title	Rule-Based Modeling Minitutorial — SIAM LS26

Rule-Based Modeling with BioNetGen

A minitutorial at SIAM Life Sciences 2026 (SIAM LS26)

This page has everything you need before, during, and after the tutorial: a schedule, software setup instructions, and links to all example models we'll walk through.

Note: This is not a hands-on coding session — you don't need to install anything to follow along. But if you'd like to try the examples yourself afterward (or follow along live), see Getting Started below.

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Schedule

Topic	Presenter
Introduction to rule-based modeling, BioNetGen VSCode extension	James Faeder
Python tools for rule-based modeling (PyBioNetGen, sensitivity analysis, parameter estimation)	Laura Strube
Network-based vs. network-free simulation, NFsim	Alex DiBiasi
Model integration and simulation pipelines (INDRA, EGFR case study)	Achyudhan Kutuva
Applications: WESTPA/WEBNG, RuleHub, and the broader ecosystem	Various

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What we'll cover

• Rule-based modeling concepts — why some biochemical systems (like multivalent ligand-receptor binding) can't be described with a fixed set of ODEs
• BioNetGen — building rule-based models with .bngl files, generating reaction networks, and simulating with ODE/SSA solvers
• Python ecosystem — PyBioNetGen, Jupyter-based workflows, sensitivity analysis, parameter estimation, identifiability
• NFsim — simulating systems whose reaction networks are too large (or infinite) to enumerate, using network-free simulation
• Applications — weighted ensemble simulation (WESTPA/WEBNG), model integration with INDRA, and the broader RuleHub model repository

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Getting started

To follow along with the example models (optional, not required for the talk itself):

1. Install BioNetGen. Follow the instructions from the BioNetGen website or install the BioNetGen VSCode extension for an integrated editing/simulation experience.
2. (Optional) Install PyBioNetGen for Python-based workflows:

   pip install bionetgen

3. (Optional) Install NFsim if you want to run the network-free examples directly — see the NFsim GitHub repo for build instructions.

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Example models

All example .bngl files discussed in the tutorial are in the models/ folder of this repo:

• one_arm_model.bngl — minimal model for learning the BNGL syntax
• lr_simple.bngl — basic L + R ⇌ LR ligand-receptor model
• tlbr.bngl — trivalent ligand / bivalent receptor model (network-free example)
• lat_aggregation.bngl — LAT-Grb2-SOS1 aggregation model
• translation_model.bngl — ribosome translation model (network-free example)
• egfr.bngl — EGFR pathway model (INDRA case study)

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Resources

• BioNetGen documentation
• RuleHub — repository of curated rule-based models
• NFsim
• WESTPA
• Slides: (link once finalized)

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Questions?

We'll have time for Q&A throughout the session — feel free to interrupt with questions. After the tutorial, you can reach us at [lab contact email] or open an issue on this repo.

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Faeder Lab, University of Pittsburgh