Skip to main content

Python-based Monte Carlo simulator for DNA/RNA duplexes.

Project description

https://travis-ci.org/fcchou/HelixMC.png?branch=master

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.

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

Project details


Release history Release notifications

History Node

0.9

This version
History Node

0.8

History Node

0.5

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
helixmc-0.8.tar.gz (11.3 MB) Copy SHA256 hash SHA256 Source None Jan 30, 2014

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page