Visual Chemical Network Editor

I have moved the chemical network editor I made for Windows and the Mac to both Linux and the Web. This was a rewrite using Rust and egui for the UI. This tool can be used to create a layout for SBML model. Such layouts are stored in the SBML itself using the standard layout extension. A number of tools can render such SBML, such as COPASI or the Python package SBMLNetwork and SBMLDiagrams. cy2sbml and EscherConverter can also read these files. 

To try it out, go to the website:

https://sys-bio.github.io/PathwayDesigner-rs/

Summary of capabilities:

To host it on another site, simply copy all the files to the other site; instructions are given at the end in the readme.md. There are no dependencies; the app is pure Rust. For the web deployment, the code is compiled to WASM.

Source code and releases can be found at

https://github.com/sys-bio/PathwayDesigner-rs

Draw reactions A → B, A + B → C, A → B + C, A + B → C + D, with stoichiometry (future versions will generalize to any number of reactants and species)

A variety of reaction renderings, such as straight lines and Bézier curves, plus an optional centered junction point for uniuni reactions.

Alisa nodes are supported, useful for species such as ATP where there may exist multiple places on the network, alias nodes avoid unnecessary clutter.

Full undo and redo

Colors, and line thickness can be set. These can only be stored in the native json format. Although SBML also has a render extension, this is a very complex standard which is difficult to implement.

Basic autolayout is provided. This is useful for SBML models that have no layout.

Models in the form of Antimony can also be input. Currently, only basic Antimony syntax is supported. A future version will have full Antimony support.

Networks can be exported as SVG, PNG, or PDF.

Update: 10/12/2026

Version 0.1.1 fixes some minor annoyances, but significantly adds the ability to draw circular pathways. To use, select the species you want in a circle, right-click and select Alignment -> Arrange in Circle. The example below was made from the default network that is loaded at startup:

YouTube Video of Iridium Platform

 

This is a brief video I made for the COMBINE 2026 meetings at Keele University this September, showing a couple of things about the Iridum simulation platform.

 Penultimate Version of Iridium Desktop Released. 

I believe I have finally reached the penultimate version of the Iridium Desktop simulator for Windows and Mac OS. The next version will be 1.0

The Iridium Desktop App is designed to be a productive and easy-to-use interactive SBML-compatible simulation environment for biochemical models. All code is open source  under the MIT license.

Mac OS and Windows binaries can be obtained from 

https://github.com/sys-bio/IridiumSimulator/releases

Click on assets to either download the Mac OS dmg file or a zip file for Windows. To use teh zip file, unzip the contents anywhere on your hard drive and run the Iridium executable. 

There is also a non-install Web Version at:

https://sys-bio.github.io/WebIridium/

Here are some screenshots of the Desktop version.

The main window is split into three sections, left to right: Control Panel, Input Panel, Output Panel. The control panel is switchable between different analysis types; these currently include Time Course simulation, Parameter Scanning, and Steady State. A variety of built-in models come with the distribution (Accessible in the bottom-left drop-down combo)

Time Course Simulation

The screenshot below shows the app operating in Time Course simulation mode. The central input panel has the antimony/SBML editor at the top and the optional slider panel at the bottom. Simulation results are shown on the plot panel to the right. 

Simulations are live in the sense that movement in any slider results in an instant change to the plotting output. All output is rendered in high definition. Output can also be captured as raw data by selecting the Text View tab on the output panel

Parameter Scan Panel

The following screenshot shows the parameter scan panel operation. Parameter scans can be with respect to any parameter of the model. The output measure can be any observable, but can also be limited to time course overlays, peak values, endpoints, and time to peak.  The slider panel is also active during a parameter scan.

Steady State Panel

The steady state panel is used to compute the steady state panel of the model. It can display the steady-state concentrations, Jacobian, and sensitivities of metabolic control analysis. The slider panel is also active in this mode. The steady state panel can display grid data or 3D plot.

Import/Export

SBML models (such as BioModels) can be imported or exported. When imported, they are automatically converted to Antimony form for easy editing.

Reproducibility

Both Time Course and Parameter Scan panels can export the last analysis as a Python script. This allows any parameter scan or time course simulation to be reproducible separately from the Iridium app.

Two sister applications are also under development:

1. Bifurcation Analysis Tool (Windows edition complete)

https://github.com/hsauro/BifurcationTool

2. A Model Fitting App for Windows and Mac OS

This is currently under development but should be released before October 2026

1. Fit SBML models to data using Antimony to edit models

2. Supports multiple data sets as well as time-course and dose-response data.

3. Implements 4 optimizers: Levenberg-Marquardt, Nelder-Mead, Swarm Particle, Differential Evolution.

3. Implements standard linear error uncertainty, profile likelihood, and bootstrap methods for uncertainty estimation.

4. Plots of the fitted model, residuals, profile likelihoods, and bootstrap estimations.

5. Differential Evolution and Particle Swarm can use multiple cores on a computer for higher performance.

6. Import/Export of PEtab.

All work on this page was supported by the NIH Center for Reproducible Biomedical Modeling

I created a number of cheat sheets for a class I did this quarter. The cheat sheets cover the topic of metabolic control. They include: 

1. General Metabolic Control 
2. Advanced Metabolic Control 
3. Linear Chains 
4. Branch Points 
5. Moiety Conserved Cycles

They are available a this GitHub repo:

https://github.com/hsauro/CheatSheets

Both the original LaTeX and pdfs files are provided.

Many years ago I wrote a windows application that could be used to build biochemical models visually. Origially called JDesigner but subsequently renamed to PathwayDesigner. Over the years the code grew larger and somewhat unwieldy. In addition it couldn't run on the Mac. I have decided therefore to rewrite it using more modern tech so that is can run on the Mac as well as Windows. Initially it won't include simulation capabilities since simulators are dime a dozen. It also won't support SBGN or the SBML layout/render standard since htey are hard to support. The GitHub repo can be found here, currenlty at version 0.1.1 https://github.com/hsauro/PathwayDesigner