A research group at the Department of Information Technology, Uppsala Universtity.
Artificial intelligence is rapidly transforming our society. Machine learning models will soon be in every digital system we use. For this reason, there is an urgent need for methods and software that allows for development of state-of-the art ML models while protecting the integrity of data owners . In this project we work on algorithms,…
Biochemical reaction networks represent complex cellular regulatory mechanisms. These networks are typically analyzed using discrete stochastic simulation models. The models typically involve numerous reactions involving a large number of chemical species, governed by highly uncertain parameters. Likelihood-free parameter inference Given existing data pertaining to a biochemical reaction network, one is often interested in inferring the…
Read More “Machine learning-assisted analysis of stochastic biochemical reaction networks” »
We currently have MSc projects available in the area of multicellular systems biology. Interested students are encouraged to contact us to learn more about the opportunities. Msc project in bone remodeling
A new semester has just started, and there is no better way to kick it off than to welcome a new group member! Anass Bouchnita has joined us for to do a postdoc in computational systems biology. He will work on multiscale methods for multicellular modeling and simulation, in a collaboration with Igor Adameyko at…
The SNIC Science Cloud (SSC) team has published a paper in the 2017 conference on IEEE eScience. SNIC Science cloud has been an infrastructure project run by the Swedish National Infrastructure for Computing (SNIC) with the purpose to assess if and how SNIC should offer cloud infrastructure to the scientific community. The project is now coming…
We are thrilled to welcome Dr. Ben Blamey as a postdoc in the group. Ben will work on our SSF-funded HASTE project, with intelligent systems for setting up and managing information hierarchies in very large volumes of image data from microscopy, read mroe about Ben and the project here: Ben Blamey joins the team to…
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…
Read More “Mesoscopic-microscopic hybrid algorithm with automatic partitioning” »
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.
