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CERENA

A toolbox for the simulation and analysis of stochastic chemical kinetics

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FAQ

Q: Should I provide the initial conditions in 
   molecule numbers or concentrations?

A: The initial conditions should always be provided in molecule numbers. 
   If the equations are to be provided for concentrations, the 
   user-provided initial conditions will be automatically
   converted to concentrations.


Q: How to evaluate a least-squares objective function together 
   with the simulation?

A: To evaluate a least-squares likelihood function, one should use the 
   llhwrapper to compile the simulation files. 
   Please refer to the llhwrapper section in the CERENA documentation 
   for more details.


Q: How can I define observables/measured variables?

A: The observables can be defined as outputs of the system. Corresponding 
   scaling and offset parameters can also be defined as additional 
   parameters of the system. 
   Please refer to the "Model definition file" section in the CERENA 
   documentation for more details.


Q: How can I change the initial condition after compiling the 
   simulation files?

A: The desired set of initial conditions can be passed to the simulation 
   MEX-file as an input argument.
   Please refer to the Numerical Simulation Chapter in the CERENA 
   documentation for more details.


Q: How do I specify the scale of the equations, e.g., molecule numbers
   or concentrations?

A: The scale of the equations depends on the selected modeling approach. 
   Some approaches provide the equations only in concentration scale, and 
   for others the desired scale can be specified. 
   Please refer to "Selection of modeling approach" section in the CERENA 
   documentation for more details.


Q: For which parameters are the sensitivity equations derived and simulated?

A: The sensitivity equations are derived for all non-constant parameters, 
   i.e. those defined as System.parameter and not as System.kappa. However, 
   when calling the simulation MEX-file, the user can specify which 
   sensitivity equations are to be solved. Please refer to 
   "Sensitivity Analysis" Section in the ACME documentation for 
   more details.