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Section: New Software and Platforms

TiSim

Tissue Simulator

Keywords: Systems Biology - Bioinformatics - Biology - Physiology

Functional Description

TiSim (Tissue Simulator) is a software for agent-based models of multicellular systems. It permits model development with centre-based models and deformable cell models; it contains modules for monolayer and multicellular spheroid simulations as well as for simulations of liver lobules. Besides agent-based simulations, the flow of blood and the transport of molecules can be modelled in the extracellular space; intracellular processes such as signal transduction and metabolism can be simulated, for example over an interface permitting integration of SBML-formulated ODE models.

TiSim is written in modern C$++$, keeping central model constituents in modules to be able to reuse them as building blocks for new models. For user interaction, the GUI Framework Qt is used in combination with OpenGL for visualisation. A non-interactive mode to use the software also exists, accepting a combination of XML and HDF5 (hierarchical data format v5) as input, which produces output data in VTP (VTK) and HDF5 format. SBML, SBML_ODESolver and sundials are deployed for the creation and solution of the differential equations of metabolic networks and signalling pathways presented in SBML data format. TiSim permits agent-based simulations of multicellular systems and can be directly fed by processed image data from TiQuant.

• Contact: Dirk Drasdo

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