Milestone Module - Glycan Pathway 1.0

Glycan pathway module

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For the implementation of the graph representation of glycans in GRITS the project is divided in three parts:

  • Object model to represent the graph in memory
  • Substructure based algorithm to represent a set of input structures in the object model
  • Interactive GUI to represent the tree in GRITS.

Object model

  • Nodes: Glycans are nodes in the graph
    • Glycan
    • (optional) Meta data => used for decorators
    • (optional) can have a level
  • Edges: Relationships between glycans are the edges in the graph
    • Relationships can be: substructure, enzymatic precursor
    • (optional) meta data => used for decorators
    • Hidden or deselected property.
  • Graph
    • Mass spec application: Directed, no multigraph, disconnected graph
    • Pathway application: Directed, no multigraph, disconnected graph, cyclic

Mass spec application: Substructure based graph generation

  • Input is a set of glycans (from several dozen to more than 1.000 glycans)
  • Calculate the substructure dependency between these glycans
  • Build the graph based on these dependencies
  • Reduce number of edges by hiding edges
    • This may include human specified rules
    • No links to grandparents and grandchildren
    • Arbitrary select one path

GUI representation in GRITS

  • Representation
    • Draw glycans as nodes
      • (not preferable) use images (png, jpg)
      • (preferable) import from SVG as intact objects
    • Draw not hidden edges as connections
      • (optional) with arrowhead for direction
    • Alignment
      • Nodes should be non-overlapping
      • If the level feature is used nodes of the same level have to be on the same horizontal/vertical line
      • (optional) Connections should cross as less as possible
  • Interaction
    • Export/print graph (e.g. pdf)
    • Hide, unhide, remove edges
    • Remove nodes => interaction with other plugins
    • (optional) Drag and drop rearrangement of the graph
Note: See TracRoadmap for help on using the roadmap.