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Tools

Tools from the Lopez Lab

pysb-swirlPySB – A Python framework for systems biology modeling.

Publication: Programming biological models in Python using PySB (Molecular Systems Biology, 2013)

GitHub repository

Documentation and Tutorials

For examples of models built with PySB, see the Models page.

Contact: Carlos Lopez

thunor Thunor – Manage, visualize, and analyze high throughput cell proliferation data.

Web interface

Demo

Introduction Video

GitHub repository

Documentation

Contact: Alex Lubbock

Core package (for standalone analysis or integration into a pipeline)

GitHub repository

Documentation

Contact: Alex Lubbock

PyDREAM – Bayesian model calibration with Python.

Publication: PyDREAM: high-dimensional parameter inference for biological models in Python (Bioinformatics, 2017)

Github repository

Documentation

Contact: Erin Shockley

cupSODA – Parallel biological simulations with GPUs and PySB.

Publication: GPU-powered model analysis with PySB/cupSODA. (Bioinformatics, 2017)

Included in PySB Github repository

Contact: James Pino

MAGINE – Network enrichment and analysis for -omics data.

Github repository

Documentation

Contact: James Pino

pybiltPyBILT – Python toolkit for analysis of lipid bilayer molecular simulation trajectories.

Github repository

Documentation

Contact: Blake Wilson

ParticleSwarmOptimization – PSO based PySB model calibration.

Github repository

Contact: James Pino

 pyvipr_logoPyViPR – Dynamic and static visualizations of PySB models.

Github repository

Contact: Oscar Ortega

TroPy – Identify signal drivers within a dynamic PySB network.

Github repository

Contact: Oscar Ortega

HypBuilder – Automatically construct multiple large physiochemical PySB models.

Github repository

Contact: Michael Kochen

QQSB – Incorporate qualitative and quantitative experimental data in model calibration.

Contact: Michael Irvin