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. 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
  • Author(s): Randy Heiland, Paul Macklin (lead)
  • URL: https://nanohub.org/tools/pc4cancerbots/ 
  • Description: Online demo of the "cancer bio-robots" example from the PhysiCell method paper. "Workers" (red) haul drug-loaded "cargo" (blue) along hypoxic gradients towards cancer cells (green). 
  • 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
• Bio-LGCA Simulator 
  • Author(s): Andreas Deutsch and Sabine Dormann
  • URL: https://imc.zih.tu-dresden.de/biolgca/#fig=9.6  
  • Description: Online demos for lattice gas models of biological pattern formation 
  • Method: Javascript implementations of lattice gas models.  
  • Reference: https://dx.doi.org/10.1007/978-1-4899-7980-3 

• microC: A 3D virtual microenvironment for perturbation biology

  • Author(s): Dimitrios Voukantsis, Kenneth Kahn, Martin Hadley, Rowan Wilson, Fracesca Buffa (lead)

  • URL: https://merlin.oncology.ox.ac.uk/microc/index.html

  • Description: Online tool to simulate perturbations in a tumor-microenvironment system (with a gene network)

  • Method: Agent-based model (in NetLogo) with a signaling network.

  • Reference: https://doi.org/10.1093/gigascience/giz010

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)