SBcoyote DOCUMENTATION

An Extensible Python-Based Reaction Editor and Viewer

Jin Xu, Gary Geng, Nhan D. Nguyen, Carmen Perena-Cortes, Claire Samuels, Herbert M. Sauro (JX and GG contributed equally)

University of Washington - Sauro Lab

SBcoyote is a visualization tool for drawing reaction networks written with wxPython (https://www.wxpython.org/) and applicable for different platforms. It can draw reactants, products, reactions, and compartments. Its features include, but are not limited to:

• Support for floating and boundary species.

• Option to display reactions using Bezier curves and straight lines.

• Plugin support, with some plugin examples: arrow designer, random network, auto layout and etc.

Contents:

• Quick Start
  • INSTALLATION FOR USERS
  • INSTALLATION OPTIONS FOR DEVELOPERS
  • RUNNING AND BUILDING FOR DEVELOPERS
  • DEVELOPMENT ON DIFFERENT PLATFORMS
• Tutorial
  • 1. Navigation Bar
  • 2. Applications Menu
  • 3. Creation Panel
  • 4. Canvas
  • 5. Information Panel
  • 6. Zoom Control
  • 7. Theme For Developers
• Plugin Development
  • Writing plugins
  • Plugin categories
• Plugin Reference
  • Plugin API Reference
  • Plugin Classes
• Internal JSON Model Format
  • Instructon
  • Information
  • Example
• Core Development
  • How do I add a field to Node/Reaction/Compartment?
• Core Reference
  • rkviewer package