A stochastic hybrid model for DNA replication incorporating protein mobility dynamics
If you find this code useful in your research, please consider citing:
@article{Windhager2019,
doi = {10.1101/583187},
url = {https://doi.org/10.1101/583187},
year = {2019},
month = mar,
publisher = {Cold Spring Harbor Laboratory},
author = {Jonas Windhager and Amelia Paine and Patroula Nathanailidou and Eve Tasiudi and Maria Rodriguez Martinez and Zoi Lygerou and John Lygeros and Maria Anna Rapsomaniki},
title = {A stochastic hybrid model for {DNA} replication incorporating protein mobility dynamics}
}
- C++11 compiler
- CMake 3.6 or newer
- Eigen 3.3.4
To clone the Eigen library directly from GitHub using git:
git clone -b 3.3.4 https://github.com/eigenteam/eigen-git-mirror.git /path/to/eigen3Replace /path/to/eigen3 with the path to your local copy of the Eigen library and execute the following commands:
git clone https://github.com/jwindhager/dna-replication.git
mkdir dna-replication/build
cd dna-replication/build
cmake -DCMAKE_BUILD_TYPE=Release -DEIGEN3_INCLUDE_DIR=/path/to/eigen3 ..
make
make installTo perform a single DNA replication simulation, call dnarepl:
Runs a single DNA replication simulation.
Client options:
-h [ --help ] Display help message
Input data:
-o [ --orifile ] arg Path to origin positions file (required)
-c [ --assyfile ] arg Path to assembly information file (required)
-s [ --structfile ] arg Path genome structure file (required)
Simulation parameters:
-r [ --rnucl ] arg Nucleus radius (required, in um)
-x [ --xnucl ] arg Nucleolus displacement (required, in um)
-q [ --rpery ] arg Periphery radius (set for peripheral particle inactivation, in um)
-z [ --rspb ] arg Spindle pole body radius (enables SPB-mediated particle activation, in um)
-n [ --npart ] arg Number of activation factors (required)
-g [ --hgrid ] arg Step size of the diffusion grid (required, in um)
-a [ --pact ] arg Activation probability (for SPB-mediated particle activation)
-d [ --dcoef ] arg Effective diffusion coefficient (required, in um2/s)
-b [ --dbind ] arg Maximal binding distance (required, in um)
-p [ --pbind ] arg Binding probability (required)
-f [ --vfork ] arg Replication fork velocity (required, in b/s)
To perform a batch of DNA replication simulations, call dnarepl-batch on any MPI-enabled environment:
Runs multiple DNA replication simulations using MPI.
Client options:
-h [ --help ] Display help message
-i [ --niter ] arg Number of iterations (required)
-w [ --outdir ] arg Path to output directory (required)
-k [ --outkey ] arg Simulation key (for output files, required)
Input data:
-o [ --orifile ] arg Path to origin positions file (required)
-c [ --assyfile ] arg Path to assembly information file (required)
-s [ --structdir ] arg Path genome structure directory (required)
Simulation parameters:
-r [ --rnucl ] arg Nucleus radius (required, in um)
-x [ --xnucl ] arg Nucleolus displacement (required, in um)
-q [ --rpery ] arg Periphery radius (set for peripheral particle inactivation, in um)
-z [ --rspb ] arg Spindle pole body radius (enables SPB-mediated particle activation, in um)
-n [ --npart ] arg Number of activation factors (required)
-g [ --hgrid ] arg Step size of the diffusion grid (required, in um)
-a [ --pact ] arg Activation probability (for SPB-mediated particle activation)
-d [ --dcoef ] arg Effective diffusion coefficient (required, in um2/s)
-b [ --dbind ] arg Maximal binding distance (required, in um)
-p [ --pbind ] arg Binding probability (required)
-f [ --vfork ] arg Replication fork velocity (required, in b/s)
This project is licensed under the terms of the MIT license.
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