## *Core App*: Diffusion
### Note: This app is pre-installed in Cytoscape 3.9 or later
**_You should not download this app_ from the store yourself. If Cytoscape detects that a new version is available in the App Store, it will notify you as it's starting and will give you a chance to download it directly.**
**_You should not download this app_ if your Cytoscape is earlier than 3.9. An earlier version of this app is pre-installed in your Cytoscape, and this app cannot replace it.**
## Background
Network propagation is an important and widely used algorithm in systems biology, with applications in protein function prediction, disease gene prioritization, and patient stratification. Propagation provides a robust estimate of network distance between sets of nodes. Operating on similar principles as Google’s search algorithms, network propagation uses the network of interactions to find new genes that are most relevant to a set of well understood genes. For instance, if we know that mutations in a particular protein cause a disease, we can also guess that mutations in related proteins are also likely to cause this disease. We can find related proteins by examining the network of interactions.
## How to Use
The Cytoscape Diffusion app turns the powerful network propagation service into an easy right click menu item.
* Select the nodes you would like to use as input heats
* Right click and select **Diffuse → Selected Nodes** which will send your network and inputs to our remote diffusion service.
* After propagation, the Diffusion app will add your results as node columns for easy filtering. A results panel will also open with some useful utilities for finding groups of nodes above and below a certain threshold, and creating styled subnets from your selections.
## Availability
The Diffusion app calls a web-based REST service to calculate network propagation. The service code and documentation is available at [https://github.com/idekerlab/heat-diffusion]
The service can be called directly from any REST-enabled client at [http://v3.heat-diffusion.cytoscape.io/]
The Diffusion app source itself is available at [https://github.com/cytoscape/Diffusion]
