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Kinetics
Additionally to a basic Boole'an simulation of networks, also "real" kinetics shall be simulatable, allowing for discrete compound concentrations/activities, .
Development has already started to simulate and visualize linear kinetics of the involved species. The central simplification is the reduction of concentrations to percentages (representing compound concentrations as numbers between 0% and 100%). Calculation will be carried out in timed steps, rather than by exact calculations (differential equations). This procedure represents a mathematical approximation, which can be justified, since we deal not with a mathematical problem but a real scenario, in which slight deviations of the precise math may also be expected from the in vivo system.
Whenever no detailed information about kinetic constants and math respectively, is known, at least a discrimination of protein-protein interactions against gen-expression is possible.
States may also be kineticly approximated according to the experimentators experience. E.g. a macroscopic state like "starvation" would have a comparably slow kinetic, since many proteins and genes are involved in it's recognition, signal transduction and consequent actions.
- linear
- exponential
- Michaelis-Menten
- Hill
At first, only linear kinetics will be implemented (in JS), see above.
Kinetics require compound concentrations/activities to be calculated time-dependendly, therefore time-graphs, showing the development of a compound concentration/activity versus time become possible and useful.
Kinetics are usually simulated using open source tool Copasi. Therefore it would be useful to implement a Copasi importer and exporter.