STRING-VRNetzer

This repository includes everything thats needed to bring protein-protein association networks from STRING DB on the VRNetzer platform:

A CytoscapeApp –VRNetzerApp – which enables the export of VRNetzer designated data format
An VRNetzer extension – StringEx – which enables the visualization of STRING specific features like multiple association evidences

Resources

VRNetzerApp

StringEx

Frozen VRNetzer backend version

Content

Installation of the VRNetzerApp
Usage of the VRNetzerApp
Installation of StringEx
Upload a STRING network
Upload an arbitrary VRNetz
Map string network on preprocessed PPI
Dependencies
License

1. Installation of the VRNetzerApp

To install it, you can use the App Manger in Cytoscape:

Apps -> App Manger -> Install from File... -> select the "VRNetzerApp-x.x.x.jar" file.

2. Usage of the VRNetzerApp

Export a network as VRNetz

Select a network you would like to export.
Export the selected network as an "VRNetz" via:
a) Apps -> VRNetzer -> Export network as VRNetz
or
b) File -> Export -> Export network as VRNetz
Select the location where to save the network, as well as a name in the prompted window. (4. When needed you can select only the link and node column you want to export. By default all link and node columns are exported.)
Click "Ok" and the network is exported.

Picture that visualizes the location of the StringEx uploader tab.

You network is now exported as an VRNetz which can be used in the VRNetzer to present your network as a 3D network.

Send a network to the VRNetzer

Select a network you would like to send.
Send the selected network to the VRNetzer via:
- Apps -> VRNetzer -> Send network to VRNetzer
Select a layout algorithm the prompted window. a) You can define the variables of the layout algorithm if you like. b) You can define a name for the layout to allow multiple layouts for the same project.
Select a project name.
Select whether you want to update an existing project, or create a new one. a) Update an existing project: All layouts with the same name are overwritten. Pick this option if you want to update an existing project with new layouts or node colors. b) Create a new project: A new project is created. Pick this option if you want to create a new project, be aware that the project name has to be unique. If a project with this name already exists, the whole project will be overwritten. (5. If the VRNetzer is not running on your local machine or on a different port than 5000, you can change the IP and port.) (6. When needed you can select only the link and node column you want to send. By default all link and node columns are sent.)
Click "Ok" and the network is sent to the VRNetzer.

Picture that visualizes the location of the StringEx uploader tab.

3. Installation of StringEx

Add the StringEx directory to your VRNetzer backend directory. The directory should be located at "extensions/StringEx".
Before the line:

python -m pip install -r requirements.txt

add the following line to the VRNetzer backend's build and run script (Windows: buildandRUN.ps, Linux: linux_buildandrun.sh, Mac: mac_buildandrun.sh) :

python -m pip install -r extensions/StringEx/requirements.txt

If you would like to use cartoGRAPHs to create layouts also add the following line:

python -m pip install -r extensions/StringEx/requirements_cartoGRAPHs.txt

It should now look something like this:

python -m pip install -r extensions/StringEx/requirements.txt
python -m pip install -r extensions/StringEx/requirements_cartoGRAPHs.txt
python -m pip install -r requirements.txt

4. Upload a Network from Cytoscape

Export a STRING network with the VRNetzerApp from Cytoscape (see above)
Start the VRNetzer backend using the script applicable to your operating system.
Navigate in your Browser to http://127.0.0.1:5000/upload (Windows/Linux) / http://127.0.0.1:3000/upload (mac)
If the StringEx is correctly installed, you should now see two new tabs. The first is the a VRNetz designated uploader
On this tab, define a project name, select the VRNetz file of your exported String network, and select the desired layout algorithm.
You can also define the respective layout variables.
Click on the "Upload" button to upload the network to the VRNetzer platform.
If the upload was successful, you'll be prompted with a success message and a link to preview the project in the designated WebGL previewer.

5. Map an exported network on a preprocessed PPI

Do the first three steps as mentioned above.

The second tab is the STRING mapper.
On this tab, define a project name, select the VRNetz file of your exported String network, and select the organism from which your VRNetz originates of.
Click on the "Map" button to map the network with the preprocessed PPI.
If the upload was successful, you'll be prompted with a success message and a link to preview the project in the designated WebGL previewer.