Bioscrape - Biological Modeling, Simulation, and Inference

Bioscrape is a Python package for deterministic, stochastic, delayed, and cell-lineage simulation of biological chemical reaction network models. It also provides parameter inference tools that can be applied to estimate model parameters from experimental data.

Features

• Fast Cython simulators for deterministic, stochastic, delayed, and cell-lineage models.

• SBML support for loading, saving, and exchanging biological chemical reaction network models.

• Python APIs for constructing models, propensities, delays, rules, and simulation workflows.

• Bayesian and deterministic parameter inference interfaces built on the Bioscrape simulation stack.

Links

• Source code: https://github.com/biocircuits/bioscrape

• Bug reports: https://github.com/biocircuits/bioscrape/issues

• Mailing list: SBTools Google Group

• Citation details: Paper and Citation

User Guide

• 1. Overview
• 2. Installation
• 3. Examples
• 4. Simulators
• 5. Propensities
• 6. Delays in Bioscrape
• 7. Sensitivity Analysis
• 8. Bioscrape Inference
• 9. SBML Support
• 10. Cell Lineage Simulation

Tutorial Examples

• Tutorial Examples

Reference Manual

• API Reference
• Paper and Citation
• Developer Notes

Indices and tables

• Index

• Module Index

• Search Page