Open PhD student position
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.
PyURDME 1.0
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 […]
ECMTB 2014 and Computational Software
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 […]
PhD and Postdoc positions
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. […]
First release of StochSS
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 […]
Back in Uppsala
After two great years as a postdoc with Linda Petzold at UCSB, I am now back in Uppsala as a senior lecturer at the division of scientific computing, department of information technology. Candidates for PhD projects, master’s thesis projects and postdoc positions are more than welcome to contact me to discuss opportunities to join the […]
Perspective: Stochastic Algorithms for Chemical Kinetics
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 […]
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 are 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 […]
URDME paper in BMC Systems Biology
Ever since the first version of URDME, a software framework based on our theoretical work on RDME simulations on unstructured meshes, was made public in 2008, we have wanted to write up a journal publication that describes the software. For variuos reasons we have not gotten around to it, until now. The paper, published in […]