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 CcmbColor 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 CcmbColor and name for the whole group; the others can no longer be controlled seperately.
Setting initial conditions
At the bottom of the window is a button labelled "regionConditionSets" Clicking that button brings up the window for the region conditions. The structure here is a little awkward because at present it relies entirely on the default user interface windows. The window lets you create and edit region conditions objects. You need one such object for each distinct set of initial conditions. Each object just contains a set of RSPoolProperties objects called "poolProps". clicking the "poolProps" button lets you edit that set. Each object in that set can specify the conditions for one pool in the reaction scheme. So, in the RSPoolPRoperties window, you need to select "new" from the top left menu for each pool with a non-zero concentration in this set of initial conditions. You get to edit the object in the lower right part of the window, wher you must set he pool it refers to, and the concentration. There is also a variable, D_rel for modifying its diffusion constant across boundaries, but this is not used yet.