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A tool that allows users to create symbolic CRNs with open rate and stoichiometric parameters which can then be solved using an SMT-ODE solver (iSAT-ODE included).

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max1s/Template-Based-Synthesis-Of-Chemical-Reaction-Networks

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CRNSynthesis

This is a python package for the Syntax-Guide Synthesis of Chemical Reaction Networks to meet formal specifications, using the method described in Syntax-Guided Optimal Synthesis for Chemical Reaction Networks..

A graphical web-interface to this library is provided by crn-designer.

Installation

Installing this package requires a Python installation: it should be compatible with both Python 2.7 and Python 3.

After downloading the code (either as a ZIP file or at the command-line using https://github.com/max1s/CRNSynthesis.git), change directory into the top-level CRNSynthesis/ directory and install using python setup.py install.

This will automatically install required dependencies (listed here).

You can either install the solver that you wish to use (iSAT or dReach) in a location that is on your $PATH (for example, by executing the command export PATH=$PATH:/some/path/dReal-3.16.09.01-linux/bin in the terminal), or provide the path to the correpsonding binary as an argument the the solver caller constructor (isat_path= to SolverCallerISAT, or dreal_path= to SolverCallerDReal).

Usage

Examples of usage are contained in the examples/ directory.

API docs (in HTML) are contained in the docs/ directory. These were generated using the rst branch of peterjc's fork of pdoc, using pdoc --html --overwrite --docformat=restructuredtext CRNSynthesis.

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A tool that allows users to create symbolic CRNs with open rate and stoichiometric parameters which can then be solved using an SMT-ODE solver (iSAT-ODE included).

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