Summary: Qualitative modeling of biological systems
ˇ The functional form of regulatory relationships and kinetic parameters
are often unknown
ˇ Increasing evidence for
ˇ robustness to changes in kinetic parameters.
Hypothesis: the kinetic details of individual interactions are less
important than the organization of the regulatory network
Network topology: identity of nodes, edge attributes (direction, sign)
Topological features such as path redundancy and feedback loops
constrain network dynamics.
First step - pseudo-dynamics: propagation of reactions in chemical
(interaction) space, starting from a source (signal)
Qualitative models are most closely based on the network topology.
Ma'ayan et al, Science 309, 1078 (2005)
Boolean modeling of biological systems
Main assumption: components have two main states :
Expressed or not expressed, active or inactive, open or closed (ion
channel), high or low level. Denote these states by ON (1) or OFF (0)
The changes in state are given by discrete (logical) rules.