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
This web2py application is designed to allow binding predictions to be run for multiple proteins, such as a whole bacterial genome.
- 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
The ncbi-blast+ tools and muscle are needed for conservation analysis. On Ubuntu type:
sudo apt-get install ncbi-blast+ muscle
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
See the help pages at http://dmnfarrell.github.io/epitopemap/help.html or inside the web application for details.