IDEPI is a domain-specific and extensible software library for supervised learning of models that relate genotype to phenotype for HIV-1 and other organisms. IDEPI makes use of open source libraries for machine learning (scikit- learn, scikit-learn.org/), sequence alignment (HMMER, hmmer.janelia.org/), sequence manipulation (BioPython, biopython.org), and parallelization (joblib, pythonhosted.org/joblib), and provides a programming interface to allow the users to engineer sequence features and select machine learning algorithms appropriate for their application.
For more information, a corresponding paper is located at http://hyphy.org/pubs/idepi/paper.pdf.
##Using IDEPI
Please look inside the examples directory for examples on how to use IDEPI to learn and apply phenotype prediction models based on viral sequences and to identify most predictive features of viral genomes.
##Quickstart
Because some of the dependencies of IDEPI (see below) can be somewhat tricky to install, we've created a virtual machine based on Ubuntu 13. It includes a complete preconfigured python environment for use with IDEPI and can be downloaded from http://hyphy.org/pubs/idepi/idepi-vm.tar.gz
Please note that this VM file is ~2GB in size and may take a bit of time to download
Virtual Machine Credentials :
- user: user
- password: reverse
To use the virtual machine:
- Decompress the downloaded file and take note of the file path on the host system
- Open VirtualBox (which can be downloaded from https://www.virtualbox.org/)
- Create a new virtual machine
- Enter a desired name, select 'Linux' as your operating system type, and 'Ubuntu(64 bit)' as your version.
- Select the desired memory size
- When prompted for hard drive options, please select Use an existing virtual hard drive file and navigate to the idepi-vm.vdi file that you have just downloaded and decompressed.
- When the machine has started, double-click the idepi launcher on the desktop
A Python virtual environment was used to create the IDEPI environment on the virtual machine. The root directory of the Python virtual environment is
/home/user/Programming/env/
##Dependencies
- Python 3.3
- BioPython (>=1.58), http://biopython.org/wiki/Main_Page
- BioExt (>=0.14.0), http://github.com/veg/BioExt
- hppy (>=0.9.5), http://github.com/veg/hppy
- sklrmmr (>=0.2.0), http://github.com/nlhepler/sklmrmr
- NumPy, http://www.numpy.org
- SciPy, http://www.scipy.org
- six, http://pypi.python.org/pypi/six
- HMMer, http://hmmer.janelia.org/
- sklearn (>=0.14.0), http://scikit-learn.org/