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Flexible Model Specification, Fast Simulation, and Bayesian Parameter Inference for Biological Circuits

The bioscrape package is a Python package for doing the types of modeling and computational tasks that are commonly required for scientists and researchers working in the field of systems biology or synthetic biology. It can be somewhat framed a Python alternative to MATLAB's SimBiology, though there are some features in the package that are not available in SimBiology (Bayesian parameter inference, many features of stochastic simulation, and support for delays), and a great number of features in SimBiology that are not part of the package. For installation, usage, examples, and other information, please use the links below. You can access the code from the repository by clicking on the link above. For citing, please see the references below.

Table of Contents

Overview

Installation

Examples

Citing and Feedback

Core Feature Documentation

• Model API

• Simulators

• Propensities

• Delays

• Cell Lineage Simulation

• Parameter Inference

• SBML Support

Citing and Feedback

If you have feedback on the software, please feel free to contact Prof. Richard M. Murray at Caltech. For citing, please cite this article.