App for modeling the effects of small binding molecules on pathways in Cytoscape
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README.md

PathInsight

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 through a series of steps and observe the affected pathway under various pre-defined conditions. PathInsight also allows for the use of visualization in Systems Biology Graphical Notation.

PathInsight is developed and maintained by Aarya Venkat (aarya@ucsd.edu) of the Gilson Lab (gilson.ucsd.edu) at UCSD.

Installation (Two Methods)

1.      Either download from http://apps.cytoscape.org/apps/pathinsight
2.      Or open Cytoscape. Click on Apps > App Manager > PathInsight
	
Download the sample network from: https://github.com/HelloAarya/PathInsight/blob/master/jakstatsbgn.cys

Function Guide:

  • PathInsight functions are located in Cytoscape under Apps > PathInsight

    • Node Analysis: An algorithmic analysis that models how a selected activated or inactivated node (or nodes) will affect their nearest neighbors. May be performed in one step (nearest neighbors) or two steps (nearest neighbors + neighbors of nearest neighbors) or N-steps (recursive algorithm that operates the number of times a user specifies).
  • Node Label:

    • Activated – Gives selected nodes a value of one.
    • Inhibited – Gives selected nodes a value of negative one.
    • Reset – Gives selected nodes a value of zero.
  • Edge Label:

    • Activating – Gives selected edges a value of one.
    • Inhibiting – Gives selected edges a value of negative one.
    • Reset – Gives selected edges a value of zero.
  • Reset Values:

    • Reset Nodes – Resets all node values to zero.
    • Reset Edges – Resets all edge values to zero.
    • Clear Images – Erases all painted images.
    • Clear Questions - Erases all question marks from edges.
  • KEGG Prepare:

    • This purely visual feature takes any edge that has previously been allocated a value of activating (+1), inhibiting (-1), or null (0) and gives it a corresponding circle, T, or diamond interaction symbol. Furthermore, if the pathway is taken directly from a KEGG source (like KEGGScape), edges are automatically changed based on provided information.
    • This function also gives any node labeled with an integer value, previously set by Node Analysis or Node Label tabs, a corresponding image of the value. Users may use this to visually model the effects of a perturbed pathway.
  • Phosphorylation

    • Phosphorylated -- visual function adding a yellow dashed line to an edge specified as phosphorylating.
    • Dephosphorylated -- visual function adding a pink dashed line to an edge specified as dephosphorylating.
  • SBGN (Systems Biology Graphical Notation)

    • Draw Chemical Node -- creates a circle shape (or replaces a node with one if a node is selected)
    • Draw Macromolecule -- Replaces a node with the SBGN value for a macromolecule
    • Draw Gene -- Replaces a node with the SBGN value for a gene
    • Draw Process Nodes -- Creates a node that represents translocation or dimerization
    • Draw AND Gate -- Creates a node that represents an AND gate
    • Draw OR Gate -- Creates a node that represents an OR gate

Example

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