OpenMiChroM
Documentation | Install | Tutorials | Forum
Overview
OpenMiChroM is a Python library for performing chromatin dynamics simulations and analyses. OpenMiChroM uses the OpenMM Python API employing the MiChroM (Minimal Chromatin Model) energy function. The chromatin dynamics simulations generate an ensemble of 3D chromosomal structures that are consistent with experimental Hi-C maps. OpenMiChroM also allows simulations of a single or multiple chromosome chains using high-performance computing on different platforms (GPUs and CPUs). It is a highly flexible framework that can be extended for chromatin modeling and simulations across different species and for general biomolecular simulations.
The chromatin dynamics simulations can be performed for different human cell lines, cell phases (interphase to metaphase), and various organisms from DNAzoo. Chromatin subcompartment annotations are available at the NDB (Nucleome Data Bank). The OpenMiChroM package accepts the chromatin sequence of compartments and subcompartments as input to create and simulate a chromosome polymer model. Examples of running the simulations and generating in silico Hi-C maps can be found here.
Usage
The following code snippet shows how to generate a single chromosome polymer model and run a chromatin dynamics simulation using OpenMiChroM:
from OpenMiChroM.ChromDynamics import MiChroM
sim = MiChroM(name='stomach_GRCh38', temperature=1.0, timeStep=0.01)
sim.setup(platform="cuda")
sim.saveFolder('stomach_GRCh38_chr10_simulation')
sim.buildClassicMichrom(ChromSeq='inputs/stomach_GRCh38.bed', chromosome='chr10')
sim.createReporters(statistics=True, traj=True, outputName=None, trajFormat="cndb", energyComponents=True, interval=10**3)
sim.run(nsteps=10**5, report=True, interval=10**4)Installation
The OpenMiChroM library can be installed via pip, conda, or compiled from source.
Install via pip
pip install OpenMiChroMNote: OpenMiChroM relies on the OpenMM API. You can install it using pip:
pip install openmm[cuda12] # For GPU
# or
pip install openmm # For CPU onlyInstall via conda
conda install -c conda-forge OpenMiChroMCitation
When using OpenMiChroM for chromatin dynamics simulations or analyses, please use this citation. We also thank Polychrom, where part of this code was inspired.