Symbolic mathematics for SBML Models.
Project description
controlSBML
controlSBML
provides: (1) a bridge between SBML models and the python control
package and (2) capabilities for the analysis and design of control systems for SBML models.
Installation
pip install controlSBML
Constructing ControlSBML
ctlsb = ControlSBML(model_reference)
where
model_reference
can be any of the following:
- path to a local file with the extension
.ant
or.xml
- a python string for an SBML or Antimony model representation
- a URL to an XML file
Key properties
species_names
is a list of species in the modelroadrunner
is the roadrunner object for the modeljacobian
is the Jacobian of the model at the current simulation time. Changes toroadrunner
can change this property.antimony
is the antimony representation of the model
Key methods
setTime(new_time)
resetsroadrunner
and runs a simulation from time zero to the time specified.makeStateSpace()
creates acontrol
state space object using the Jacobian of the model at the current simulation time.plotTrueModel
plots a roadrunner simulation.plotLinearApproximation
plots the linear approximation provided by an ${\bf A}$ matrix. The default ${\bf A}$ matrix is the Jacobian of the currentRoadRunner
instance. You can either specify a different ${\bf A}$ or set theRoadRunner
instance to a different time.
Example
This notebook illustrates how to use controlSBML
.
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