Spatial Stochastic Simulation of the Hes1 gene regulatory network

Individual mouse embryonic stem cells have been found to exhibit highly variable differentiation responses under the same environmental conditions. Recent experimatal evidence suggest that the noisy cyclic expression of Hes1 and its downstream genes areĀ  responsible for this, but the mechanism underlying this variability in expression is not well understood. Together with Mark Chaplain’s group, […]

URDME 1.2 Released

We are happy to announce the release of URDME 1.2. New features include support for Comsol 4.1, 4.2 and 4.3. We have also added the ability to compile the solvers independently of Matlab libraries. This will greatly simplify deployment of URDME jobs by StochSS down the line. To get URDME 1.2: www.urdme.org Or visit us […]

Multiscale and hybrid algorithms for stochastic chemical kinetics

Many biochemical network models display scale separation with respect to reaction rates and/or molecular copy numbers. Depending on the type of question under study, different models are best suited to simulate the system. For some parts of the system, a macroscopic model might be appropriate. For other parts, a mesoscopic model may provide additional insight […]