Tools
Tools from the Lopez Lab
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: Lolab
Thunor – Manage, visualize, and analyze high throughput cell proliferation data.
Web interface
Contact: Lolab
Core package (for standalone analysis or integration into a pipeline)
Documentation
Contact: Lolab
PyDREAM – Bayesian model calibration with Python.
Publication: PyDREAM: high-dimensional parameter inference for biological models in Python (Bioinformatics, 2017)
Contact: Lolab
cupSODA – Parallel biological simulations with GPUs and PySB.
Publication: GPU-powered model analysis with PySB/cupSODA. (Bioinformatics, 2017)
Included in PySB Github repository
Contact: Lolab
MAGINE – Network enrichment and analysis for -omics data.
Contact: Lolab
PyBILT – Python toolkit for analysis of lipid bilayer molecular simulation trajectories.
Contact: Lolab
ParticleSwarmOptimization – PSO based PySB model calibration.
Contact: Lolab
PyViPR – Dynamic and static visualizations of PySB models.
Contact: Lolab
TroPy – Identify signal drivers within a dynamic PySB network.
Contact: Lolab
HypBuilder – Automatically construct multiple large physiochemical PySB models.
Contact: Lolab
QQSB – Incorporate qualitative and quantitative experimental data in model calibration.
Contact: Lolab