EDITH-CSA 2024 presentation Tomas Kulhanek
Created by Tomas Kulhanek
Bodylight.js & eGolem - Methods and tools for scientific models in medical simulation education
acknowledgment
team current and past
What language/technology do you use for modeling?
1. Science - mathematical models
3. Use cases - medical simulators for education
2. Technology - how to simulate models
Is it a model? equations
Elena Zappon Efficient Reduced Order Modeling for Coupled Problems in Cardiac Electrophysiology, CompBioMed2023, 13th September 2023
Is it a model? component diagram
Magdalena Otta et al. A 0D model of lower limb haemodynamics: sensitivity analysis, CompBioMed2023, 13th September 2023
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.
explanatory models
to explain:
- equations
- way of computation
- physical reality
who is the audience?
- mathematician/computer scientist
- biomedical engineer
- other domain expert
- clinicians, physicians
- healthcare staff
- students of medicine
- patient
model of glucose insulin regulation - explain equations
model of glucose insulin regulation - block schema - explain computation
model of glucose insulin regulation - acausal and component modeling (compartment modeling) - explain physical reality
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
Guyton's original scheme
implementation in component and acausal modeling language
Frank-Starling law is much more visible in component model - "force of the heart muscle depends on pressure of incoming blood".
Physiolibrary & Chemical
https://physiolibrary.org
free open-source Modelica library designed for modeling physical chemistry & human physiology.
Physiomodel
Complex model of physiology in Modelica based on HumMod and Physiolibrary
https://physiomodel.org
>60 000 equations
who is the audience?
- mathematician/computer scientist
- biomedical engineer
- other domain expert
- clinicians, physicians
- healthcare staff
- students of medicine
- patient
from model to web simulator and where bodylight.js fills the missing pieces
bodylight.js
- scripts translate model - FMU (standard C-source,C-binary following API) to WebAssembly
- javascript library
- custom element for model
- custom element for animation
- custom element for other useful web libraries and simplified elements
- Optional tools (composer, editor) to simplify creating and deploying web simulators
1. export model to FMU with C source code
2.compile to WebAssembly
Configuration and scripts to facilitate compilation with emscripten
emcc … -O3 –closure 0 …
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
webcomponents - custom elements
- custom tag for model: fmi
- custom tag for chart
webcomponents - custom elements animation
simulator with web components - src
<script src=" bodylight.bundle.js" ></script>
...
<body aurelia-app="webcomponents">
...
we can put HTML/CSS styling
simulation education
4369 students, most of them general medicine and dentistry, >3500 study in Czech language (including >500 non-Czech nationality), >800 study in English (India,Israel,Iran,United Kingdom, ...)
lecture supported by simulators
physiology and pathophysiology
web simulators in a browser / desktop/tablet
co-simulation of multiple models
blood-gas exchange
respiration
hemodynamics of cardiovascular system
simulator of glucose/insulin
native mobile apps
control HW mannequin
bring virtual reality to life
WebGL+WebXR Unity+WebView
medical simulators - products
https://egolem.online/irm
simulator of iron metabolism: https://egolem.online/irm
digital appendix of scientific paper
Mazumder, Nikhilesh R et al. (2023). “Portal Venous Remodeling Determines the Pattern of Cirrhosis Decompensation: A Systems Analysis.” In: Clinical and Translational Gastroenterology. DOI: 10.14309/ctg.0000000000000590.
summary
- Science - Physiomodel, Physiolibrary - open source MIT license
- Modelica language - open source, interoperable via FMI standard
- Modelica tools - open source OpenModelica, commercial Dymola,...
- Technology - Bodylight.js - library to enable in-browser simulation
bodylight.physiome.cz (with source codes at GITHUB)
- Use cases - eGolem - digital textbook with web simulators
- HTML or Markdown with bodylight.js webcomponents
- seek economical/business model to maintain science, technology and use cases
- Value - dissemination of scientific results to educate students, domain experts, patients
explanatory simulators
GI equation
model of circulation and its regulation
