tugHall version 1.1

tugHall (tumor gene-Hallmark) is cancer-cell evolution model simulator, wherein gene mutations are linked to the tumor cell behaviors, which are influenced by the hallmarks of cancer.

This is an R-based script to simulate the cancer cell evolution in the framework of the model proposed by Prof. Mamoru Kato, Head of Bioinformatics Department, Research Institute, National Cancer Center, Tokyo, JAPAN.

Authors and contributor list:

Iurii Nagornov

Mamoru Kato

Department of Bioinformatics, Research Institute, National Cancer Center Japan, Tokyo, Japan

All questions and requests can be sent to inagonov@ncc.go.jp

Project source can be downloaded from websites

https://github.com/tugHall/Cell-based - the stable version;

https://github.com/tugHall/Clone-based - the stable version based on the clone (tugHall 2.0 and 2.1).

https://github.com/tugHall/CNA - the new (developing) version based on clone with copy number alteration in output data.

Cite this code

Iurii S Nagornov, Mamoru Kato. tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes. Bioinformatics, V.36, N11, June 2020, pp. 3597–3599

• Clone-based version of tugHall 2.0 and 2.1 with the acceleration of calculation speed

Nagornov, I., Nishino, J., Kato, M. (2020). tugHall: A Tool to Reproduce Darwinian Evolution of Cancer Cells for Simulation-Based Personalized Medicine. In: Mathematical and Computational Oncology. ISMCO 2020. Lecture Notes in Computer Science, vol 12508. Springer

Short description

The wide availability of recent cancer genomic data requires a coherent model that can sort out the relevant findings to systematically explain the clonal evolution and resultant intra-tumor heterogeneity (ITH). Here, we present a new mathematical model designed to computationally simulate the evolution of cancer cells. The model connects well-known cancer hallmarks with the specific mutational states of tumor-related genes. The cell behavior phenotypes are stochastically determined and the hallmarks interfere probabilistically with the phenotypic probabilities. In turn, the hallmark variables depend on the mutational states of tumor-related genes. Thus, it is expected our software can be used to deepen our understanding of cancer-cell evolution and generation of ITH.

Content of package

• User-Guide-tugHall.Rmd and User-Guide-tugHall.html are the user guides to install, run, and use tugHall simulator in R Markdown and html formats.
• User-Guide-Analysis.Rmd and User-Guide-Analysis.html are the user guide to analyze the results of a single simulation in R Markdown and html formats.
• /tugHall/ is a directory with the program code, input, and output data.
• /FOR_DEVELOPMENT/ is a directory for development.