Tools
Tools from the center
PySB – A Python framework for systems biology modeling.
Publication: Programming biological models in Python using PySB (Molecular Systems Biology, 2013)
For examples of models built with PySB, see the Models page.
Contact: Carlos Lopez
Thunor – Manage, visualize, and analyze high throughput cell proliferation data.
Web interface
Contact: Alex Lubbock
Core package (for standalone analysis or integration into a pipeline)
Documentation
Contact: Alex Lubbock
PyDREAM – Bayesian model calibration with Python.
Publication: PyDREAM: high-dimensional parameter inference for biological models in Python (Bioinformatics, 2017)
Contact: Erin Shockley
MAGINE – Network enrichment and analysis for -omics data.
Contact: James Pino
PyViPR – Dynamic and static visualizations of PySB models.
Contact: Oscar Ortega
HypBuilder – Automatically construct multiple large physiochemical PySB models.
Contact: Michael Kochen