CyberUnits Bricks: An Implementation Study of a Class Library for Simulating Nonlinear Biological Feedback Loops

Abstract

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.