Tonight I started watching the KBase session “Exploring Plant Gene Linkages using Random Walk with Restart Tools.” Kyle Sullivan, a scientist from Oak Ridge National Labs, is working on these apps. The webinar was recorded January 31, 2024. The team developed a series of tools and a narrative. The genome wide association studies (GWAS) and tools to explore networks were described by Sullivan. The Random Walk with Restart (RWR) algorithm was applied on multiplex networks. With this process, networks can be explored with “restart” to prevent getting stuck. Sullivan described gene-to-gene network layers with over 3.8 million connections for Arabidopsis thaliana. They generated these multiplex networks with supercomputing. The networks are pre-constructed and available on KBase. For example, RNA seq data from a leaf sample was used for one multiplex network. Data sets from several sources were included, such as knock-out gene phenotypes/transcriptomes. Sullivan described how networks are linked based on similar functions or ontologies, for example. This was a dense explanation of networks before getting into the use case. I paused here to focus on my talk tomorrow!
