Indiana University

Indiana University is a prominent member of the OpenVT community, recognized for developing the CompuCell3D and PhysiCell frameworks. CompuCell3D specializes in cellular Potts modeling, while PhysiCell focuses on center modeling, both offering detailed simulations of cellular dynamics and enable practitioners to investigate a variety of biological scenarios, from tumor growth to tissue regeneration, reinforcing Indiana University's role as a leader in blending engineering, computer science, and biology for virtual tissues.

CompuCell3D PhysiCell

University of Florida

The University of Florida excels in the OpenVT community with its Tissue Forge framework, designed for detailed particlebased modeling in physics, chemistry, and biology. This robust platform facilitates dynamic modeling of tissue structures across multiple scales, supported by extensive customization via Python and C/C++ APls. Tissue Forge empowers researchers to simulate complex biological processes, solidifying the University of Floridas reputation as a global leader in blending engineering, computer science, and biology for advanced multicellular virtual tissues.

Tissue Forge

University of Washington

The Center for Reproducible Biomedical Modeling at The University of Washington supports OpenVT. This Center focuses on enhancing simulations and models of biological systems from cellular processes to entire bodies. The center develops technologies that improve the accuracy, scalability, and reproducibility of models, ensuring their reliability for clinical use. It helps scientists annotate and verify models, promoting best practices in systems biology and multi-scale modeling. This is transforming complex system modeling in the scientific community.

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University of Melbourne

Chaste

University of Connecticut

The Center for Cell Analysis and Modeling at UConn Health is advancing the OpenVT community with Vivarium, a versatile software tool for integrative multiscale modeling. Vivarium offers an interface for converting individual simulators into modules, which can then be combined into large composite simulators, parallelized across computing nodes, and cosimulated across multiple spatial and temporal scales. This modular approach promotes interoperability, reusability, and composability, cementing UConn's role as a pioneer in advanced computational biological modeling.

Vivarium Collective

Technische Universität Dresden, Germany

The Center for Interdisciplinary Digital Sciences (CIDS) at Technische Universität Dresden, Germany, hosts Morpheus.lab and supports OpenVT. Morpheus allows to simulate multicellular dynamics based on the cellular Potts formalism with coupling to intracellular and extracellular ODEs (SBML-encoded) and PDEs. The Morpheus framework provides a user-friendly GUI, online course materials, the parameter estimation tool FitMultiCell and a model repository using the modeling language MorpheusML, which separates the complete model definition from the simulation code.

Modeling and simulation framework Morpheus Bayesian parameter estimator FitMultiCell for stochastic multicellular models MorpheusML model repository Plans for modular standard MultiCellML including SBML extension packages Standardization community COMBINE

Goethe-Universität Frankfurt, Germany

Coming soon...

Radboud University Nijmegen, Netherlands

Artistoo

Swiss Institute of Bioinformatics (SIB), Basel, Switzerland

SimuCell3D PolyHoop

Utrecht University, Utrecht, Netherlands

The Theoretical Biology and Bioinformatics division within the Institute for Biodynamics and Biocomplexity at Utrecht University has a long-standing focus on advancing the development and application of the cellular Potts modeling. Researchers from this institute actively contribute to the OpenVT community, and collaborate closely with Leiden University in development of the Tissue Simulation Toolkit. A platform for multiscale modeling of multicellular systems integrating biophysical, mechanical, and biochemical processes. This is done by combining cellular Potts with ordinary differential equations (ODEs) and fiber-based models of extracellular matrix (ECM), enabling advanced modeling of multicellular systems.

Tissue Simulation Toolkit VirtualLeaf