BioCRNpyler 0.9.0

A chemical reaction network compiler for generating large biological circuit models

BioCRNPyler -- Biomolecular Chemical Reaction Network Compiler

Python toolbox to create CRN models in SBML for biomolecular mechanisms

BioCRNPyler is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.

• Website: https://github.com/BuildACell/BioCRNPyler
• Mailing list: TBA
• Source: https://github.com/BuildACell/BioCRNPyler
• Bug reports: https://github.com/BuildACell/BioCRNPyler/issues
• Documentation biocrnpyler.readthedocs.io

Simple example

Building a simple reaction network

from biocrnpyler import *
# let's build the following CRN
# A -->[k1] 2B
# B -->[k2] B+D
# Species
A = Species("A")
B = Species("B")
C = Species("C")
D = Species("D")

#Reaction Rates
k1 = 3.
k2 = 1.4

#Reaciton Objects
R1 = Reaction.from_massaction([A], [B, B], k_forward = k1)
R2 = Reaction.from_massaction([B], [C, D], k_forward = k2)

#Make a CRN
CRN = ChemicalReactionNetwork(species = [A, B, C, D], reactions = [R1, R2])
print(CRN)

More advanced examples can be found in the example folder, here's the first file in the Tutorial series: Building CRNs

Installation

Install the latest version of BioCRNPyler::

$ pip install biocrnpyler

Install with all optional dependencies::

$ pip install biocrnpyler[all]

Further details about the installation process can be found in the BioCRNPyler wiki.

Bugs

Please report any bugs that you find here. Or, even better, fork the repository on GitHub, and create a pull request (PR). We welcome all changes, big or small, and we will help you make the PR if you are new to git (just ask on the issue and/or see docs/CONTRIBUTING.md).

Versions

BioCRNpyler versions:

• 1.0.0 (latest stable release): To install run pip install biocrnpyler
• 0.2.1 (alpha release): To install run pip install biocrnpyler==0.2.1

License

Released under the BSD 3-Clause License (see LICENSE)

Copyright (c) 2020, Build-A-Cell. All rights reserved.