Use Case Name : ../AutoDrawBioPax

For Feature : MIMEditor

Editors: DavidKane

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A user wants to see a Kohn representation of a BioPAX pathway.

Step-by-Step User Action

  1. User selects a BioPAX document to view
  2. The system uses an automated layout program to generate a map using the Kohn notation

Visual Aides

Requirements for Cytoscape



Although many of the use cases are cast in terms of editing, this use case could provide a good shorter-term capability that could be useful to both BioPAX-oriented users, and work out the implementation details for representing the Kohn notation.

Other Examples

Many software engineering tools have these sorts of autodraw features from underlying models. E.g. drawing a class diagram from XMI or drawing an ERD from an underlying database.


Shared ../MimEditorUseCaseComments

Used by ../AssistedLayout

AllanKuchinsky - 2007-01-22 05:29:23

Assume this can be handled by programmatic calls to one or more of the Cytoscape automated layout routines? Is incremental/interactive layout via BubbleRouter applicable as well?

Molecular_Interaction_Maps/AutoDrawBioPax (last edited 2009-02-12 01:03:12 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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