PathwayDesigner

This is a rewrite of the original PathwayDesigner application. This version will run on Windows and Mac OSX

Overview

PathwayDesigner is a GUI tool for drawing and editing biochemical networks. Visualization is simple in that it doesn't support the SBGN standard but offer a clean view of a network. Models can be imported in Antimony format and eventually SBML. The applicaton has its own JSON format that is used to store all the graphical information.

Getting Started

An initial binary release is available in the releases section, version 0.1.0 for windows only. Mac binaries (DMG files) will be made if there are requests.

Vession 0.1.0

This version supports:

• Adding, deleting and moving species nodes
• Adding and deleting reactions
• Zoom and pan
• Creating alias species
• Select straight line or Bezier curves (basic support so far)
• Import/Export a subset of Antimony syntax
• Save and load to a json format that can store visualization information
• Autolayout, useful for model imported from Antimony

Version 0.1.1

This version adds:

• Undo/redo
• Much better control over bezier curves

Version 0.1.2

This version adds:

• Export to SBML including SBML layout. This means file can be imported into SBML packages suchas SBMLLayout that support drawing of networks.
• Fixed a number of bugs in Antimony import
• Some experimental support for setting colors of species nodes

Version 0.2

• Added right-click popup menu to align species nodes: left, middle, right, top, center, bottom, distribute vertically, and distribute horizontally
• Further improvements to the autolayout functions.
• Added a side text area where antimony syntax can be entered directly and the network drawn.
• Added hover feature to get concentrations of species and ids of reactions

Version 0.22

• Fixed small bug in antimony parsing
• Added basic printing support
• Added saving if networks as pdf or png files.

Versiion: 0.30

• Changing properties of species and reactions significantly improved
• Added ability to show or hide reaction junction point
• Create new color palette selection popup
• Changed color format in json to hex RRGGBBAA

Versiion: 0.31

• Bug fixes

Versiion: 0.32

• When confronted with a reaction such as -> A, it now adds a null species instead of leaving it empty.
• The start of a preferences form was added. One option was added. This option decides what it does with reactions of the form A -> A + B, kAB, with the option on it will change the reaction to -> B; kAB and add a modifier from A to the reaction.

Versiion: 0.37

• Add initial support for modifiers
• Allow users to edit the rate law
• Autosync changes in the rate law with the diagram, especially for modifiers.
• Fixed bugs in SBMLLayout export, fixed bug in tooltips colliding with delete species or reaction

Versiion: 0.38

• Added preferences option to show or hide a null node
• Improved handling of bezier curves usingthe Deckard autolayout with reactions such A -> A + B
• Added more control to the positioning of the reaction arrow head.
• Fixed bug in converting A -> A + B to -> B

Not yet supported

• Set font sizes for species names
• Select different species node shapes
• Positioning of species labels
• Styling, such as Echer style
• Cicularlize a set of nodes
• Interchange between json format and Alcuin human reable format
• Visualize compartments

Contributing

Bug reports and feature requests are welcome!

Screenshots

v0.3

License

MIT License

Copyright (c) 2026 Herbert M Sauro

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.