ChronoRepair

ChronoRepair is a research-oriented C++17 toolkit for modelling the time evolution of radiation-induced DNA damage, repair and misrepair processes, and resulting cellular outcomes. It supports damage-site kinetics, foci evolution, cell survival, and protracted-irradiation scenarios.

This repository is a curated snapshot of the dev-DPuerta development branch from the Bertolet Lab repository, shared with the laboratory's permission. It is intended for technical review and research-software evaluation.

Capabilities

• Object-oriented models of cells, DNA damage sites, repair, and misrepair
• Time-resolved simulation of damage evolution and cellular outcomes
• Repeated-simulation workflows with summary statistics and uncertainty estimates
• Survival and foci modelling modes
• Protracted-damage event scheduling
• Standard Damage Data (SDD) input handling
• A stdin/stdout interface for coupling the C++ simulator to Python fitting workflows

Requirements

• A C++17-compatible compiler
• CMake 3.25 or newer
• Python 3 and NumPy for the optional Python interface

Build

cmake -S . -B build -DCMAKE_BUILD_TYPE=Release
cmake --build build

The default target builds mains/main_fittinginterface_SimulationGeneral.cpp as the ChronoRepairPlus executable.

Run the fitting interface

./build/ChronoRepairPlus \
  <sdd_path> <foci|survival> <number_of_dose_points> \
  <dose_1> [<dose_2> ...] <add_protracted_damage>

After initialization, the executable prints READY and receives simulation parameter sets through standard input.

The Python helper python/auxiliary_functions.py launches the default executable from build/ChronoRepairPlus. A different executable may be supplied through its executable_path argument.

Selected entry points

• mains/main_fittinginterface_SimulationGeneral.cpp: general fitting interface
• mains/main_fittinginterface_ExtrapolateDoses.cpp: dose-extrapolation workflow
• mains/main_manysimulations.cpp: repeated-simulation example
• mains/main_simulation.cpp: single-simulation example
• mains/main_sdd.cpp: SDD reader example
• mains/main_damagesite.cpp: damage-site example

To build another entry point, change MAIN_FILE in CMakeLists.txt.

Scope

This showcase contains the current toolkit sources and representative entry points. Development archives, thesis-specific analysis scripts, experiment-specific configurations, and generated numerical results are intentionally excluded. The complete research snapshot remains archived separately.

Licence

ChronoRepairPlus is distributed under the MIT License. See LICENSE.

Research-software status

This is research software under active development. Interfaces may change, and users should independently validate the model and outputs for their application.