Commit aa205897 authored by Pascal Carrivain's avatar Pascal Carrivain

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......@@ -84,8 +84,8 @@ You can imagine to model small part of an *epigenome* or the whole genome confin
Purpose of Module
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Recently, the epigenetic and the tri-dimensional structure of fly genome is studied by means of *block-copolymer*.
The *block-copolymer* is made of more than one monomer species.
The epigenetic and the tri-dimensional structure of fly genome is studied by means of *block-copolymer*.
The *block-copolymer* is a polymer made of more than one monomer species.
The epigenetic information do not involve alterations in the DNA but `histone <https://en.wikipedia.org/wiki/Histone>`_ tails modifications.
This uni-dimensional information can be projected along the contour of a *block-copolymer* model.
Then, every pairwise of monomers interacts according to the epigenetic states leading to specific pattern of interactions.
......@@ -94,13 +94,16 @@ Since 2000, biologists can produce the same kind of data thanks to the *high-thr
Recently, biologists shown the interactions pattern is correlated with the epigenetic information.
However, the strength and model of interactions between epigenetic states are not always clearly known.
In addition to the *high-throughput-sequencing* methods, we can study the spatial distances inside part of the genome with the help of FISH `<https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization>`_ and high-resolution methods.
All the spatial distances can be simply extracted from the model built with the help of OpenMM_Copolymer module.
The module we propose uses the OpenMM software with GPU acceleration to sample as many as possible epigenetic parameters.
It is possible to use effective interactions (gaussian overlap or Lennard-Jones potential) to model the epigenetic.
The module introduces the possibility to replace effective epigenetic interactions with `binders model <https://www.ncbi.nlm.nih.gov/pubmed/22988072>`_ too.
In this case, the binder is like a protein that can bind to a specific site of the genome.
A simple input file is enough to tell the script about the binder-binder and monomer-binder interactions.
The present module assists with simulation of a *block-copolymer* model and assist with the analysis of the data (`HPC Dask <https://dask.org/>`_ and `Python compiler Numba <http://numba.pydata.org/>`_).
The present module assists with simulation of a *block-copolymer* model and assists with the analysis of the data (`HPC Dask <https://dask.org/>`_ and `Python compiler Numba <http://numba.pydata.org/>`_).
In particular, it assists the creation of polymer described by FENE bond and WCA repulsive potential to resolve the excluded volume constraints.
On top of that, it builds the epigenetic interactions based on a simple input file.
It can be used by polymer physicists, biophysicists for epigenetic modeling, to understand the link between epigenetic and tri-dimensional structure of a genome, to estimate first-passage-time encounter of two locii.
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