https://github.com/open2c/polychrom

Chromosome polymer simulations and in silico capture experiments
https://github.com/open2c/polychrom

chromatin chromosomes hi-c loop-extrusion polymer simulation

Last synced: 5 months ago
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Chromosome polymer simulations and in silico capture experiments

• Host: GitHub
• URL: https://github.com/open2c/polychrom
• Owner: open2c
• License: mit
• Created: 2019-03-30T20:30:23.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2025-04-16T23:30:31.000Z (6 months ago)
• Last Synced: 2025-04-24T01:13:50.180Z (5 months ago)
• Topics: chromatin, chromosomes, hi-c, loop-extrusion, polymer, simulation
• Language: Python
• Homepage:
• Size: 19.7 MB
• Stars: 48
• Watchers: 8
• Forks: 16
• Open Issues: 9
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# polychrom

[![DOI](https://zenodo.org/badge/178608195.svg)](https://zenodo.org/badge/latestdoi/178608195)

## Open2C polymer simulation library

This library is designed to easily set up polymer simulations of chromosomes subject to a set of forces or constraints. 

Polychrom is designed to build mechanistic models - i.e. models that simulates a biological process. 

We then compare results of the simulation to Hi-C maps or microscopy, and to other sources of data. 

Polychrom is not designed to make a simulation based on a Hi-C map alone, without a hypothesis in mind. 

For distinction between mechanistic and data-driven models see https://pubmed.ncbi.nlm.nih.gov/26364723/ 

Polychrom documentation is hosted on readthedocs. 

https://polychrom.readthedocs.io/en/latest/

One of the main uses of polychrom now is to simulate loop extrusion. An example loop extrusion simulation is presented here.

https://github.com/mirnylab/polychrom/tree/master/examples/loopExtrusion . It is a good starting point for loop extrusion simulations. 

Simplest example simulation that does nothing, which is a good starting point for novel simulations or polymer physics projects.  

https://github.com/mirnylab/polychrom/blob/master/examples/example/example.py

### Transitioning from openmm-polymer ("openmmlib")

Compared to openmm-polymer, it has a new storage format described here: https://github.com/mirnylab/polychrom/blob/master/examples/storage_formats/hdf5_reporter.ipynb

For backwards compatibility with analysis routines, we have legacy reporter that saves into openmmlib format 

https://github.com/mirnylab/polychrom/blob/master/examples/storage_formats/legacy_reporter.ipynb

polychrom.polymerutils.load function  is backwards compatible with both new and old style 

format. https://github.com/mirnylab/polychrom/blob/master/polychrom/polymerutils.py#L22