Summary

Simulations of hematopoietic stem cells to accompany our paper "Cell lineage tracing with molecular clocks based on fluctuating DNA methylation."

The provided .jar file is used to exectue the model while the two accompanying files (run_simulations.sh and GeneratePlots.py) allow you to recreate the plots used within the paper.

Dependencies

1. Python (>=3.6)
2. Java 1.8
3. Java JDK

Execution

1. Clone the repository: git clone https://github.com/MathOnco/ticktockblood.git

2. Navigate into the directory from the commandline cd ticktockblood

3. Execute the simulations bash run_simulations.sh

4. Once simulations have completed, run the python script to generate figures using the following command python GeneratePlots.py Normal 2500 ALL.0.9 300 ALL.0.5 300 ALL.0.2 300 CL.0.9 1500 CL.0.5 1500 CL.0.2 1500 CHIP.0.9 2500 CHIP.0.5 2500 CHIP.0.2 2500

This will produce two .png files from the simulations.

Additional informaiton

To execute the model using any parameter set you want refer to the help menu from the jar file:

java -jar ./TickTockBlood.jar --help

Source code is located within the ./src/ directory. This includes dependencies within the HAL framework and those required for the jar file build.