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Online interactive cancer simulations and demos by Paul Macklin

This is a curated collection of interactive, online cancer simulations and demos. It will be actively updated to include new and emerging cloud-hosted tools that demonstrate discrete and agent-based models in cancer biology and oncology.

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This is a curated collection of interactive, online cancer simulations and demos. It will be actively updated to include new and emerging cloud-hosted tools that demonstrate discrete and agent-based models in cancer biology and oncology. If you spot an online simulator to include here, please contact Paul Macklin. See http://MathCancer.org/Contact.php.

Online simulators

The following are cloud-hosted, runnable cancer simulators. You can set parameters, run simulations remotely, and visualize the results in your browser.  

  • pcISA : invader-scout-attacker multicellular system
    • Author(s): Paul Macklin (lead), Randy Heiland
    • URL: https://nanohub.org/tools/pcisa/ 
    • Description: Online demo of the of an invader-scout-attacker multicellular system, to showcase chemical communication. Invaders (red) could be cancer cells, scouts (green) could be macrophages, and attackers could be activated T-cells. All agents in this simulation communicate through chemical signals. 
    • Method: Off-lattice agent-based model built from PhysiCell and Jupyter notebooks.  User interface was auto-generated by xml2jupyter
    • Reference: Ghaffarizadeh et al. (2018). DOI: 10.1371/journal.pcbi.1005991
  • pc4nanobio : cancer nanotherapy simulator
    • Author(s): Randy Heiland, Paul Macklin (lead), Eric Bower, Daniel Mishler, Tyler Zhang
    • URL: https://nanohub.org/tools/pc4nanobio/ 
    • Description: Online tool to design and explore phase-changing nanoparticles conjugated to novel cancer therapeutics. 
    • Method: Off-lattice agent-based model built from PhysiCell and Jupyter notebooks. 
    • Reference: (in preparation)
  • pc4cancerbots : cancer biorobots simulation
  • Bio-LGCA Simulator 
  • microC: A 3D virtual microenvironment for perturbation biology

Downloadable simulators and games

The following are user-friendly, downloadable simualtion games and apps. You can explore cancer models and potential treatments. Please note that these may or may not be available on all platforms.  

  • Cancer Crusade
    • Author: Integrative Mathematical Oncology (IMO) at the Moffitt Cancer Center, directed by Alexander R.A. Anderson
    • URL: http://cancercrusadegame.com/ 
    • Platforms: Android and iPhone 
    • Description: Downloadable cancer therapy "game" based upon earlier published simulation models. Users can try their own therapy designs, and watch the impact in an evolving (and mutating!) cancer landscape. 
    • Method: Cellular automaton cells coupled with (finite difference) PDE solvers  
    • Reference: (in preparation)

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Paul Macklin

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