A visualization tool for reaction networks

Gary Geng, Carmen Perena-Cortes, Dr. Herbert M. Sauro, Jin Xu, Claire Samuels

University of Washington - Sauro Lab

PyRKViewer is a visualization tool for drawing the reaction networks written by wxPython (https://www.wxpython.org/) and applicable for different platforms.

• It can draw reactants, products, reactions and compartments. Its features are listed below but not limited to:

• It supports floating and boundary species.

• Reactions can be displayed using Bezier curves and straight lines.

• It has plugin support, with some plugin examples: ArrowDesigner, RandomNetwork, Antolayout and etc. For the next version, we are going to add simulations of reaction networks.

• This is the first version of this application, done in the Sauro Lab in the University of Washington.

Contents:

• Quick Start
  • RUNNING AND BUILDING
  • Building an Executable with Pyinstaller:
  • USING ON DIFFERENT PLATFORMS
• Tutorial
  • 1. Navigation Bar
  • 2. Applicaions Menu
  • 3. Creation Panel
  • 4. Canvas
  • 5. Information Panel
  • 6. Zoom Control
• Plugin Development
  • Writing plugins
• Plugin Reference
  • Plugin API Reference
  • Plugin Classes
• Core Development
  • How do I add a field to Node/Reaction/Compartment?
• Full Reference
  • rkviewer package