We are looking for a talented individual to join our efforts on creating smart and scalable cloud services to support simulation-driven scientific discovery via large-scale computational experiments such as parameter sweeps. This is a classic and very important problem that we will approach in new ways, leveraging recent advances in cloud computing, data-intensive computing and machine […]
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 […]
We are very happy to welcome Fredrik Wrede, MSc. in Bioinformatics, to the group. Fredrik was accepted as a PhD student in CIM, the Center for Interdisciplinary Mathematics. His project will center around intelligent cloud services for processing and making sense of massive amounts of data, for example generated by large computational experiments in systems […]
Last week brought some great news. I am awarded the Göran Gustafsson Prize 2016 from the Gustafsson Foundation (KTH/UU). In the proposed project titled Smart Services for Scientific Discovery we will look into new and more productive ways to combine simulation software and cloud computing infrastructure to build intelligent applications for e.g. exploring an underlying model’s essential […]
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 […]