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controlSBML-1.0.9
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Control analysis of SBML models
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | controlSBML-1.0.9 |
| نام | controlSBML |
| نسخه کتابخانه | 1.0.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | - |
| ایمیل نویسنده | Joseph Hellerstein <joseph.hellerstein@gmail.com> |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/controlSBML/ |
| مجوز | MIT License Copyright (c) 2022 Joseph Hellerstein Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
# controlSBML
The [Systems Biology Markup Language (SBML)](https://co.mbine.org/standards/sbml) is a community standard for representing
simulations of biological models, especially chemical reaction networks.
``controlSBML`` is a package that does control analysis and design of SBML models using
the [CalTech ``control`` package](http://python-control.sourceforge.net/manual/).
``controlSBML`` uses the following "systems characterization" of an SBML model:
* state variables are floating species;
* inputs are reaction fluxes;
* outputs are a subset of the state variables.
We note that reaction fluxes cannot be manipulated directly. Thus,implementation requires a mapping from a reaction flux to an *effector*, typically a chemical
species such as an enzyme that is specific to the reaction.
The keyword ``effector_dct`` refers to a python dictionary that does this mapping.
(See the ``makeNonlinearIOSystem`` method of ``ControlSBML``.)
``controlSBML`` interfaes to the ``control`` package by creating two kinds of ``control`` objects for an SBML model:
* ``NonlinearIOSystem``, which wraps the actual simulation of the SBML model; and
* ``StateSpace``, which is a linear MIMO model approximation of the SBML model at a specified time in the simulation.
These objects can be used in combination with other ``control`` objects to analyze system properties,
design controllers, and construct closed loop systems.
``controlSBML`` also provides analyses of SBML models as well as a means to manipulate
elements of the SBML model.
## Installation
``pip install controlSBML``
To find the current version:
```
import controlSBML as ctl
ctl.__version__
```
### Installing ``slycot`` (optional)
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_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
## Technical Summary
### ``ControlSBML``
#### Properties
* ``roadrunner`` is the roadrunner object for the SBML 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 represented as a pandas DataFrame.
* ``B_df`` is the ${\bf B}$ matrix in the linear system represented as a pandas DataFrame.
* ``C_df`` is the ${\bf C}$ matrix in the linear system represented as a pandas DataFrame.
* ``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.
#### 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.
* ``makeNonlinearIOSystem()`` creates a ``NonlinearIOSystem`` object that simulates the SBML model.
* ``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.
### Other Functions
* ``makeTS`` creates a time series object from an array. A time series object is a DataFrame whose index in time (in integer milliseconds),
and the columns are variable names.
* ``simulateSystem`` provides a simplified way to simulate a system (which may be an ``interconnect``) by creating the times and initial,
returns a time series DataFrame.
* ``plotOneTS`` plots a single time series DataFrame.
* ``plotManyTS`` plots multiple time series DataFrames structured so that each column is a separate plot that compares the different times series.
## Example
[This notebook](https://github.com/ModelEngineering/controlSBML/blob/main/notebooks/Using-Control-SBML.ipynb) 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``.
1. To generate a new release, update the version in pyproject.py and in
_version.py.
## Version History
* 1.0.11
* 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.
نیازمندی
| مقدار | نام |
|---|---|
| - | coverage |
| - | control |
| - | docstring-expander |
| - | jupyterlab |
| - | lmfit |
| - | matplotlib |
| - | numpy |
| - | pandas |
| - | pip |
| - | pylint |
| - | python-libsbml |
| - | seaborn |
| - | symmathSBML |
| - | sympy |
| - | tellurium |
| - | twine |
| - | urllib3 |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl controlSBML-1.0.9:
pip install controlSBML-1.0.9.whl
نصب پکیج tar.gz controlSBML-1.0.9:
pip install controlSBML-1.0.9.tar.gz