Hellander recently received the VR Young Researcher grant, for a project titled: From Single Cells to Cancer Tumors: Multiscale Simulation of Multicellular Systems. This means that we will be expanding the group with another PhD student in early 2016. Interested candidates are encouraged to contact me to discuss opportunities.
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 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 […]
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 […]