heavywatal / tumopp

🦀 Tumor growth simulation in C++/R

tumopp

tumopp is a fast and flexible tumor growth simulator. The core library is written in C++. It can be installed and run via R package.

Requirements

• Unix-like environment (macOS, Linux, WSL, MinGW on MSYS2, etc.)
• C++17 compiler (clang++ >= Apple LLVM 12, g++ >= 8)
• CMake (>= 3.15.0)

The following libraries are optional or automatically installed:

• clippson
• cxxwtl
• sfmt-class
• zlib

Installation

See tumopp R package.

Alternative installation for command-line execution

The easiest way is to use Homebrew. The following command installs tumopp with its dependencies:

brew install heavywatal/tap/tumopp

You can manually install the latest version from source code to an arbitrary DESTINATION:

git clone https://github.com/heavywatal/tumopp.git
cd tumopp/
DESTINATION=${HOME}/local
cmake -S . -B build -DCMAKE_INSTALL_PREFIX=$DESTINATION
cmake --build build -j 2
cmake --install build -j 2
PATH=${DESTINATION}/bin:$PATH

Example:

tumopp -h
tumopp -N20000 -D3 -Chex -k100 -d0.1 -m0.5 -o OUTPUT_DIR

API Document

• Online documentation generated with doxygen
• @ref params

Reference

Watal M. Iwasaki and Hideki Innan (2017) "Simulation Framework for Generating Intratumor Heterogeneity Patterns in a Cancer Cell Population" PLOS ONE 12(9): e0184229

Project page on GitHub