Integrative Scalable Computing Laboratory
A research group at the Department of Information Technology, Uppsala Universtity.
To make it easy to try StochSS, our software for rapid model development and simulation of stochastic regulatory networks, we are now providing it as a service on http://try.stochss.org. To use it, simply follow the link to set up your account. Since this only require a modern browser and a valid email address (no software installation), we hope…
I will be spending Feb 15-March 17 at the Isaac Newton Institute, Cambride, UK, for a program on Stochastic Dynamical Systems in Biology: Numerical Methods and Applications. Big thanks to the organizers,Radek Erban (Oxford), David Holcman (ENS – Paris), Samuel Isaacson (Boston) and Konstantinos Zygalakis (Southampton) for organizing this amazing opportunity to gather many creative people in…
New capabilities of Version 1.6 include: Spatial visualization now supports animation, wireframe rendering, and mesh slicing FlexCloud: run ‘cloud’ jobs on dedicated hardware (in addition to using EC2) Import SBML models Many bug fixes and stability enhancements Details and instructions on how to obtain the code can be found on the Download page Tutorials are…
We are excited to announce the release of StochSS 1.4 Version 1.4 includes spatial stochastic simulation capabilities powered by PyURDME (http://www.pyurdme.org/). Details and instructions on how to obtain the code can be found on the Download page Tutorials are available on the Documentation page Linda Petzold and Chandra Krintz – University of California Santa Barbara Per Lotstedt and Andreas Hellander – Uppsala…
Read More “StochSS 1.4: Introducing Spatial Stochastic Modeling and Simulations” »
The Center for Applied Mathematics (CIM) in Uppsala are looking for up to 3 PhD students in applied mathematics. Within this call there is an opportunity to joint the group working on the project From cell-cell interactions to embryo development: Multiscale models and simulation in systems biology. This project is a collaboration with Carolina Wählby….
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” »
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…
Read More “Multiscale and hybrid algorithms for stochastic chemical kinetics” »
