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Section: New Software and Platforms
TiSim
Tissue Simulator
Keywords: Systems Biology - Bioinformatics - Biology - Physiology
Scientific Description: TiSim (Tissue Simulator) is a versatile and efficient simulation environment for tissue models. TiSim is a software for agent-based models of multicellular systems. It permits model development with center-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. The simulation code is in the process of being published. The modeling strategy and approaches slowly reach systems medicine and toxicology. The diffusion of software is a fundamental component as it provides the models that are complex and difficult to implement (implementing a liver lobule model from scratch takes about 2-2.5yrs) in form of a software to the developer and users who like to build upon them. This increases significantly the speed of implementing new models. Moreover, standardization is indispensible as it permits coupling different software tools that may have implemented models at different scales / levels.
Functional Description: TiSim is a software that permits agent-based simulations of multicellular systems. - center-based lattice-free agent-based model - modular - C++, Qt, OpenGL, GUI, batch mode - permits multiscale simulations by integration of molecular pathways (for signaling, metabolisms, drug) into each individual cell - applications so far: monolayer growth, multicellular spheroids - Boolean networks (development time = coding time ( 60 MMs) + model development time ( 264 MMs)) - in follow-up version 1: - liver lobule regeneration - SBML interface - in follow-up version 2: - deformable cell model (by triangulation of cell surface) - deformable rod models - extracellular matrix - vascular flow and transport TiSim can be directly fed by processed image data from TiQuant.