We have developed a multiscale method coupling the mesoscopic and microscopic scales. On the mesoscopic scale, systems are modeled as discrete jump processes on a structured or unstructured grid, while on the microscopic scale, molecules are modeled by hard spheres diffusing in continuous space. Microscopic simulations are accurate but computationally expensive. In this paper we […]
We are welcoming Lovisa Lugnegård to the group this semester. Lovisa will be doing a MSc thesis project of relevance to the HASTE project. She will design and prototype a cloud-based simulator capable of streaming already generated microscopy data, varying a wide range of parameters and emulating realistic scenarios when running high-content imaging platforms.
We are delighted to have Stefan Hellander join the lab! Stefan obtained his Ph.D. in scientific computing from Uppsala University in 2013, with the thesis “Stochastic Simulation of Reaction-Diffusion Processes”, advised by Prof. Em. Per Lötstedt. He then went on to work as a postdoc in the lab of Prof. Linda Petzold at UCSB, […]
Fredrik Wrede presented a poster titled “Smart systems for model exploration with application in computational systems biology” at the Machine Learning in Systems Biology (MSLB) 2017 Workshop held as a special session of ISMB 2017, Prague, Czech Republic, on July 25, 2017.
Our project Hierarchical Analysis of Spatial and TEmporal Data (HASTE) is granted 29 MSEK funding from SSF. The project, with PI Carolina Wählby and co-PIs Andreas Hellander, Ola Spjuth and Mats Nilsson, will explore new ways to gain insight from massive amounts of spatial and temoral image data through hierarchical analysis models and smart cloud systems […]
We are looking for a postdoc to work on development of new simulation methods for cell-level modeling of developmental processes.
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 […]