File: Dsmts.htm

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<html>
<head>
<title>DSMTS</title>
</head>
<body>
<h1>Discrete Stochastic Models Test Suite</h1>

<p>
The <a href="http://dsmts.googlecode.com/">DSMTS</a>
is a test suite of discrete stochastic models in 
<a href="http://sbml.org/">SBML</a> format,
distributed under the 
<a href="http://www.gnu.org/licenses/lgpl.html">GNU LGPL</a>.
Version 3.1 of the software
is included in the Cain distribution in the directory 
<tt>examples/sbml/dsmts31</tt>. 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 <tt>examples/cain/dsmts31</tt>.
</p>

<p>
General issues with SBML files:
<ul>
  <li>
  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.
  <li>
  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
  <img src="launch.png">&nbsp; will result in a custom solver being
  compiled and then launched.
  For example, consider the reaction <em>X &rarr; Y</em> with
  propensity function
  <em>K*X</em>. 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 <em>K</em>.
  For the second order reaction
  <em>2 X &rarr; Y</em> with propensity function
  <em>0.5*K*X*(X-1)</em> the MA field will be checked, and
  the propensity field will be set to <em>K</em>.
  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.
  <li>
  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.
  <li>
  Cain does not have support for boundary conditions.
</ul>
</p>


</body>
</html>