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A reaction scheme is composed of various pools and the reactions between them, constructed by the usual tear-and-stick process. Catalyzed reactions, and those of the form A+B -> C are included as special cases. Others can be built up by linking pools in an equation-like manner.
The editor allows you to construct a reaction diagram much as you would draw it on paper. Pools can be torn off the prototype on the top left. Each is initially assigned a random color which can be set rom the menu under the "catacomb.RSpool" button on the top right. Each pool also has a name and an initial concentration C-0.
Pools are linked with the six connector types on the top row which have the following functions:
1. Equilibrium: defined by forward and reverse rates. The reactants and/or products may be groups linked with addition connections. For reactions of the form nA <--> mB the number of reactants n or products m may be set by highlighting the reaction and using the sliders at the bottom right.
2. Equilibrium: functionally as (2) but it is drawn with a curve for the layout.
3. Two to one reactions: this is a shorthand for the case A + B <--> C which could instead be implemented with an addition link. The two halves of one end of the arrow are connected to the two reactants and the other end to the product as usual.
4. Catalysed or enzyme reactions using Michaelis Menten Kinetics. The catalyst is connected to the pink arm and catalysies the reaction in the direction of the arow. Three parameters are required: the maximal transition rate v-max, the catalyst concentration for half maximal activity k-m and ratio of reverse to forward exit from the catalyst plus reactant complex, k-r-by-v-max. Often realistic reactions are insensitive to this parameter (Bhalla - see chapter2 of the models section) which defaults to 4.
5. External: the reqction uses an external method to calculate the forward and reverse rates. The method is given an array of the concentrations of all species in the network as its argument.
6. Addition: to link multiple reactants or products as in A <--> B + C + D
7. Identity: One pool may fugure in several reactions, in which case using addition connections leads to ambiguity. In this case the pool must be duplicated for each reaction with the duplicates linked by identity connectors. It may also be conveneint for layout purposes for the same pool to occur in different parts of the diagram. Once pools are identified, one sets the color and name for the whole group; the others can no longer be controlled seperately.