A web application for visualizing MHC binding predictions
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ABOUT
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startepitopeapp

README.md

epitopemap

A web application for visualizing mhc binding predictions

Note: It is now recommended that you use the epitopepredict tool instead: https://github.com/dmnfarrell/epitopepredict

Background

This web2py application is designed to allow binding predictions to be run for multiple proteins, such as a whole bacterial genome.

Installation

  • Install web2py
  • Unzip web2py and place in the folder where you wish to run it
  • Download eptiopemap by cloning this repo
  • place under web2py/applications
  • Start the server using python web2py.py -i localhost -a password -p 8000 -K epitopemap -X
  • Go to http://localhost:8000/epitopemap in your browser

Other software

The ncbi-blast+ tools and muscle are needed for conservation analysis. On Ubuntu type:

sudo apt-get install ncbi-blast+ muscle

Python dependencies

Setup currently requires you to install the Python libraries yourself. This is a cleaner approach than providing them with the application and is now simple on linux. In addition we recommend you use easy_install or pip to install the packages rather than the OS package manager (e.g. apt-get) but both methods should work. On Ubuntu type the following on the command line to install the Python modules:

sudo apt-get install python-pip
sudo pip install numpy pandas matplotlib biopython bokeh mpld3

Usage

See the help pages at http://dmnfarrell.github.io/epitopemap/help.html or inside the web application for details.