OpenMiChroM 0.0.2

Open-Michrom lib for chromosome simulations

Open-MiChroM is a Python library for performing chromatin dynamics simulations and analyses. Open-MiChroM 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. Open-MiChroM also allows simulations of a single or multiple chromosome chain using High-Performance Computing in different platforms (GPUs and CPUs).

The chromatin dynamics simulations can be performed for different human cell lines, cell phases (interphase to metaphase), and different organisms from DNAzoo. Chromatin subcompartment annotations are available at the NDB (Nucleome Data Bank). Open-MiChroM package receives the chromatin sequence of compartments and subcompartments as input to create and simulate a chromosome polymer model. Examples of running the simulations and generating the in silico Hi-C maps can be found here