/Chromosome_modelling

C++ software tool for 3D chromosome modelling using HiC data

Primary LanguageC++

Chromosome_modelling

C++ software tool for 3D chromosome modelling using HiC data

Table of Contents

• About ‘Chromosome-condensation’

• Getting Started

• Tutorial

• Output & visualization

• Documentation

• License

• Contact

• Acknowledgements

About ‘Chromosome-reconstruction’

‘Chromosome-reconstruction’ code is a C++ biophysical software designed for 3D chromosome modelling from HiC data.

Getting Started

This is an example of how you may set up the code running for your projects locally.

Prerequisites

  • C++ built-in
  • Visualization software such as Chimera, VMD or PyMOL

Installation

  1. You can download the code (initConfig.hpp, initConfig.cpp, initDynamics.hpp, initDynamics.cpp, chromoCell.cpp, Makefile, chromosome_real.numberBead, chromosome_real.normMatrix)
  2. Or you can clone the repo: git clone https://github.com/FrancisCrickInstitute/Chromosome-Condensation

Tutorial

First, create a folder where you want to run simulations:

mkdir test_reconstruct

cd test_reconstruct

Make sure you copy all the code files from chromo_3D_code to the folder where you want to run simulations:

cp path_to_code_folder/chromo_3D_code/* ./

Next, set up parameters in the initConfig.hpp (for parameter description see Documentation) and then compile the code:

make

Prepare normalized matrix of a single chromosome or whole genome to be modelled and name it chromosome_real.normMatrix. You can find a template of single chromosome normalized Matrix together with other files. Also, do include number of reconstructed chromosomes and number of bins for each in chromosome_real.numberBead.

Run the simulation:

./chromo _chromosome_real

Output & visualization

The main output of code are PDB files from specific timepoints with coordinates of reconstructed chromosomes. These can be visalized using Chimera, VMD or PyMOL.

Documentation – parameters

The ‘Chromosome-condensation’ code consists of several files:

  • initConfig.hpp = includes parameter settings and declaration of functions that initialise the chromatin chain
  • initConfig.cpp = includes definition of functions that initialise the chromosome(s)
  • initDynamics.hpp = includes declaration of functions that describe the dynamical evolution of chromosome chain(s)
  • initDynamics.cpp = includes definition of functions that describe the dynamical evolution of chromosome chain(s) to converge to energy minimum
  • chromoCell.cpp = includes functions to call functions in files above to simulate the dynamical evolution and convergence

General parameter set up can be adjusted in initConfig.hpp file. README_parameters_chromo_modelling.xlsx contains more in-depth description of polymer simulation parameters.

Optional output files and their corresponding parameters are: • chromoPDB*.pdb = PDB file format of chromatin chain with binders/condensin in selected time point

License

Distributed under The Francis Crick Institute License.

Contact

Acknowledgements

This code was developed under the Biomolecular Modelling Laboratory https://www.crick.ac.uk/research/labs/paul-bates at Francis Crick Institute (https://www.crick.ac.uk/). Please cite our paper (doi:10.21203/rs.3.rs-757454/v1) when using the code.