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...
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| Format: | Article |
| Language: | English |
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Ediciones Universidad de Salamanca
2024-08-01
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| Series: | Advances in Distributed Computing and Artificial Intelligence Journal |
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| Online Access: | https://revistas.usal.es/cinco/index.php/2255-2863/article/view/31762 |
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| author | Johannes W. Dietrich Nina Siegmar Jonas R. Hojjati Oliver Gardt Bernhard O. Boehm |
| author_facet | Johannes W. Dietrich Nina Siegmar Jonas R. Hojjati Oliver Gardt Bernhard O. Boehm |
| author_sort | Johannes W. Dietrich |
| collection | DOAJ |
| 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. |
| format | Article |
| id | doaj-art-11b94b81d336435293e3e53b1f0f46dc |
| institution | Kabale University |
| issn | 2255-2863 |
| language | English |
| publishDate | 2024-08-01 |
| publisher | Ediciones Universidad de Salamanca |
| record_format | Article |
| series | Advances in Distributed Computing and Artificial Intelligence Journal |
| spelling | doaj-art-11b94b81d336435293e3e53b1f0f46dc2025-01-23T11:25:18ZengEdiciones Universidad de SalamancaAdvances in Distributed Computing and Artificial Intelligence Journal2255-28632024-08-0113e31762e3176210.14201/adcaij.3176237243CyberUnits Bricks: An Implementation Study of a Class Library for Simulating Nonlinear Biological Feedback LoopsJohannes W. Dietrich0Nina Siegmar1Jonas R. Hojjati2Oliver Gardt3Bernhard O. Boehm4Diabetes, Endocrinology and Metabolism Section, Department of Medicine I, St. Josef University Hospital, UK RUB, Gudrunstr. 56, D-44791 Bochum, Germany.Diabetes, Endocrinology and Metabolism Section, Department of Medicine I, St. Josef University Hospital, UK RUB, Gudrunstr. 56, D-44791 Bochum, Germany.Diabetes, Endocrinology and Metabolism Section, Department of Medicine I, St. Josef University Hospital, UK RUB, Gudrunstr. 56, D-44791 Bochum, Germany.Rheumatology Section, Department of Medicine I, Blankenstein Hospital, Im Vogelsang 5–11, D-45527 Hattingen, GermanyLee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Singapore 308232, SingaporeFeedback 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.https://revistas.usal.es/cinco/index.php/2255-2863/article/view/31762modelling and simulationsystems biologyobject pascalnonlinear systemscomputational biomedicine |
| spellingShingle | Johannes W. Dietrich Nina Siegmar Jonas R. Hojjati Oliver Gardt Bernhard O. Boehm CyberUnits Bricks: An Implementation Study of a Class Library for Simulating Nonlinear Biological Feedback Loops Advances in Distributed Computing and Artificial Intelligence Journal modelling and simulation systems biology object pascal nonlinear systems computational biomedicine |
| 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 | modelling and simulation systems biology object pascal nonlinear systems computational biomedicine |
| url | https://revistas.usal.es/cinco/index.php/2255-2863/article/view/31762 |
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