https://github.com/dmnfarrell/epitopemap
A web application for visualizing MHC binding predictions
https://github.com/dmnfarrell/epitopemap
Last synced: 12 months ago
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A web application for visualizing MHC binding predictions
- Host: GitHub
- URL: https://github.com/dmnfarrell/epitopemap
- Owner: dmnfarrell
- License: apache-2.0
- Created: 2014-12-16T20:23:05.000Z (over 11 years ago)
- Default Branch: master
- Last Pushed: 2019-07-10T10:47:08.000Z (almost 7 years ago)
- Last Synced: 2025-04-22T07:01:19.831Z (about 1 year ago)
- Language: JavaScript
- Homepage:
- Size: 5.53 MB
- Stars: 6
- Watchers: 3
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
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.