As a metabolic network reaches from a state to a steady state, a subset of its fluxes gradually change. The sequence of intermediate states, called the dynamic state, shows the pa...
Background: We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our appro...
Motivation: High-throughput methods for detecting molecular interactions have produced large sets of biological network data with much more yet to come. Analogous to sequence alig...
Background: The Distributed Annotation System (DAS) has proven to be a successful way to publish and share biological data. Although there are more than 750 active registered serv...
Bernat Gel, Andrew M. Jenkinson, Rafael C. Jimenez...
Background: In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state...