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Cells initialized in cube secrete VEGF and are themselves attracted to VEGF (i.e., they chemotax to high concentrations of VEGF), causing angiogenesis.
This is a 3D simulation, you can select a plane to view or the 3D view on the "Graphics" window. Note, important: Before switching to 3D disable the visualization of cell borders in the menu "Visualization->Cell Borders", attempting to render cell borders in 3D is slow and may cause a crash.
You can also visualize the chemical concentration from the drop-drown menu on the "Graphics" window (2D: heat-map; 3D: iso-curves).
You can create new "Graphics" windows by selecting the menu "Window-> New Graphics Window"
CompuCell3D is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in-silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials. CompuCell3D models have been used to solve basic biological problems, to develop medical therapies, to assess modes of action of toxicants and to design engineered tissues. CompuCell3D intuitive and make Virtual Tissue modeling accessible to users without extensive software development or programming experience. It uses Cellular Potts Model to model cell behavior.
Part of the nanoBio group https://nanohub.org/groups/nanobio
This project is currently funded by generous support from the U.S. National Science Foundation (NSF) and National Institutes of Health (NIH). Grants: NSF- 1720625, “Network for Computational Nanotechnology - Engineered nanoBIO Node” and NIH- R01 GM122424, “Competitive Renewal of Development and Improvement of the Tissue Simulation Toolkit”.
Cite this work
Researchers should cite this work as follows:
Multi-Scale Modeling of Tissues Using CompuCell3D – M. Swat, Gilberto L. Thomas, Julio M. Belmonte, A. Shirinifard, D.Hmeljak, J. A. Glazier, Computational Methods in Cell Biology, Methods in Cell Biology 110: 325-366 (2012)