tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes

SUMMARY: The flood of recent cancer genomic data requires a coherent model that can sort out the findings to systematically explain clonal evolution and the resultant intra-tumor heterogeneity (ITH). Here, we present a new mathematical model designed to computationally simulate the evolution of cancer cells. The model connects the well-known hallmarks of cancer with the specific mutational states of tumor-related genes. The cell behavior phenotypes are stochastically determined, and the hallmarks probabilistically interfere with the phenotypic probabilities. In turn, the hallmark variables depend on the mutational states of tumor-related genes. Thus, our software can deepen our understanding of cancer-cell evolution and generation of ITH. AVAILABILITY AND IMPLEMENTATION: The open-source code is available in the repository https://github.com/nagornovys/Cancer_cell_evolution. CONTACT: mamkato@ncc.go.jp SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.