Table 2. List of actions performed in the use case workflow.
| Action | Workspace | URL | Sample Parameters |
|---|---|---|---|
| Download | Broad firehose
web site |
http://firebrowse.org/api/v1/Analyses/Mutation/MAF | format=‘tsv’
cohort=‘BRCA’ |
| Build
network |
Cytoscape | http://localhost:1234/reactomefiviz/v1/buildFISubNetwork | file=‘BRCA.maf’
sampleCutoffValue=4 |
| Cluster | Cytoscape | http://localhost:1234/reactomefiviz/v1/cluster | none |
| Partition by
overlap |
Python
notebook |
n/a | cutoff=.05 |
| Annotate | Cytoscape | http://localhost:1234/reactomefiviz/v1/ReactomePathwayEnrichment | data=[‘ABCA1’, ‘ACL2’,
..., ‘ZNF462’] |
| Export
diagram |
Cytoscape | http://localhost:1234/reactomefiviz/v1/exportPathwayDiagram | dbId=68877
pathwayName=‘Mitotic Prometaphase’ fileName=‘Mitotic Prometaphase.pdf’ |