CyberUnits bricks: an implementation study of a class library for simulating nonlinear biological feedback loops
Feedback loops and other types of information processing structures play a pivotal role in maintaining the internal milieu of living organisms. Although methods of biomedical cybernetics and systems biology help to translate between the structure and function of processing structures, computer simul...
| Main Authors: | , , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2024
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| Online Access: | https://hdl.handle.net/10356/181767 |
| _version_ | 1826123516720709632 |
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| author | Dietrich, Johannes W. Siegmar, Nina Hojjati, Jonas R. Gardt, Oliver Boehm, Bernhard Otto |
| author2 | Lee Kong Chian School of Medicine (LKCMedicine) |
| author_facet | Lee Kong Chian School of Medicine (LKCMedicine) Dietrich, Johannes W. Siegmar, Nina Hojjati, Jonas R. Gardt, Oliver Boehm, Bernhard Otto |
| author_sort | Dietrich, Johannes W. |
| collection | NTU |
| description | Feedback loops and other types of information processing structures play a pivotal role in maintaining the internal milieu of living organisms. Although methods of biomedical cybernetics and systems biology help to translate between the structure and function of processing structures, computer simulations are necessary for studying nonlinear systems and the full range of dynamic responses of feedback control systems. Currently, available approaches for modelling and simulation comprise basically domain-specific environments, toolkits for computer algebra systems and custom software written in universal programming languages for a specific purpose, respectively. All of these approaches are faced with certain weaknesses. We therefore developed a cross-platform class library that provides versatile building bricks for writing computer simulations in a universal programming language (CyberUnits Bricks). It supports the definition of models, the simulative analysis of linear and nonlinear systems in the time and frequency domain and the plotting of block diagrams. We compared several programming languages that are commonly used in biomedical research (S in the R implementation and Python) or that are optimized for speed (Swift, C++ and Object Pascal). In benchmarking experiments with two prototypical feedback loops, we found the implementations in Object Pascal to deliver the fastest results. CyberUnits Bricks is available as open-source software that has been optimised for Embarcadero Delphi and the Lazarus IDE for Free Pascal. |
| first_indexed | 2025-03-09T13:31:36Z |
| format | Journal Article |
| id | ntu-10356/181767 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2025-03-09T13:31:36Z |
| publishDate | 2024 |
| record_format | dspace |
| spelling | ntu-10356/1817672024-12-22T15:39:49Z CyberUnits bricks: an implementation study of a class library for simulating nonlinear biological feedback loops Dietrich, Johannes W. Siegmar, Nina Hojjati, Jonas R. Gardt, Oliver Boehm, Bernhard Otto Lee Kong Chian School of Medicine (LKCMedicine) Computer and Information Science Medicine, Health and Life Sciences Computational biomedicine Systems biology Feedback loops and other types of information processing structures play a pivotal role in maintaining the internal milieu of living organisms. Although methods of biomedical cybernetics and systems biology help to translate between the structure and function of processing structures, computer simulations are necessary for studying nonlinear systems and the full range of dynamic responses of feedback control systems. Currently, available approaches for modelling and simulation comprise basically domain-specific environments, toolkits for computer algebra systems and custom software written in universal programming languages for a specific purpose, respectively. All of these approaches are faced with certain weaknesses. We therefore developed a cross-platform class library that provides versatile building bricks for writing computer simulations in a universal programming language (CyberUnits Bricks). It supports the definition of models, the simulative analysis of linear and nonlinear systems in the time and frequency domain and the plotting of block diagrams. We compared several programming languages that are commonly used in biomedical research (S in the R implementation and Python) or that are optimized for speed (Swift, C++ and Object Pascal). In benchmarking experiments with two prototypical feedback loops, we found the implementations in Object Pascal to deliver the fastest results. CyberUnits Bricks is available as open-source software that has been optimised for Embarcadero Delphi and the Lazarus IDE for Free Pascal. Published version 2024-12-17T02:31:22Z 2024-12-17T02:31:22Z 2024 Journal Article Dietrich, J. W., Siegmar, N., Hojjati, J. R., Gardt, O. & Boehm, B. O. (2024). CyberUnits bricks: an implementation study of a class library for simulating nonlinear biological feedback loops. Advances in Distributed Computing and Artificial Intelligence Journal, 13, e31762-. https://dx.doi.org/10.14201/adcaij.31762 2255-2863 https://hdl.handle.net/10356/181767 10.14201/adcaij.31762 2-s2.0-85204298850 13 e31762 en Advances in Distributed Computing and Artificial Intelligence Journal © 2024 PD Dr. med. Johannes W. Dietrich, Nina Siegmar, Jonas R. Hojjati, Oliver Gardt, Bernhard O. Boehm. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. application/pdf |
| spellingShingle | Computer and Information Science Medicine, Health and Life Sciences Computational biomedicine Systems biology Dietrich, Johannes W. Siegmar, Nina Hojjati, Jonas R. Gardt, Oliver Boehm, Bernhard Otto CyberUnits bricks: an implementation study of a class library for simulating nonlinear biological feedback loops |
| title | CyberUnits bricks: an implementation study of a class library for simulating nonlinear biological feedback loops |
| title_full | CyberUnits bricks: an implementation study of a class library for simulating nonlinear biological feedback loops |
| title_fullStr | CyberUnits bricks: an implementation study of a class library for simulating nonlinear biological feedback loops |
| title_full_unstemmed | CyberUnits bricks: an implementation study of a class library for simulating nonlinear biological feedback loops |
| title_short | CyberUnits bricks: an implementation study of a class library for simulating nonlinear biological feedback loops |
| title_sort | cyberunits bricks an implementation study of a class library for simulating nonlinear biological feedback loops |
| topic | Computer and Information Science Medicine, Health and Life Sciences Computational biomedicine Systems biology |
| url | https://hdl.handle.net/10356/181767 |
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