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Frameworks

The nanoBIO node has many apps and tools built from external frameworks. Please see the related webpages for more information.

PhysiCell

PhysiCell aims to provide a robust, scalable code for simulating large systems of cells in 3-D tissues on standard desktop computers. Many multicellular systems problems can only be understood by studying how cells move, grow, divide, interact, and die. Tissue-scale dynamics emerge from systems of many interacting cells as they respond to and influence their microenvironment. The ideal "virtual laboratory" for such multicellular systems simulates both the biochemical microenvironment (the "stage") and many mechanically and biochemically interacting cells (the "players" upon the stage). PhysiCell was developed to work in concert with BioFVM to fill this role as a virtual laboratory.

CompuCell3D

CompuCell3D allows biomodelers  to effectively use a multi-scale, multi-cell simulation environment to build, test, run and post-process simulations of biological phenomena occurring at single cell, tissue or even up to single organism levels. Simulations of tissues, organs and organisms require one to simplify and adapt single cell simulations to apply them efficiently to study, in-silico, ensembles of several million cells. To be useful, these simplified simulations should capture key cell-level behaviors, providing a phenomenological description of cell interactions without requiring prohibitively detailed molecular-level simulations of the internal state of each cell. While an understanding of cell biology, biochemistry, genetics, etc. is essential for building useful, predictive simulations, the hardest part of simulation building is identifying and quantitatively describing appropriate subsets of this knowledge. In the excitement of discovery, scientists often forget that modeling and simulation, by definition, require simplification of reality.

v. 4 is now available here.

Fury

Fury is a Python library available for scientific visualization. The library is available via PyPi or Anaconda package system. Go here for more information.