Transform to Stochastic Capable

This section describes the Tools -> Transform to Stochastic Capable menu option. One problem with deriving stochastic appications from a general VCell BioModel is that the reaction kinetics are introduced in the model as deterministic. The unambigous interpretation of the terms of Poisson stochastic processes is possible only for the mass action kinetics, and even in this case, the reversible reactions should be decoupled into two separate processes. To address this issue, the "Transform To Stochastic Capable" tool is used to automatically map reaction rates of mass-action reactions to probabiilistic propensities and facilitate the mapping of other reactions. In the BioModel interface, VCell offers a number of kinetic types including a ‘general kinetics’ option that allows for arbitrary rate expressions. The tool identifies the kinetic type of a reaction or membrane flux and in the case of general kinetics, automatically determines, by parsing the rate expression, whether the mechanism might be a combination of individual Poisson processes (e. g. if they are passive fluxes). It then informs the user which of the mechanisms with kinetics other than mass action can be directly translated into probabilistic propensities (and asks permission to do it) and which have to be recast manually by the user into the mass-action type.

Clicking on Tools -> Transform to Stochastic Capable menu option brings up a warning to the user about potential changes to the model if the tool is used.

Clicking Cancel will cancel the transform operation. Clicking OK will open the "Transform to Stochastic Capable Model" dialog. This dialog displays a table of all the reactions in the model.

For each reaction, the table shows the name, type (reaction or flux), kinetic type, reaction rate expression, forward and reverse rate (if they exist or are transformable). The "Transform" column in the table displays a checkbox (non-editable) for each reaction indicating if the reaction kinetics can be transformed into mass action kinetics for being stochastic capable. Rows that are highlighted in red indicate that that reaction failed to be transformed to mass action type. Any comments/errors from the transformation process is displayed in the "Remarks" column of the table.