Systems Biology in ModelingToolkit

07/29/2021, 12:40 PM — 12:50 PM UTC


Systems Biology Markup Language (SBML) and CellML are extensible markup languages (XML) widely used throughout the biological modeling community. In this talk we showcase new packages (SBML.jl and CellMLToolkit.jl) for importing models from these languages to the ModelingToolkit.jl format for the full suite of SciML tools to simulate and analyze!


Back in my day, systems biologists used MATLAB and Python for RK4. But in 2021 we can now run downhill both ways and make our biological models zoom with CellMLToolkit.jl and SBMLToolkit.jl in Julia! We will demonstrate importing CellML and SBML models into ModelingToolkit and how we get these model analysis and simulation tools "for free" in an acausal symbolic component model. We will show a few examples of how (biological) researchers may benefit from the broader SciML ecosystem, including parameter estimation and global sensitivity analysis. Short comparisons with de facto SBML and CellML modeling programs will be drawn to demonstrate how a biologists’ workflow may differ with SciML. The audience will leave with a firm understanding of how the Julia simulation environments will lead the next generation of biological modeling and simulation.

Platinum sponsors

Julia Computing

Gold sponsors

Relational AI

Silver sponsors

Invenia LabsConningPumas AIQuEra Computing Inc.King Abdullah University of Science and TechnologyDataChef.coJeffrey Sarnoff

Media partners

Packt Publication

Fiscal Sponsor