In bioinformatics, biochemical pathways can be modeled by many differential equations. It is still an open problem how to fit the huge amount of parameters of the equations to the...
We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms. Each per...
Background: Genome-scale metabolic reconstructions under the Constraint Based Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the metabolic capabili...
Jan Schellenberger, Junyoung O. Park, Tom M. Conra...
We provide a logical model of biochemical reactions and show how hypothesis generation using weakest sufficient and strongest necessary conditions may be used to provide addition...
Patrick Doherty, Steve Kertes, Martin Magnusson, A...
Kinetic models for biochemical systems often comprise a large amount of coupled differential equations with species concentrations varying on different time scales. In this paper w...