IBUsage
- Access the Interaction Browser from its homepage at http://sysbio.soe.ucsc.edu/nets . There is a tutorial that describes the basic functions at pages linked from there.
- A network can be visualized directly by including node and track requests in the URL's query string. Use the following example:
- http://sysbio.soe.ucsc.edu/nets/NetVizTest.html?organism=worm&biodes=lin-23,lin-39,F29C12.4,Y48E1B.5,ZC395.10,mrp-5,F54C9.6,exo-3,T09A5.5,ogt-1,lin-2,C27F2.10,bar-1,lin-35,efl-1,B0432.3,lin-7,T20B12.7,ubc-18,T01E8.6,prx-5&tracks=Weirauch08,wormbase_genetic
- The interaction browser interprets the parameters in the query string.
- organism is the organism from which organism to look up nodes.
- biodes is a comma-separated list of gene identifiers that the Interaction Browser servlets will attemp to look up.
- tracks is a comma-separated list of tracks to turn on. The names in this list must match exactly to a track name. Track names can be retrieved by querying the Interaction Browser servlets as described in /IBServlets
- active subnetworks
- This feature allows a user to start with just a set of genes. The IB will take the query set of genes and attempt to identify a subnetwork for it, adding additional genes and turning on tracks as needed.
- To make a gene set for initial testing, we attempt to identify significantly mutated genes in cancer with a poisson-like model. Here's a whiteboard that outlines this method:
