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arXiv · 2302.09151

SBcoyote: An Extensible Python-Based Reaction Editor and Viewer

Jin Xu·Gary Geng·Nhan D. Nguyen·Carmen Perena-Cortes·Claire Samuels·Herbert M. Sauro
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Abstract

SBcoyote is an open-source cross-platform biochemical reaction viewer and editor released under the liberal MIT license. It is written in Python and uses wxPython to implement the GUI and the drawing canvas. It supports the visualization and editing of compartments, species, and reactions. It includes many options to stylize each of these components. For instance, species can be in different colors and shapes. Other core features include the ability to create alias nodes, alignment of groups of nodes, network zooming, as well as an interactive bird-eye view of the network to allow easy navigation on large networks. A unique feature of the tool is the extensive Python plugin API, where third-party developers can include new functionality. To assist third-party plugin developers, we provide a variety of sample plugins, including, random network generation, a simple auto layout tool, export to Antimony, export SBML, import SBML, etc. Of particular interest are the export and import SBML plugins since these support the SBML level 3 layout and render standard, which is exchangeable with other software packages. Plugins are stored in a GitHub repository, and an included plugin manager can retrieve and install new plugins from the repository on demand. Plugins have version metadata associated with them to make it install plugin updates. Availability: https://github.com/sys-bio/SBcoyote.

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BibTeXRIS

Jin Xu, Gary Geng, Nhan D. Nguyen, Carmen Perena-Cortes, Claire Samuels, Herbert M. Sauro. 2023-02-17. SBcoyote: An Extensible Python-Based Reaction Editor and Viewer. https://doi.org/10.1016/j.biosystems.2023.105001

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