README

HelixMC

HelixMC is a software package for Monte-Carlo (MC) simulations of DNA/RNA helices using the base-pair level model, coded with Python. HelixMC is distributed under the GPLv3 licence.

The project is authored by Fang-Chieh Chou in 2013, under the supervison of Dr. Rhiju Das, at the Biochemistry Department of Stanford Unviersity.

Links

• Source code: https://github.com/fcchou/HelixMC
• HTML documentation: http://helixmc.readthedocs.org/
• Publication: Chou F-C, Lipfert J, Das R (2014) Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque. PLoS Comput Biol 10(8): e1003756. Link
• Das Lab @ Stanford: http://daslab.stanford.edu

Dependencies

The required dependencies to build the software are Python >= 2.7, Numpy >= 1.6, Matplotlib >= 1.1.0, and a working C/C++ compiler.

Install

The easiest way to install is to use pip install:

$ pip install helixmc

Alternatively, one can download the source code from the latest GitHub repository. And install using setup.py:

$ python setup.py build
$ sudo python setup.py install

Instead of installing using setup.py, you can just add your HelixMC folder into the system's $PATH and $PYTHONPATH. In bash this can be done by adding the following lines to your ~/.bashrc:

export PATH=$PATH:<HelixMC Path>
export PYTHONPATH=$PYTHONPATH:<HelixMC Path>

Then build the Cython extension. Under the helixmc/ folder, run:

$ python _cython_build.py build_ext --inplace

Note that this requires you to have Cython installed. Otherwise you can choose to build the c source file, then you do not need Cython:

$ python _c_build.py build_ext --inplace