Tag: Cancer Diagnosis

MaBoSS is a simulation software for continuous time Boolean modeling. The model is described by a network, where nodes have Boolean states. Transitions between the node states are governed by logical equations, with an associated rate (a real number ∈[0,∞[⁠).

COBRA (Constraint-Based Reconstruction and Analysis) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many orders of magnitude. Data values also have greatly varying magnitudes. Standard double-precision solvers may return inaccurate solutions or report that no solution exists. Exact simplex solvers based on rational arithmetic require a near-optimal warm start to be practical on large problems (current ME models have 70,000 constraints and variables and will grow larger).