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A simple birth-death agent-based model of tumor evolution (with lineage tracking) built in HAL.
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README.md

HAL + EvoFreq tutorial

Click here for the blog tutorial associated with this repository

This is the open-source code repository for the passenger driver model of tumor evolution. This is a two-dimensional on lattice agent-based model.

Before you start

TumorEvolution.java uses the open-source agent-based modeling platform called HAL. In order to run this code base, you'll need to download the latest version of Java and an editor (we suggest using IntelliJ Idea).

Setting up the project in IntelliJ Idea

  1. Open Intellij Idea and click "create project from existing sources" ("file/ new/ project from existing sources" from the main GUI) and direct it to the unzipped AgentFramework Source code directory.
  2. Continue through the rest of the setup, click next until it asks for the Java SDK:
  • "/Library/ Java/ JavaVirtualMachines/" on Mac.
  • "C:\ Program Files\ Java" on Windows.
  1. Once the setup is complete we will need to do one more step and add some libraries that allow for 2D and 3D OpenGL visualization:
  2. open the Intellij IDEA main gui
  3. go to "file/ project structure"
  4. click the "libraries" tab
  5. use the minus button to remove any pre-existing library setup
  6. click the plus button, and direct the file browser to the "HAL/ lib" folder.
  7. click apply or ok

References

  1. Chandler D. Gatenbee, Ryan O. Schenck, Rafael Bravo, Alexander R.A. Anderson. EvoFreq: Visualization of the Evolutionary Frequencies of Sequence and Model Data. 2019. bioRxiv.

  2. Jeffrey West, Ryan Schenck, Chandler Gatenbee, Mark Robertson-Tessi, Alexander RA Anderson. Tissue structure accelerates evolution: premalignant sweeps precede neutral expansion. 2019. bioRxiv.

  3. Hybrid Automata Library: A modular platform for efficient hybrid modeling with real-time visualization Rafael Bravo, Etienne Baratchart, Jeffrey West, Ryan O. Schenck, Anna K. Miller, Jill Gallaher, Chandler D. Gatenbee, David Basanta, Mark Robertson-Tessi, Alexander R. A. Anderson bioRxiv 411538.

Magma RPlot

Colored By HAL Scheme RPlot

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