Toolkit for playing around with systems biology models. Based around problem sets from An Introduction to Systems Biology by Uri Alon as well as material from Systems Biology: Properties of Reconstructed Networks by Bernhard Palsson.
Transcription network models are built up from nodes (SimpleProduct and LogicProduct) and edges (Switch) that specify the connectivity and interaction rules for the time evolution of the system.
Metabolic network models are represented as flux matrices (StoichioMatrix) with chemical rows and pathway columns specifying the mass transfer through the system.
- NumPy
- matplotlib