Comet

Computational modeling of evolving tumors

Comet is built on Tumopp, a single-cell based, flexible and efficient spatial tumor growth simulator written in C++.

The differences between Comet and the original tumopp packages are:

• passenger mutations are generated and printed out for each cell
• all dead cells and lineages are printed out (for lineage tracing)
• Metastatic seeding cells are sampled randomly over time (removed from the growing tumor)

Test

Requirements

• Unix-like environment (macOS, Linux, WSL, MinGW on MSYS2, etc.)
• C++14 compiler (clang++ >= Apple LLVM 8.1, g++ >= 5.3)
• CMake (>= 3.8.0)

The following libraries are optional or automatically installed:

• clippson
• cxxwtl
• sfmt-class
• zlib

Installation

git clone https://github.umn.edu/sunpath/Comet.git
cd Comet/
mkdir build
cd build/
DESTINATION=${HOME}/local
cmake -DCMAKE_INSTALL_PREFIX=$DESTINATION ..
make -j2
make install
PATH=${DESTINATION}/bin:$PATH

Example:

comet -h
comet -N1000000 -D3 -Cmoore -k1 -u 0.15 -b 0.25 -d 0.18 --ub 0.0005 --mb 0.05 --extinction 100000 --local linear --seedingSize 5000 -o $OUTPUT_DIR

Reference:

Ruping Sun and Athanasios N. Nikolakopoulos
Elements and Evolutionary Determinants of Genomic Divergence Between Paired Primary and Metastatic Tumors,
bioRxiv 2020.08.24.262378,
☕DOI: 10.1101/2020.08.24.262378

Author:

Ruping Sun, Athanasios Nikolakopoulos