DSMTS

# Discrete Stochastic Models Test Suite

The DSMTS is a test suite of discrete stochastic models in SBML format, distributed under the GNU LGPL. Version 3.1 of the software is included in the Cain distribution in the directory `examples/sbml/dsmts31`. In this chapter we reproduce some of its results. Note that Cain does not parse all SBML constructs. After importing the SBML files, we note how to edit the results within Cain to obtain valid models. The Cain XML files that correspond to those in the DSMTS are in the directory `examples/cain/dsmts31`.

General issues with SBML files:

- Cain assumes that all species amounts are given is substance units (number of molecules). If an SBML model uses concentration units you will have to correct the initial amounts in the species editor.
- Reaction propensity functions are typically imported correctly. Furthermore, mass action kinetic laws are often automatically recognized as such. Recall that if a model has only mass-action kinetic laws then one can use the pre-compiled mass-action solvers. Otherwise, clicking the launch button will result in a custom solver being compiled and then launched. For example, consider the reaction X → Y with propensity function K*X. In most cases, Cain will recognize this as a mass-action law. The MA (Mass-Action) field will be checked, and the propensity factor will be K. For the second order reaction 2 X → Y with propensity function 0.5*K*X*(X-1) the MA field will be checked, and the propensity field will be set to K. However, there are some cases in which Cain will not perform this conversion. (For example, when the rate law has local parameters.) In these cases, one may manually perform the conversion in the reactions editor.
- SBML events are not imported. For models with events one must use the time events editor and/or the trigger events editor to add the events.
- Cain does not have support for boundary conditions.