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.