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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Main Authors: Johannes W. Dietrich, Nina Siegmar, Jonas R. Hojjati, Oliver Gardt, Bernhard O. Boehm
Format: Article
Language:English
Published: Ediciones Universidad de Salamanca 2024-08-01
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.
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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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