CeCe is a platform for advanced simulation of cells and cell signalling in 2D. It includes a physical engine, stochastic chemical reactions, cell-cell bonding, diffusion, hydrodynamics, and a growth model.
Design experiments to differentiate interaction graph models
An activation model for the full TAM receptor family.
Influence graph analysis, consistency check, diagnosis, repair and prediction
PAR2 Activation and calcium signaling Reaction Model in PySB
Convolutional Neural Network for Dynamics EXploration (CODEX) is a method for mining time-series dataset by leveraging CNN features.
Python pipeline to build empirical kinase networks and identify kinase signalling communities from quantitative phosphoproteomics data.
Maximum Entropy (MaxEnt) parameter inference in biological networks.
Source code for "Coupling dynamics of 2D Notch-Delta signalling", by Francisco Berkemeier and Karen M. Page
napari-plugin to analyse collective signalling events
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