Welcome to openNucleome’s documentation!

OpenNucleome is an open-source software designed for conducting molecular dynamics (MD) simulations of the human nucleus. This software streamlines the process of setting up whole nucleus simulations through just a few lines of Python scripting. OpenNucleome can unveil intricate, high-resolution structural and dynamic chromosome arrangements at a 100 KB resolution. It empowers researchers to track the kinetics of condensate formation and fusion while also exploring the influence of chemical modifications on condensate stability. Furthermore, it facilitates the examination of nuclear envelope deformation’s impact on genome organization. The software’s modular architecture enhances its adaptability and extensibility. Leveraging the power of OpenMM, a GPU-accelerated MD engine, OpenNucleome ensures efficient simulations.

Environment

We recommend using openmm 7.5.1 for using openNucleome, as openNucleome is built based on openmm 7.5.1.

Install openmm 7.5.1 with the following command: conda install -c conda-forge openmm=7.5.1

Other required packages: numpy, pandas, scipy, scikit-learn, MDAnalysis, mdtraj.

Getting Started

• Installation
  • Install via pip
• Introduction

OpenNucleome:

• openNucleome
  • openNucleome.whole_nucleus_model
  • openNucleome.chromosome
  • openNucleome.speckle
  • openNucleome.nucleolus
  • openNucleome.lamina
  • openNucleome.utils.DamID_TSASeq_calculation
  • openNucleome.utils.coor_transformation
  • openNucleome.utils.final_frame

Tutorials

• Sphere Model: Langevin Dynamics
  • Import the necessary packages
  • Important parameters
  • Initialize the system
  • Add the force field
  • Perform the simulation
  • Post-process the output files
• Sphere Model: Brownian Dynamics
  • Import the necessary packages
  • Important parameters
  • Initialize the system (A larger damping coefficient for the Brownian Dynamics)
  • Add the force field
  • Perform the simulation
  • Post-process the output files
• Nuclear Deformation Simulation
  • Import the necessary packages
  • Important parameters
  • Initialize the system
  • Add the force field
  • Perform the simulation
  • Post-process the output files
• Tutorials: Configuration Generation
  • Import the necessary packages
  • Import the necessary reference files
  • Generate the raw configs of chromosomes
  • Generate Speckle and Nucleolus beads
  • Generate Lamina beads
  • Generate the initial configuration files used in the simulation
• Tutorials: Configuration Relaxation
  • Import the necessary packages
  • Important parameters
  • Initialize the system
  • Add the force field
  • Perform the simulation
  • Post-process the output files
• Tutorials: Configuration Selection
  • Import the necessary packages
  • Load data for the selection
  • Iteration
• Tutorials: Contact Probability Computation
  • Import the necessary packages
  • Compute the simulated DamID and TSASeq
  • Visualization
  • Compute the chromosome contact probabilities
• Tutorials: Chromosome Chromosome Optimization
  • Import the necessary packages
  • Important parameters
  • Adam optimization
  • Start to update the parameters
• Tutorials: Chromosome Nuclear Landmarks Optimization
  • Import the necessary packages
  • Compute the simulated DamID and TSASeq
  • Load the experimental DamID and TSASeq
  • Adam optimization
  • Save the new parameters

Indices and tables

• Index

• Module Index

• Search Page

Citations

“OpenNucleome for high resolution nuclear structural and dynamical modeling”, eLife (in press), doi: 10.1101/2023.10.16.562451