controlSBML

controlSBML is a python packag that assists with control engineering of biological systems that are characterized by models in the Systems Biology Markup Language (SBML), a community standard for representing models of biological models, especially chemical reaction networks. controlSBML provides the following:

• Read SBML models, viewing candidate inputs, and outputs, and running simulations.
• System identification, including the creation of (SISO) transfer function objects from the python control systems library
• Creating Antimony simulations of closed loop systems
• Design of closed loop systems

Examples of usage are in this directory

Installation

pip install controlSBML

To find the current version:

import controlSBML as ctl
ctl.__version__

Version History

• 1.3.0 2/10/2025
  • Add draw to API
  • Change colors for plots to make them more visible
• 1.2.4 2/2/2025
  • Add colour to requirements
• 1.2.3 1/21/2025
  • Fix update bug
• 1.2.2 1/21/2025
  • Update to most current API
• 1.2.1 5/23/2024
  • Eliminated the save_path feature since it conflicted with usage in colab.
• 1.2.0 5/22/2024
  • Implemented differential control
  • Extended noise model to include lognormal distribution, offset, and slope
  • Implemented several examples, some of which are based on student projects
  • Two algorithms for fitting. gpz fits the transfer function in order by gain (g), poles (p), zeroes (z). poly fits a polynomial in s to the simulations.
• 1.1.03 1/20/2024
  • Better error checking
  • API uses parameter names kI, kP, kF
• 1.1.02 12/27/2023
  • Fix bug in dependencies. Update header documentation.
• 1.1.01 12/27/2023
  • Complete change in the architecture. Instead of using NonlinearIOSystems in the python control package, controlSBML generates Antimony code to implement staircase functions and closed loops.
  • Creation of a consistent API.
• 1.0.11 3/1/2023
  • Ensure that state variables are never negative.
• 1.0.10
  • Fixed bug with unequally spaced times
  • Fixed bug so can start a simulate at a time other than 0 and the correct initial state is obtained.
• 1.0.9 2/14/2023
  • Use temporary directory for plots created in tests
• 1.0.8 2/14/2023
  • Avoid error if Jacobian cannot be calculated.
  • Better handling of warnings
• 1.0.7 2/11/2023
  • Add missing dependency (lmfit)
• 1.0.6 2/11/2023
  • ControlSBML.makeSISOTransferFunctionBuilder creates a SISOTransferFunctionBuilder object. The plotStaircaseResponse method of SISOTransferFuntionBuilder indicates the controlability of an input for the output. fitTransferFunction fits a transfer function to the outputs produced by a staircase input.
  • plotStaircaseResponse shows effect of a staircase input on outputs
  • Remove cruft from effector_dct
  • Added plot option writefig which takes arguments, True, False, str (path)
• 1.0.5 1/22/2023
  • Fix bugs in NonlinearIOSystem relating to states and calculations in updfcn.
  • Changes to documentation
• 1.0.4
  • Fix bug so that makeStateSpace honors the time argument
  • Updated Sphinx documentation
  • Fix bug with version
• 1.0.3
  • Fix bug with file path in _version
• 1.0.1
  • src directory contains all pcakages
• 1.0.0
  • Redefined inputs as species adjustment (positive or negative)
  • ControlSBML.equals has an option to do a "quick check"
  • Deprecated the use of an effector dictionary
• 0.2.23 12/18/2022
  • Updates for using toml files
• 0.2.22
  • IOSystemFactor.makeStateFilter creates a vector of filters between 2 systems
  • SISOClosedLoopSystem.makeFullStateController creates multiple filters if kf != 0
• 0.2.21 5/30/2022
  • NonlinearIOSystem creates a logger.
  • SISOClosedLoopSystem.makeFullStateSystem has option for filters
  • Changed legend of step respoinse plot to use "reference" instead of "step"
• 0.2.20 5/27/2022
  • Fix bug in SISOClosedLoopSystem.evaluateControllability because scipy didn't handle nan values.
• 0.2.19 5/27/2022
  • Fix bug in SISOClosedLoopSystem.evaluateControllability because scipy didn't handle nan values.
• 0.2.18 5/26/2022
  • Fix small bug
• 0.2.17 5/26/2022
  • Deleted the callback_log implemented in 0.2.14.
• 0.2.16 5/24/2022
  • Refactored SISOClosedLoopSystem
  • Implemented SISOClosedLoopSystem.makeFullStateController
  • Fixed bug with makePIDController where ki, kd are ineffective.
• 0.2.15 5/21/2022
  • Fix bug in reverting the semantics of control input to be setting the species as a static.
• 0.2.14 5/11/2022
  • Provide callback for each manufactured IOsystemFactory
  • Reverted semantics of control input to a NonlinearIOSystem to be setting the value rather than adding or subtracting a value.
• 0.2.13 5/9/2022
  • SISOClosedLoopSystem provides a way to construct a closed loop system for an SBML model. The system has a PID controller and a filter.
  • IOSysemFactory has a log
• 0.2.12 5/3/2022
  • IOSystemFactory creates IOSystem objects for Adder, Multiplier, Filter, PIDController, Sinusoid, Constant, Passthru
  • State inputs add to state, not replace the state value.
• 0.2.11 4/25/2022
  • Fix bug in calculating transfer function that incorrectly considered state
• 0.2.9 4/19/2022
  • Fluxes can be outputs
  • Construction of transfer function includes atol option for simplification
• 0.2.8 4/17/2022
  • Added options to plotTrueModel
  • Updated Using ControlSBML with an example of doing feedback
• 0.2.7 4/11/2022
  • Species can be inputs
  • makeStateSpace, makeTransferFunction have timepoint argument
• 0.2.6 4/10/2020
  • Default for constructor: is_reduced=False
  • makeTransferFunction
• 0.2.5 4/8/2022
  • Improve performance by not recalculating Jacobian
  • Fix bugs related to implementation of is_reduced as applied on NonlinearIOSystem
• 0.2.4 3/31/2024 - Create reduced A matrix
  • mat2Df - fixed bug with printing column names
  • Create reduced A matrix for makeStateSpace so that A is non-singular Default output_names is all floating species
• 0.2.3, 3/22/2022 - Bug fix for mat2DF
• 0.2.2, 3/22/2022 - Bug fix
• 0.2.1, 3/22/2022 - Bug fix
• 0.2.0, 3/22/2022 - Version for class
  • ppMat - pretty print a matrix
  • plotMat - display a heatmap for a matrix
  • mat2TS - convert a matrix to a timeseries
  • mat2DF - convert a matrix to a dataframe
• 0.1.6, 3/16/2022
  • Using-Control-SBML.ipynb has an example of doing feedback control design with controlSBML.
  • control.NonlinearIOSystem wraps an SBML model. Can be used in the construction of systems using control.interconnect and in simulations using control.input_output_response. One caveat is that this may work poorly for models implemented as SBML rate rules.
• 0.1.5, 3/5/2022.
  • More options for plotting and simulations
  • plotBode
  • Inputs are identified by reaction Ids
• 0.1.3, 2/13/2022. First release.