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#SLiMscape SLiMScape, a Cytoscape plugin, is a platform for performing short linear motif analyses of protein interaction networks by integrating motif discovery and search tools in a network visualization environment. This aims to aid in the discovery of novel short linear motifs, as well as visualisation of the distribution of known motifs.

##Installation To install, simply navigate to the Cytoscape App Store and click the install button. This will add the app to your local Cytoscape version.

##Input The minimum input for SLiMScape is an interaction network which contains a Uniprot attribute for each node OR a run ID from the UNSW servers. At the moment, the name of the node needs to be its Uniprot ID or Accession Number for the server to know what to do with it.

An example input with Uniprot IDs is:

name

P54253

O35147

Q61337

P04049

Q99683

Q9EPK5

An example input with a run ID is:

Run ID:

15020400003 (SLiMProb run)

More specific documentation for each program is available on the program page.

Once a search has been completed, the nodes that contain SLiMs will change from the default blue circles to red diamonds. The rest of the nodes will remain as they were.

If you want to pre generate a job on the Slimsuite servers, you can do that from here. If you do this, you can input the generated run ID to Cytoscape, and a graph will be generated for you! It's also handy for larger jobs that may take a while to finish.