Table of Contents

Getting Started

• Installation
  • Install via conda
  • Install via pip
• Introduction

Open-MiChroM Modules

• OpenMiChroM
  • OpenMiChroM.ChromDynamics
  • OpenMiChroM.Optimization
  • OpenMiChroM.CndbTools
  • OpenMiChroM.Integrators

Tutorials

• Single Chromosome Simulation
  • Chromatin Dynamics Simulations on Chromosome 10 of GM12878 Cell Line
  • Trajectory analysis using cndbTools
• Multiple Chromosome Simulation
  • Chromatin Dynamics Simulations on Chromosome 10 and Chromosome 11 of GM12878 Cell Line
• Tutorial: Single chromosome optimization using OpenMiChroM
  • This tutorial performs optimization in the MiChroM Parameters (Second-order optimization -> Hessian inversion)
  • 1# Types Interaction Opmization
  • 2# Ideal Chromosome Interaction Opmization
• Full Inversion Method for a single chromosome using OpenMiChroM
  • This tutorial enables performing Full Inversion Method using Adam (First-order optimization)
• Pulling Simulations
  • Part 1: Constant-Force Pulling
  • Part 2: Constant-Distance Pulling
  • Simulation Parameters:
  • Function that retrieves pull coordinate:
  • Functions to create pin, slide, and pull forces
  • Sets up simulation and loads initial structure
  • Define pull groups.
  • WARNING! – Orient Initial Structures
  • Native Simulation
  • Constant Force
  • Release Simulation
  • Plot Pull Coordinate
• Temporally Correlated Active Noise Simulation Tutorial
  • Introduction
  • Simulations

Reference

• How to cite OpenMiChroM
• References
• License

Indices and tables

• Index

• Module Index

• Search Page