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Cytoscape interface to STRING and STITCH
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Basic idea: three "modes" Mode 1: build an initial network from String/Stitch 1) Add to web service interface: get a list of identifiers. Will also need to be able to use slider to change confidence cut-offs, a drop-down list of species, and buttons for evidence types. 2) Take list of identifiers and use resolveList on String web site to get the possible matches. If the preferredName matches the user input, use that. If not, provide the user with a dialog to choose which identifier to select. 3) Once the list of identifiers are known, use the API to get a tsv file with all of the interactions. Use this to build the network. Once the network is built, go back to string/stitch to get the additional annotations (currently don't have a good way to do this). Mode 2: expand an existing network from String/Stitch 1) Select a group of nodes, right-click on any node and pull the list of String identifiers from selected nodes, then query string to fetch additional interactions and nodes Mode 3: Grow network 1) Like expand, but explicitly send the entire network and ask for more interactors. Mode 3: "Send to Cytoscape" button in String/Stitch