Dataset of tugHall simulations of cell evolution for colorectal cancer
Dataset contains results of multiply parallel calculations using the tugHall simulator. Output data of simulations are variant allele frequencies for four genes (APC, KRAS, TP53, and PIK3CA) related to colorectal cancer. During each simulation tugHall stochastically reproduces Darwinian evolution for cancer cells and calculates clonal heterogeneity. The probabilities of stochastic processes depend on a correspondence matrix between genome information and cancer hallmarks. As a result, tugHall records variant allele frequencies for the final stage of evolution. The number of trials is several million to get rich statistics of stochastic processes. These data can be used for approximate Bayesian computation and other statistical methods to get personalized coefficients for patients with colorectal cancer. The procedure of usage data is explained in our papers [Bioinformatics, 36, 11 (2020) 3597; ISMCO 2020: Mathematical and Computational Oncology (2020) 71] in which the part of these data was used.
Steps to reproduce
Unzip Dataset.zip file to get dataset with 8 files. Description of files and it's meaning, please, kindly read in description.pdf file. array_jobs.zip file contains files and directories of the code and input files to make simulation using supercomputer of Human Genome Center, the University of Tokyo (see References).