Evolutionary Telomere Dynamics

Author: Kent Horvath, MD PhD kenthorvath@gmail.com
Date: October 6, 2016
GitHub Repository: https://github.com/kenthorvath/evolutionary-telomere-dynamics
License: MIT (see LICENSE file)

Description:

Here we provide a Monte Carlo simulation to model evolutionary telomere dynamics across generations. For an in depth description of epidemiological and theoretical considerations of our model, please refer to [1].

Requirements:

The following open source libraries and packages are required for compiling and running this software. Installation instructions are provided for MacOS via homebrew.

  • Java Runtime Environment (via: brew cask install java)
    • tested with Open JDK Runtime Environment 18.9
  • sbt 1.2.6+ (via: brew install sbt)
  • scala 2.12 (via: brew install scala)

Compile:

Compile the project from the project root directory using sbt assembly.

Run:

Run the Simulator from the project root via: scala -cp ./target/scala-2.12/pac-effect-assembly-1.0.jar Simulator <pacAgeCenter> <crossOverYear> <brinkEffect> <cancerIncidenceAdjustment> <maternalInheritance> <initialPopulationTL> <runLength> <numberOfTrials> <outputFileName>

Parameters:

  • <pacAgeCenter> (None or a Double): PAC in years above which TL is added, below which subtracted
  • <crossOverYear> (None or an Int): Year that PAC model is switched on during simulation
  • <brinkEffect> (Boolean): Whether or not to include a brink effect in the model
  • <cancerIncidenceAdjustment> (Double): Scaling factor for cancer incidence (0.0 -> implies no cancer incidence)
  • <maternalInheritance> (Double): Weight of inherited maternal birth TL (range -> 0.0 to 1.0)
  • <initialPopulationTL> (Int): Given in base pairs
  • <runLength> (Int): Given in years
  • <numberOfTrials> (Int): Must be greater than or equal to 1
  • <outputFileName> (String): path to write CSV output

Example: scala -cp ./target/scala-2.12/pac-effect-assembly-1.0.jar Simulator 34.2 500 True 1.0 0.5 10000 1000 1 output.csv

References

  1. Paternal Age and Transgenerational Telomere Length Maintenance: A Simulation Model, Horvath, K. Eisenberg, D., Stone, R., Anderson, J., Kark, J., Aviv, A., Nature Scientific Reports (accepted)