controlSBML 0.1.1

Symbolic mathematics for SBML Models.

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_referencecan 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 model
• roadrunner is the roadrunner object for the model
• jacobian is the Jacobian of the model at the current simulation time. Changes to roadrunner can change this property.
• antimony is the antimony representation of the model

Key methods

• setTime(new_time) resets roadrunner and runs a simulation from time zero to the time specified.
• makeStateSpace() creates a control 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 current RoadRunner instance. You can either specify a different ${\bf A}$ or set the RoadRunner instance to a different time.

Example

This notebook illustrates how to use controlSBML.