydrogenase
Transporters and Pumps involving Biochemical Reactants
NADH-ubiquinone oxidoreductase (Complex I)
Ubiquinol-cytochrome c reductase (Complex III)
ATP/magnesium phosphate carrier
Inorganic Cation Transport
Calcium rapid uptake pathway