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 […]
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 […]
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 […]
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, […]
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 […]
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 […]
The RDME will break down in the limit of vanishing voxel sizes, in the sense that contributions from bimolecular reactions will be lost. The problem sets on earlier (for larger voxels), the more diffusion limited the reaction is. This is a problem that has attracted a lot of interest since it was pointed out by […]
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 […]