Experience with Teaching Different Modeling Techniques on the example of Glucose Insulin Regulation Model

In order to teach different modeling techniques we demonstrate equation-based, block-schema based, compartment and component-based modeling using acausal and object-oriented modeling language - Modelica. Hands-on implementation using all these techniques and comparing them towards same system (in our case glucose-insulin regulation) we teach pros and cons of each technique. Equation-based or block-schema based may be rapidly implemented from literature. However, compartment based or component-based models brings better understanding of modeled reality. When students have such experience, they tend to assess published papers more critically and do more complex system analysis.

Development of In-Browser Simulators for Medical Education: Introduction of a Novel Software Toolchain

Background

Simulators used in teaching are interactive applications comprising a mathematical model of the system under study and a graphical user interface (GUI) that allows the user to control the model inputs and visualize the model results in an intuitive and educational way. Well-designed simulators promote active learning, enhance problem-solving skills, and encourage collaboration and small group discussion. However, creating simulators for teaching purposes is a challenging process that requires many contributors including educators, modelers, graphic designers, and programmers. The availability of a toolchain of user-friendly software tools for building simulators can facilitate this complex task.

Objective

This paper aimed to describe an open-source software toolchain termed Bodylight.js that facilitates the creation of browser-based client-side simulators for teaching purposes, which are platform independent, do not require any installation, and can work offline. The toolchain interconnects state-of-the-art modeling tools with current Web technologies and is designed to be resilient to future changes in the software ecosystem.

Methods

We used several open-source Web technologies, namely, WebAssembly and JavaScript, combined with the power of the Modelica modeling language and deployed them on the internet with interactive animations built using Adobe Animate.

Results

Models are implemented in the Modelica language using either OpenModelica or Dassault Systèmes Dymola and exported to a standardized Functional Mock-up Unit (FMU) to ensure future compatibility. The C code from the FMU is further compiled to WebAssembly using Emscripten. Industry-standard Adobe Animate is used to create interactive animations. A new tool called Bodylight.js Composer was developed for the toolchain that enables one to create the final simulator by composing the GUI using animations, plots, and control elements in a drag-and-drop style and binding them to the model variables. The resulting simulators are stand-alone HyperText Markup Language files including JavaScript and WebAssembly. Several simulators for physiology education were created using the Bodylight.js toolchain and have been received with general acclaim by teachers and students alike, thus validating our approach. The Nephron, Circulation, and Pressure-Volume Loop simulators are presented in this paper. Bodylight.js is licensed under General Public License 3.0 and is free for anyone to use.

Conclusions

Bodylight.js enables us to effectively develop teaching simulators. Armed with this technology, we intend to focus on the development of new simulators and interactive textbooks for medical education. Bodylight.js usage is not limited to developing simulators for medical education and can facilitate the development of simulators for teaching complex topics in a variety of different fields.

Physiomodel - an integrative physiology in Modelica

Physiomodel (http://www.physiomodel.org) is our reimplementation and extension of an integrative physiological model called HumMod 1.6 (http://www.hummod.org) using our Physiolibrary (http://www.physiolibrary.org). The computer language Modelica is well-suited to exactly formalize integrative physiology. Modelica is an equation-based, and object-oriented language for hybrid ordinary differential equations (http:// www.modelica.org). Almost every physiological term can be defined as a class in this language and can be instantiated as many times as it occurs in the body. Each class has a graphical icon for use in diagrams. These diagrams are self-describing; the Modelica code generated from them is the full representation of the underlying mathematical model. Special Modelica constructs of physical connectors from Physiolibrary allow us to create diagrams that are analogies of electrical circuits with Kirchhoff's laws. As electric currents and electric potentials are connected in electrical domain, so are molar flows and concentrations in the chemical domain; volumetric flows and pressures in the hydraulic domain; flows of heat energy and temperatures in the thermal domain; and changes and amounts of members in the population domain.

The Atlas of Physiology and Pathophysiology: Web-based multimedia enabled interactive simulations

The paper is a presentation of the current state of development for the Atlas of Physiology and Pathophysiology (Atlas). Our main aim is to provide a novel interactive multimedia application that can be used for biomedical education where (a) simulations are combined with tutorials and (b) the presentation layer is simplified while the underlying complexity of the model is retained. The development of the Atlas required the cooperation of many professionals including teachers, system analysts, artists, and programmers. During the design of the Atlas, tools were developed that allow for component-based creation of simulation models, creation of interactive multimedia and their final coordination into a compact unit based on the given design. The Atlas is a freely available online application, which can help to explain the function of individual physiological systems and the causes and symptoms of their disorders.

Prevalence of tidal expiratory flow limitation in preschool children with and without respiratory symptoms: application of the negative expiratory pressure (NEP) method

Negative expiratory pressure (NEP) applied at the mouth during tidal expiration provides a non-invasive method for detecting expiratory flow limitation. Forty-two children were studied, i.e. 25 children with different respiratory symptoms (R) and 17 without any respiratory symptoms (NR). Children were examined without any sedation. A preset NEP of -5 cm H(2)O was applied; its duration did not exceed duration of tidal expiration. A significance of FL was judged by determining of a flow-limited range (in % of tidal volume). FL was found in 48 % children of R group. No patient of the NR group elicited FL (P<0.001 R vs. NR). The frequency of upper airway collapses was higher in R group (12 children) than in NR group (5 children). In conclusion, a high frequency of tidal FL in the R group was found, while it was not present in NR group. A relatively high frequency of expiratory upper airway collapses was found in both groups, but it did not differ significantly. NEP method represents a reasonable approach for tidal flow limitation testing in non-sedated preschool children.

Evaluation of mitochondrial membrane potential using a computerized device with a tetraphenylphosphonium-selective electrode

Mitochondrial membrane potential (Deltapsi(m)) plays important roles in the normal function of cells and in pathobiochemical situations. The application of ion-selective electrodes for the measurement of Deltapsi(m) is important for studying normal biological reactions and pathways and mitochondrial diseases. We constructed and optimized a computerized device for real-time monitoring of the Deltapsi(m), which included modification of tetraphenylphosphonium (TPP(+))-selective membrane that improved reproducibility of the TPP(+)-selective electrode. Application of MATLAB software increased the sensitivity of the system. We tested our improved device for membrane potential measurements of isolated mitochondria (in absolute scale of millivolts). In addition, we assessed relative changes of Deltapsi(m) (as changes in TPP(+) concentration) of digitonin-permeabilized cells (hepatocytes, control transmitochondrial cybrids, HeLa G and BSC-40) after addition of substrates, inhibitors, and uncoupler of respiratory chain. Our system can be successfully used for studies of many aspects of the regulation of mitochondrial bioenergetics and as a diagnostic tool for mitochondrial oxidative phosphorylation disorders.

Spike encoding mechanisms in the sound localization pathway

Two distinct neural circuits calculate the direction of incoming sound in mammals. Lower frequency sounds are processed in the medial superior olive (MSO) and higher frequencies are processed in the lateral superior olive (LSO); together they constitute the superior olivary complex. We show that the spike generation mechanisms of coincidence detection (CD) are employed in both these branches of sound localization pathway. Our description uses the concepts of probabilistic spike generation and spike timing jitter. We explain the notch in sound localization sensitivity described in human psychophysics. We estimate the processing time in the superior olivary complex and discuss possible spike processing mechanisms. Among them, we distinguish between the excitatory coincidence detection (ECD) and the inhibitory coincidence detection (ICD). We compare the latter to the mechanism of firing rate subtraction traditionally attributed to the lateral superior olive.