EMBO 2023 - Bodylight.js

Created by Tomas Kulhanek

#modeling, #physiology, #simulation

Tomáš Kulhánek - Bodylight.js

Bodylight.js – toolchain for in-browser simulation of simple and complex mathematical models.

code in programming language

Model

equations

block schema

component modeling (compartment modeling)

components

Tomas Kulhanek, Jiri Kofranek. Experience with Teaching Different Modeling Techniques on the example of Glucose Insulin Regulation Model,

Annu Int Conf IEEE Eng Med Biol Soc. 2020 Jul;2020:6024-6027. doi: 10.1109/EMBC44109.2020.9176535

OpenModelica, Dymola (by Dassault Systemes), System Modeler (by Wolfram) ...

component (compartment) model (having DAE or ODE) follows physical reality

Is it a model? block schema

A C Guyton, T G Coleman, H J Granger, Circulation: overall regulation, Annu Rev Physiol.1972;34:13-46.doi: 10.1146/annurev.ph.34.030172.000305.

Correction after reimplementation in 2010

J.Kofránek, et al., Restoration of Guyton‘s Diagram for Regulation of the Circulation ...Physiol Res. 2010;59(6):897-908.doi: 10.33549/physiolres.931838.

Physiomodel

https://physiomodel.org >60 000 equations

Mateják, M., Kofránek, J. (2015), Physiomodel – An Integrative Physiology in Modelica, Proceedings of 37th AnnualInternational Conference of the IEEE Engineering in Medicine and Biology Society, IEEE, Milano (It), pp. 1464-1467, ISSN: 1557- 170X.

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circulatory dynamics

implementation in component and acausal modeling language

Frank-Starling law

Frank-Starling law is much more visible in component model - "force of the heart muscle depends on pressure of incoming blood".

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Physiolibrary, Chemical

https://physiolibrary.org

Marek Mateják, Tomáš Kulhánek, Jan Šilar, Pavol Privitzer, Filip Ježek, Jiří Kofránek: Physiolibrary - Modelica library for Physiology, In Conference Proceeding,

#1 award for best open-source library - for Physiolibrary 10th International Modelica Conference, March 12, 2014, Lund, Sweden, (DOI:10.3384/ECP14096499)

#1 award for best open-source library - for Chemical 11th International Modelica Conference, 2015, September 21-23, 2015, Paris, France

compile code to executable

Simulation

specialized modeling simulation tool

portable application

Why simulation?

missing pieces for portable web application

1. export model to FMU with C source code

bodylight.js

scripts to translate model from FMU (co-simulation mode with C source code) to WebAssembly
webcomponents - javascript library with reusable and configurable custom elements
1. for model simulation
2. for animation
3. for other visualisation/communication etc.
optional tools (composer, editor) to simplify creating and deploying web simulators

2.compile to WebAssembly

Configuration and scripts to facilitate compilation with emscripten

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https://github.com/creative-connections/Bodylight.js-FMU-Compiler

3. download JS with WebAssembly and use it in <bdl-fmi> web component

webcomponents - HTML elements

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webcomponents - custom elements animation

export animation from Adobe Animate to JS library
follows CreateJS API
custom tag for animation

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webcomponents - custom elements

custom tag for range

range

custom tag for model: fmi
custom tag for chart

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in-browser simulator - INDEX.HTML

1. download or refer bodylight.bundle.js

EITHER <script src=" bodylight.bundle.js" ></script>
OR npm -i bodylight-components

2.include web components in HTML source:

...

we can put HTML/CSS styling

HTML + webcompontens = in-browser simulator

simulator of glucose/insulin

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simulator of iron metabolism

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simulator of hemodynamics

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co-simulation of multiple models

respiration

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blood-gas exchange

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hemodynamics of cardiovascular system

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native mobile apps

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digital appendix of scientific paper

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give life to VR/AR

simulator of cardiorespiratory treated with ECMO

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REST API

control HW mannequin

hwmanequin

summary

Bodylight.js – toolchain for in-browser simulation of simple and complex mathematical models.

Tomáš Kulhánek, Ph.D.

(seek for collaboration, contract, visit, job)

future: AI / ML assisted modeling - SciML - physiology informed neural network

value of simulation based on scientific models for educational and clinical app

https://bodylight.physiome.cz

https://egolem.online/demo

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supported FMI export

Dymola
- CVODE with source code
OpenModelica
- EULER
- CVODE - in roadmap

+

or

performance - WASM 12% slower than native code

WASM1 ~ requestAnimationFrame( () -> {
  ...
  fmiDoStep();
  ...
})
WASM3 ~ requestAnimationFrame( () -> {
  ...
  fmiDoStep();
  fmiDoStep();
  fmiDoStep();
  ...
})

+

simulator1

static HTML pages - GITHUB pages

simulator2

Supporting tools

Bodylight.js-FMU-Compiler

Configuration and scripts to facilitate compilation with emscripten

emcc … -O3 –closure 0 …

https://github.com/creative-connections/Bodylight.js-FMU-Compiler

Bodylight Editor

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Bodylight VirtualMachine

Physiolibrary

https://physiolibrary.org