BioCRNPyler - Biomolecular Chemical Reaction Network Compiler

BioCRNpyler (pronounced “bio compiler”) is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex biochemical networks. BioCRNpyler compiles high-level design specifications for biochemical processes – represented using a modular library of biochemical parts, mechanisms, and contexts – to CRN implementations.

Features

  • Automated constructions of CRN representations to Systems Biology Markup Language (SBML) models compatible with numerous simulators

  • Library of modular biochemical components allows for different architectures and implementations of biochemical circuits to be represented succinctly with design choices propagated throughout the underlying CRN automatically

  • High-level design specifications can be embedded into diverse biomolecular environments, such as cell-free extracts and in vivo systems

  • Includes a parameter database that allows users to rapidly prototype large models using very few parameters that can be customized later in the development cycle

Links:

How to cite

An article about the package is available in PLOS Computational Biology. If the BioCRNpyler package helped you in your research, please cite:

@article{biocrnpyler2022,
  title={{BioCRNpyler}: {Compiling} chemical reaction networks from
         biomolecular parts in diverse contexts},
  author={W. Poole and A. Pandey and A. Shur and Z. A. Tuza and
          R. M. Murray},
  journal = {PLOS Computational Biology},
  year = {2022},
  month = {04},
  volume = {18},
  url = {https://doi.org/10.1371/journal.pcbi.1009987},
  pages = {1-19}
}

or the GitHub site: https://github.com/BuildACell/BioCRNPyler.

User Guide

Reference Manual

Indices and tables