Use Case Name : Protein Complexes

For Feature : Groups

Editors: Alex Pico

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We would like to be able to represent two or more proteins as macromolecular complexes in pathways. The representation of complexes will help simplify the visualization of complicated biological systems. Furthermore, complexes themselves have properties and interactions that we'd like to support and store.

Step-by-Step User Action

Creating a New Complex

  1. Select two or more nodes
  2. Choose "Form complex" from a context menu, main menu or toolbar
  3. Automatically view collapsed view of complex with default label (editable)
  4. Be able to expand complex as vertically stacked set of nodes by a very simple mechanism (e.g., click on a plus/minus icon)
    1. perhaps other restricted views of the children will be allowed:
      1. horizontal stack
      2. block (e.g., 2x2, 3x4)
      3. overlapping "clump" of nodes packed into a some defined circular area
      4. new network
  5. Be able to destroy complex
  6. Be able to expand-all or collapse-all complexes in a given network

Loading a Network with a Complex

  1. Same as 3-6 above

Visual Aides


In this GenMAPP pathway, stacked gene objects help indicate complex and paralog groups. For example, Rhoa + Racgap1 and Gsk3b + Apc

Requirements for Cytoscape


This is a very important use case, critical to almost every pathway. The typical user would expect quick, intuitive control over this feature, mainly for simplifying (or digging deeper into) a given pathway representation.

Other Examples


AllanKuchinsky - 2006-11-27 07:16:15

This suggests a sub-project to define a set of "visual formalisms" for the view aspect of Groups.  Visual formalisms are "diagrammatic notations with well-defined semantics for expressing relations.  They ae based on simple visual notations such as tables, graphs, plots, panels, and maps.  Versions of such visual notations that define a precise semantics become truly formal".   This is described in Nardi and Zarmer, 1990, which is attached nardiZarmer.pdf

AllanKuchinsky - 2006-11-27 07:33:55

The idea would be to build a small set of visual formalisms, e.g. vertical/horizontal stacks, tables, that could be readily specialized to views for complexes, paralogs, protein domains, etc.

groupAPI/UseCase_2A (last edited 2009-02-12 01:03:56 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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