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A central aim of systems biology is to elucidate the complex dynamic structure of biological systems within which functioning and control occur. The success of this endeavour requires a dialogue between the two quite distinct disciplines of life science and systems theory, and so drives the need for graphical notations which facilitate this dialogue.… (More)
BACKGROUND A gene-regulatory network (GRN) refers to DNA segments that interact through their RNA and protein products and thereby govern the rates at which genes are transcribed. Creating accurate dynamic models of GRNs is gaining importance in biomedical research and development. To improve our understanding of continuous deterministic modeling methods… (More)
This paper reviews a variety of different graphical notations currently in active use for modelling dynamic processes in bioinformatics and biotechnology, and crystallises from these notations a set of properties essential to any proposal for a modelling language seeking to provide an adequate systemic description of biological processes.
Living organisms regulate the expression of genes using complex interactions of transcription factors, messenger RNA and active protein products. Due to their complexity, gene-regulatory networks are not fully understood, however, various modeling approaches can he used to gain insight into their function and operation. This paper describes an ongoing study… (More)
OBJECTIVE Living organisms regulate the expression of genes using complex interactions of transcription factors, messenger RNA and active protein products. Due to their complexity, gene-regulatory networks are not fully understood.However, by building computational models it is possible to gain insight into their function and operation. METHODS… (More)
BACKGROUND Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs), which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate… (More)
The authors introduce a graphical notation for representing general dynamical systems and demonstrate its use in three commonly occurring systems in the biosciences. They also indicate how the notation is used to facilitate the acquisition and transfer by students of skills in constructing equations from a verbal description of a system. 1 Modelling in the… (More)