To the best of our knowledge, it was 1993 that Reddy et al. introduced
Petri nets for the qualitative modelling of biochemical networks. Since that time, just a few
papers appeared every year with similar approaches in order to model and/or analyse biochemical
pathways, dealing with metabolism, gene regulation, or signal transduction, respectively. Only
recently, there seems to be an increasing interest in that research topic, at least as far we
can tell from the total number of published papers.
A quick search through the papers found reveals a quite large variety of Petri net extension,
for qualitative modelling:
as well as for quantitative modelling and simulation:
- time dependency: discrete, continuous, hybrid,
- self-modification, in different variations, and
- fuzzy Petri nets.
All these kinds of Petri nets are used on all levels of biological abstraction, for example
for the modelling of the relationships between biochemical substances, cell components, cells,
organs, individuals, species, organism classes, and populations.
In chemistry, applications seem to be restricted to the control and regulation of process
technologies and installations. Just Kuroda et al. used Petri nets for modelling more complex
Also, many applications are conceivable in the field of stuff and energy flows, ecological
systems, population dynamics and evolution. Suzuki introduces spatial hybrid Petri nets for that
In medicine, the majority of the published applications come from the field of management
processes, for instance the passing on of patients, diagnosis preparation, display preparation,
and therapy. But, there are also a few applications, modelling the development of some diseases.
A central topic of almost all investigated publications is the demonstration of a methodology
how to use Petri nets for the chosen application area, often associated with the presentation of
related software tools. Accordingly, almost all published applications seem to rely on
demonstration examples only. Therefore, a major break through of a Petri net based technology for
modelling and analysis in applications related to biology, chemistry, or medicine can´t be
M. Heiner, I. Koch, J. Will: Model Validation of Biological Pathways Using
Petri Nets - Demonstrated for Apoptosis"; in Priami, Corrado (ed.): Computational Methods in
Systems Biology (CMSB 2003), Lect. Notes Comput. Sci. 2602 (2003) 173 und BioSystems 75 (2004)
This paper demonstrates the first steps of a new integrating methodology
to develop and analyse models of biological pathways in a systematic manner using well
established Petri net technologies. The whole approach comprises step-wise modelling, animation,
model validation as well as qualitative and quantitative analysis for behaviour prediction. In
this paper, the first phase is addressed - how to develop and validate a qualitative model, which
might be extended afterwards to a quantitative model.
The example used in this paper is devoted
to apoptosis, the genetically programmed cell death. Apoptosis is an essential part of normal
physiology for most metazoan species. Disturbances in the apoptotic process could lead to several
diseases. The signal transduction pathway of apoptosis includes highly complex mechanisms to
control and execute programmed cell death. This paper explains how to model and validate this
pathway using qualitative Petri nets. The results provide a mathematically unique and valid
model enabling the confirmation of known properties as well as new insights in this pathway.
ind Energy (e.g. Wind-Hamster
- A single computer programming language should be possible, which combines all known universal
- A computer programming language should be possible, which allows to describe mathematical
algorithms as by formulas and short texts in a book.
- Higher speeds of computing would be possible with novel analog computers that work with for example
electrical, magnetical or optical fields.
- Reflect on winning a thunderstorm's lightning energy by creating the lightning.
- Reflect on creating a locally restricted wind vortex like tornado vortices to winning wind energy.
(I don't mean the Yen tornado tower.)
- Reflect on hanging up a very long funnel tube at a high mountain to increase an upwind power
- Is there a spray for self-defense possible which has an awfully nasty smell (like butyric acid or
- Would an everywhere portable little camera protect someone against criminal attack?
- Protection against remote ignition of a bomb could be possible by
using a Faraday cage.
- Try to make photos (at a stand) from an aircraft's model.
- Would it be possible to change the form of a thing (car, aircraft, air foil or so) continuously?
- Could catching fishes be possible by attracting them with sound?
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