An open-source Cytoscape application that models the effects of small binding molecules in pathways in Systems Biology Graphical Notation


PathInsight is an open-source Cytoscape application created to aid in modeling the upstream and downstream signaling effects of small molecule binders in a biological pathway. Users may perturb a given system and observe the affected pathway under various user-defined conditions.

PathInsight is developed and maintained by Aarya Venkat of the Gilson Lab at UCSD.

Installation (two methods):

1. Either download from

2. Or open Cytoscape. Click on Apps > App Manager > PathInsight

  • Version Preview (1.1.0):

New in this version is the algorithm's ability to model SBGN pathways. Systems Biology Graphical Notation (SBGN) is a new format for pathway representation, created to maintain visual consistency in research.

To Do List:

  • Add function for N number of steps during Node Analysis
  • Add better designs for dual-state functionality
  • Add Uniprot and BindingDB functions - for ease of access to binding data for all nodes

External Links:

Gilson Lab




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