An interactive simulator for integrating biochemical models with experimental data
Abstract
Biological models based on mathematical simulations (e.g., ordinary differential equations) are hugely beneficial for understanding biological processes and predicting the outcomes of experiments. Such models are built using a variety of sophisticated modeling tools. Unfortunately, the complexity of these tools is often a barrier to use by experimental biologists. To improve the usability and impact of biological models, we have created a desktop platform (DeskIridium) and a web-based simulator (WebIridium, hosted as a GitHub page) that, in combination, provide features that promote ease of use by experimental biologists, including: human-readable editing of models via the Antimony syntax; sliders for adjusting parameter values while simultaneously displaying simulation results in real time; zero-install distribution; AI chat integration; and generation of standalone Python implementations of SBML models to support reproducibility. The desktop version uses the well-established libroadrunner simulation package; the web-based application uses an Emscripten translated version of COPASI. Both simulators are SBML-compatible, allowing users to easily import previously built models or edit existing models using the easy-to-use antimony language. We used modern AI methods for software development and share the lessons we learned. Binaries, source code, and the web interface are available at: https://github.com/sys-bio/IridiumSimulator and https://github.com/sys-bio/WebIridium.
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BibTeX
@misc{sauro2026interactive,
title = {{An interactive simulator for integrating biochemical models with experimental data}},
author = {Herbert M. Sauro and Dan Nguyen and Long Nguyenle and Steven S. Andrews and Frank T. Bergmann and Joseph L. Hellerstein and Lucian P. Smith and H. Steven Wiley},
howpublished = {arXiv},
year = {2026},
month = sep,
doi = {10.48550/arxiv.2609.34186},
eprint = {2609.34186},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2609.34186},
note = {CC BY 4.0},
}
RIS
TY - UNPB
TI - An interactive simulator for integrating biochemical models with experimental data
AU - Herbert M. Sauro
AU - Dan Nguyen
AU - Long Nguyenle
AU - Steven S. Andrews
AU - Frank T. Bergmann
AU - Joseph L. Hellerstein
AU - Lucian P. Smith
AU - H. Steven Wiley
PY - 2026
DA - 2026/09/28
PB - arXiv
DO - 10.48550/arxiv.2609.34186
UR - https://arxiv.org/abs/2609.34186
AB - Biological models based on mathematical simulations (e.g., ordinary differential equations) are hugely beneficial for understanding biological processes and predicting the outcomes of experiments. Such models are built using a variety of sophisticated modeling tools. Unfortunately, the complexity of these tools is often a barrier to use by experimental biologists. To improve the usability and impact of biological models, we have created a desktop platform (DeskIridium) and a web-based simulator (WebIridium, hosted as a GitHub page) that, in combination, provide features that promote ease of use by experimental biologists, including: human-readable editing of models via the Antimony syntax; sliders for adjusting parameter values while simultaneously displaying simulation results in real time; zero-install distribution; AI chat integration; and generation of standalone Python implementations of SBML models to support reproducibility. The desktop version uses the well-established libroadrunner simulation package; the web-based application uses an Emscripten translated version of COPASI. Both simulators are SBML-compatible, allowing users to easily import previously built models or edit existing models using the easy-to-use antimony language. We used modern AI methods for software development and share the lessons we learned. Binaries, source code, and the web interface are available at: https://github.com/sys-bio/IridiumSimulator and https://github.com/sys-bio/WebIridium.
ER -