controlSBML 0.1.4

Control analysis and design 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

To find the current version:

import controlSBML as ctl
ctl.__version__

Installing slycot (a control package dependency)

To get the full set of capabilities from the control package, you need to install slycot, a package that addresses requirements for more sophisticated manipulation of MIMO models (e.g., solving algebraic Ricotti equations).

The best way is to install slycot is from binaries using anaconda. However, at the present time, anaconda is difficult to set up on Google Collaboratory.

Otherwise, you need to install from source. Below are the instructions for Ubuntu.

• install cmake: pip install cmake --upgrade
• install sikit-build: pip install scikit-build
• install fortran: sudo apt-get install gfortran
• provide path to fortran: export FC=`which gfortran
• install BLAS: sudo apt-get install libatlas-base-dev
• clone Sylcot: git clone --recurse-submodules https://github.com/python-control/Slycot.git
• cd Slycot
• python setup.py install

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

• roadrunner is the roadrunner object for the model
• jacobian_df is the full Jacobian of the model at the current simulation time. Changes to roadrunner can change this property.
• antimony is the antimony representation of the model
• A_df is the ${\bf A}$ matrix in the linear system
• B_df is the ${\bf B}$ matrix in the linear system
• C_df is the ${\bf C}$ matrix in the linear system
• state_names is a list of floating species that constitute the state vector
• input_names is a list of reaction names that specify the input vector
• output_names is a list of floating species that constitute the output vector

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.
• plotBode constructs bode plots for the SISO systems formed by all combinations of inputs and outputs.

Example

This notebook provides a simple example of using controlSBML.

Developer Notes

1. The package works with and without slycot. So two virtual environments are needed for testing: ctl includes slycot and ctl_tst does not. Note that continuous integration is done only without slycot.

Version History

• 0.1.4,
  • More options for plotting and simulations
  • plotBode
  • Inputs are identified by reaction Ids
• 0.1.3, 2/13/2022. First release.