Likelihood-free parameter inference

Biochemical reaction networks represent complex cellular regulatory mechanisms. These networks are typically analyzed using discrete stochastic simulation models. The models may involve numerous reactions involving a large number of chemical species, governed by highly uncertain parameters. Given existing data pertaining to a biochemical reaction network, one is often interested in inferring the values of the […]

Hierarchical Analysis of Spatial and Temporal Data

The HASTE project, a SSF-funded project on computational science and big data, takes a holistic approach to new, intelligent ways of processing and managing very large amounts of microscopy images to leverage the imminent explosion of image data from modern experimental setups in the biosciences. One central idea is to represent datasets as intelligently formed […]

Scalable simulation of stochastic multicellular systems

In multicellular systems, cells of different types interact in various ways, both mechanically and chemically, to regulate complex processes. There is a large computational gap between detailed models of sub-cellular, molecular processes in single cells, and models of multicellular systems comprising of large numbers of interacting cells such as bacterial colonies, tissue and tumors. In […]

Intelligent model exploration

The integration between on the one hand data, modeling and algorithms, and on the other hand the specification, coordination and execution of large scale and data-intensive computational experiments poses a fundamental problem in all scientific disciplines relying on modeling and simulation. Today it is largely left to the modeler or engineer to manually tune models […]

StochSS: Stochastic Simulation Service

StochSS is an integrated development environment (IDE) for discrete stochastic biochemical simulations. Users make use of a graphical user interface (GUI) to define their problem, including its domain (geometry, volume), molecular interactions (stoichiometry, rate constants), and simulation goals (single trajectory, histogram, probabilities of rare events). The platform transparently executes model workflows using local resources (laptops, […]

Multiscale simulations of chemical kinetics

Life spans in size from small organisms consisting of single cells to complex organisms built up of billions of cells. Even the single-cell organisms are challenging to fully understand and study—their function is dependent on a rich set of reaction networks. Important molecules inside a cell may exist in only a few copies, and that […]