AOPXplorer

Driving Biological Understanding of Data By Coupling Adverse Outcome Pathway Networks, R and Cytoscape

Installation Instructions

AOPXplorer requires the following to work properly:

Install Fuseki

First, get the AOPXplorer Fuseki instance. Drop it onto your hard drive (and remember where it is).

On Mac, find the aopxplorer_fuseki.command file and double click it.

On Windows, find the aopxplorer_fuseki.bat file and double click it.

On Linux, run the aopxplorer_fuseki.sh file from the terminal.

If these don't work, you should check to see if you need to make the file executable. Use the Terminal (Mac/Linux) to run:

chmod +x aopxplorer_fuseki.command
chmod +x aopxplorer_fuseki.sh
chmod +x aopxplorer_fuseki.bat

Once the Fuseki server is up and running, you can navigate to http://localhost:3030 in your browser

Get the AOPOntology Up and Running in Fuseki

Download the AOPOntology.

If you download the zip from Github, make sure to open and unzip it someplace on your hard drive.

With your browser at http://localhost:3030, you can upload the AOPOntology file. Click on the "add data" button for the /ds dataset. Select the aopo.owl file from the location where you saved the AOPOntology zip file. Press the "upload all" button. Fuseki is now ready to be queried by the AOPXplorer.

Install AOPXplorer

In R, make sure you install devtools (run this within R):

install.packages("devtools")

Next, you'll install the AOPXplorer package from Github. Within R run the following:

library(devtools)
install_github("DataSciBurgoon/aopxplorer2", build_vignettes=TRUE)

The AOPXplorer will be ready for release soon. It is in the final streth of development, testing, and documentation. We expect a release around September 2016 (probably sooner).

Email Lyle Burgoon to get notifications about AOPXplorer's launch.