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VirtualTumorEvolution

A Python script to simulate 3D tumor growth and multi-region sequencing data via an agent-based model. Deme subdivision is assumed in order to model cell mixing and spatial contraint

  • Spatial model: peripheral growth

Author

  • Zheng Hu in Curtis lab@Stanford
  • Release Date: 2/23/2017

Requirements

Python packages: numpy,sys,math,random,collections,sets

Usage

  • Simulation of a typical tumor (~10^9 cells) is computationally costly. We suggest to run this script on HPC cluster.
  • The memory cost is also large, e.g. it costs about ~40G when the final_tumor_size = 10^9 and mut_rate = 0.6.

To run the script

$ python 3DTumorSimul_MultiRegionSeq.py deme_size mut_rate adv_rate s_coef repl
e.g., python 3DTumorSimul_MultiRegionSeq.py 5000 0.6 0.00001 0.1 0