Metadata-Version: 1.0
Name: TADphys
Version: 0.1
Summary: Tadphys is a Python library that allows to model and explore single or time-series 3C-based data.
Home-page: UNKNOWN
Author: Marco Di Stefano
Author-email: marco.di.distefano.1985@gmail.com
License: GPLv3
Description: 
        
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        | Current version: pipeline_v0.2.722  |
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        TADphys.
        
        Documentation
        *************
        
        **Install LAMMPS as a shared library**
           | 1 - Download lammps
           | git clone -b stable https://github.com/lammps/lammps.git mylammps
           
           | 2 - Install lammps as a shared library
           | cd ../../src/
           | include "-DLAMMPS_EXCEPTIONS" in the LMP_INC line in src/MAKE/Makefile.mpi
           | make yes-molecule
           | make mpi mode=shlib
           | make install-python
        
           | cd ../../
        
        **Install packages**
           | conda install -y scipy           # scientific computing in python
           | conda install -y numpy           # scientific computing in python
           | conda install -y matplotlib      # to produce plots
           | conda install -y -c https://conda.anaconda.org/bcbio pysam # to deal with SAM/BAM files
        
        **Install TADphys**
           | 1 - Download TADphys from the Github repository
           | git clone https://github.com/MarcoDiS/TADphys.git -b TADphys TADphys
        
           | 2 - Install TADphys
           | cd TADphys
           | python setup.py install
           | cd ..
        
        **Try TADdyn**
           | cd test/
           | python test_TADphys.py
        
        Citation
        ********
        Please, cite this article if you use TADphys.
        
        Marco Di Stefano, Ralph Stadhouders, Irene Farabella, David Castillo, François Serra, Thomas Graf, Marc A. Marti-Renom.
        **Dynamic simulations of transcriptional control during cell reprogramming reveal spatial chromatin caging.**
        *bioRxiv* 642009; `doi: https://doi.org/10.1101/642009`_
        
        Methods implemented in TADphys
        -----------------------------
        In the actual implementation, TADphys relies on TADbit for the models' analysis
        and on LAMMPS [Plimpton]_ for the implementation of the simulations.
        
        Bibliography
        ************
        
        .. [Plimpton] Plimpton, S. Fast Parallel Algorithms for Short-Range Molecular Dynamics. J Comp Phys 117, 1-19 (1995) and Fiorin, G., Klein, M.L. & Hénin, J. Using collective variables to drive molecular dynamics simulations. Molecular Physics 111, 3345-3362 (2013).
        
Platform: OS Independent
