Integrative Scalable Computing Laboratory
A research group at the Department of Information Technology, Uppsala Universtity.
We are currently hiring a PhD student to work on the project From Single Cells to Tumors – Multiscale Simulation of Stochastic (multi)cellular Systems . Deadline for application: March 15. Instructions for how to apply can be found here: Instructions for application.
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” »
We have an opening for a PhD student in computational systems biology. Interested candidates are encouraged to contact me for more details. Apply to the position here.
After more than a year of development, we are happy to announce the release of PyURDME 1.0.0! PyURDME is a Python module for spatial stochastic simulation model development and simulation. PyURDME is connected to URDME in that is uses a modified version of its core solver. While URDME is mainly designed as an interactive Matlab…
I attended this years ECMTB 2014. Apart from many interesting sessions on mathematical modeling, I attended this minisymposia on software for multicellular simulations. All the speakers had done a great job developing software for the application community, but the impression was that they managed to do this despite being productive methods researchers, not as a…
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….
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” »