Random Walk with Restart Toolkit

These apps allow users to explore networks of multiplex data in an interactive network visualization using the Random Walk with Restart Toolkit (RWRtools).

Apps

• Find Functional Context using Lines of Evidence with RWRtools LOE: uses Random Walk with Restart (RWR) to rank genes in the network starting from a Feature Set.

• Find Gene Set Interconnectivity using Cross Validation with RWRtools CV: performs cross validation on a single gene set, finding the RWR rank of the left-out genes.

Inputs

The input for this app is an annotated Genome.

The network data is maintained by KBase behind the scenes and can be found here.

Narratives

• RWRtools Exascale and Petascale Network Analysis Demo Narrative – was created as part of the software publications for the RWRtoolkit (manuscript in preparation).

  • Created and made public by Kyle Sullivan of Oak Ridge National Laboratory

• Microbial Genomics in KBase: Gene Feature Analysis – provides further examples of creating and working with FeatureSets derived from Genomes.

Tutorial webinar

Tutorial webinar presented by Kyle Sullivan, Oak Ridge National Laboratory

SFA Collaboration page

These apps were developed as part of the Exascale Network project led by Dan Jacobson. To learn more about this collaboration, see: https://www.kbase.us/research/user-working-groups/#datascience.