Stochastic integration of trajectories of molecular content

'langil' is a C++ code that integrates stochastic trajectories of different interacting molecular species using the Gillespie algorithm or a continuous stochastic differential equation description.

Files

• langil.cpp Definition of the langil class containing the main integration routines. Particular description of its usage can be found for the HIV example
• langil.h Headers for the langil class and definition of the reaction class defining the different types of reactions that can be used by langil
• species.h Definition of the species class that contains the different types of the molecular species used by langil
• cell_cycle.h Definition of the cell_cycle class used to incorporate cell cycle properties (cell cycle phases of different stochastic duration including material division at bipartition). Examples using it can be found in the CellCycleVariability example
• examples Folder containing different projects using the langil class

Compilation

There is an example Makefile provided to compile the code, to compile the langil class run

make

To compile the code and the examples provided run

make examples

To clean all the object files run

make clean

Examples

• HIV Example for a simple model of HIV cell population infection. It contains a detailed description of the use of the langil class
• Cell Cycle Variability Code used in R. Perez-Carrasco, C. Beentjes, R. Grima, Effects of cell cycle variability on lineage and population measurements of mRNA abundance. JRS Interface 17:168 (2020) to simulate mRNA abundance in cells with a stochastic cell cycle duration

Prerequisites

langil uses the random number generation routines of the GNU Scientific Library.

Author

• Ruben Perez-Carrasco - 2piruben

License

This project is licensed under the MIT License - see the LICENSE.md file for details