Integrative Scalable Computing Laboratory
A research group at the Department of Information Technology, Uppsala Universtity.
We are excited to announce the first release of StochSS: Stochastic Simulation Service. StochSS is an integrated development environment featuring state of the art algorithms for discrete stochastic biochemical simulation. StochSS is designed to enable you to easily scale up your simulations in complexity, deploying compute resources as needed. The current version includes algorithms for…
In a new paper in the Journal of Chemical Physics, Dan Gillespie, myself and Linda Petzold review theory and algorithms for well-mixed and spatial mesoscopic chemical kinetics. In an associated podcast, available in the journal’s Perspectives collection, we share some of our views on the grand challenges facing us as methods developers as the field…
Read More “Perspective: Stochastic Algorithms for Chemical Kinetics” »
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 are responsible for this, but the mechanism underlying this variability in expression is not well understood. Together with Mark Chaplain’s group,…
Read More “Spatial Stochastic Simulation of the Hes1 gene regulatory network” »