There are three branches you might be interested in -
-
mastercontains some extra Mathematica code + data files for visualization -- these are not present in the other branches. -
fix-mc-boundary- It has not been merged intomaster, as we were mid-refactoring before leaving the project. -
danilo- contains latest version of code for molecular dynamics
Dependencies
The source code for the Monte Carlo uses the @ matrix multiplication operator,
so it needs Python 3.5 or later.
Apart from the usual Python scientific suite, additional packages required
for the Monte Carlo simulation
include
numba,
seaborn,
xarray
and optionally
hypothesis
and
pytest for running tests.
These can be easily installed using conda
(numba in particular recommends using conda):
conda install numba seaborn xarray hypothesis pytest
There is an additional package nbstripout which is useful for
working with Jupyter notebooks. Before using git commit, you can run the
backup_nb.py file (it is executable) so that it will generate new copies
of notebooks without output. These can be put in version control without
large file sizes. For some reason, the conda version of nbstripout
doesn't seem to be working properly, so you should install it using pip.
pip install nbstripout
# if that doesn't work, try sudo -H pip install nbstripout
Tests can be run by cd-ing into src and running pytest.
Bibliography
The source code comments sometimes refer to papers for values etc. The bibliography for those references is given here for easy cross-verification.
[B] Bancaud et al. - Structural plasticity of single chromatin fibers revealed by torsional manipulation
[DS] Daniels and Sethna - Nucleation at the DNA Supercoiling transition
[F] Forth et al. - Abrupt Buckling Transition Observed during the Plectoneme Formation of Individual DNA Molecules