Hypoxia Simulator

This model simulates the dynamics of tumor cells in a microenvironment subject to intratumoral hypoxia.

Legend:

•   DsRed+/GFP- cell
•   DsRed+/GFP+ cell
•   DsRed-/GFP+ cell
•   Necrotic cell

Modeling description

In this model, we simulate the evolution of a tumor subject to hypoxia. The tumor microenvironment is initially composed of a cluster of cells at the center of the domain. The oxygen concentration is diffused in the environment, providing viability for the cells until a specific moment, where the cells begin to suffer stress due to the lack of oxygen and enter the state of hypoxia. The cells that experience hypoxia have a permanent mark, and they respond to the migratory stimulus differently.

GUI Overview

• Config Basics tab:    input parameters common to all models (e.g., domain grid, simulation time, choice/frequency of outputs)
• Microenvironment tab:   microenvironment parameters that are model-specific
• User Params tab:      user parameters that are model-specific
• Out: Plots tab:           output display of cells and substrates
• Animate tab:              generate an animation of cells

Edit the domain size and simulation length in the Config Basics tab. Edit diffusion parameters in the Microenvironment tab, and model-specific parameters in the User Params tab. Once you are satisfied with your settings, click the Run button to start the simulation. (After the run starts, the the Run button is replaced with a Cancel button.)

As the simulation runs, an "Output" widget can be clicked/expanded to reveal the progress (text) of the simulation. Model outputs can be visualized in the Out: Plots tab while the simulation is running. The "# cell frames" will be dynamically updated as the simulation progresses. Note that the simulation images (SVG files) and raw output data (in MultiCellDS format) can be downloaded in this tab once the simulation is done.

Once the simulation is done running, use the Animate tab to create a movie. Please be patient: it may take a few minutes for the script to finish running before the movie is embedded in the tab. You can download the generated movie once it's done.

This software is powered by PhysiCell [1-2], a powerful simulation tool that combines multi-substrate diffusive transport and off-lattice cell models. PhysiCell is BSD-licensed, and available at:

• GitHub releases: https://github.com/MathCancer/PhysiCell/releases
• SourceForge downloads: https://sourceforge.net/projects/physicell/

It is a C++, cross-platform code with minimal software dependencies. It has been tested and deployed in Linux, BSD, OSX, Windows, and other environments, using the standard g++ compiler. 

See http://PhysiCell.MathCancer.org.

The Jupyter-based GUI was auto-generated by xml2jupyter [3], a technique to create graphical user interfaces for command-line scientific applications.

1. Ghaffarizadeh A, Heiland R, Friedman SH, Mumenthaler SM, Macklin P (2018) PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems. PLoS Comput Biol 14(2): e1005991. https://dx.doi.org/10.1371/journal.pcbi.1005991
2. Ghaffarizadeh A, Friedman SH, Macklin P (2016) BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations. Bioinformatics 32(8):1256-8. https://dx.doi.org/10.1093/bioinformatics/btv730

Researchers should cite this work as follows:

• Lima Da Rocha, Heber, Paul Macklin (2020), "PhysiCell model for tumor hypoxia," https://nanohub.org/resources/pc4tumorhypoxia. (DOI: 10.21981/6SNT-7K48).

  BibTex | EndNote

1. cells
2. hypoxia
3. nano/bio
4. NanoBio Node at Indiana
5. PhysiCell
6. Tumors