Starts with a brief review of the history and the application areas considered in the literature. The author then proceeds with introductory modeling examples, behavioral and structural properties, three methods of analysis, subclasses of Petri nets and their analysis. In particular, one section is devoted to marked graphs, the concurrent system model most amenable to analysis. Introductory discussions on stochastic nets with their application to performance modeling, and on high-level nets with their application to logic programming, are provided. Also included are recent results on reachability criteria. Suggestions are provided for further reading on many subject areas of Petri nets. >

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Petri nets: Properties, analysis and applications

Data Mining Practical Machine Learning Tools and Techniques

https://cmi.ac.in/~madhavan/courses/verification-2011/alur-dill-tcs-94.pdf

A theory of timed automata

物件導向軟體之架構(Object-Oriented Software Construction)探討

The Temporal Logic of Reactive and Concurrent Systems: Specification

Subset languages of petri nets part ii: closure properties

Gene Assembly in Ciliates: Molecular operations

Boolean nets are a family of Petri net models with very simple markings which are sets of places. We investigate several classes of boolean nets distinguished by different kinds of individual connections between places and transitions, as well as different ways in which these connections are combined in order to specify the effect of executing steps of transitions. The latter aspect can be captured by connection monoids. A key advantage of using connection monoids is that by describing the step semantics of a class of Petri nets in terms of a connection monoid, one can apply results developed within a general theory of Petri net synthesis. In this paper, we provide an extensive classification of boolean nets which can be described by connection monoids. This classification is based on the realisation that the different ways of interpreting combinations of connections can be made explicit using a higher level monoid. Moreover, we demonstrate that connection monoids can capture other behavioural properties of boolean nets, such as structural conflicts between transitions.

Step semantics of boolean nets

In recent years, several strategies for DNA based molecular computing have been investigated. An important area of research is the detection and analysis of output molecules. We demonstrate how DNA computing can be extended with in vivo translation of the output. In the resulting proteins, the information per kilogram is about 15-fold higher than in the original DNA output. The proteins are therefore of correspondingly smaller mass, which facilitates their subsequent detection using highly sensitive mass spectrometry methods. We have tested this approach on an instance of the Minimal Dominating Set problem. The DNA used in the computation was constructed as an open reading frame in a plasmid, under the control of a strong inducible promoter. Sequential application of restriction endonucleases yielded a library of potential solutions to the problem instance. The mixture of plasmids was then used for expression of a protein representation. Using MALDI-TOF mass spectrometry, a protein corresponding to the correct solution could be detected. The results indicate the feasibility of the extension of DNA computing to include protein technology. Our strategy opens up new possibilities for both scaling of DNA computations and implementations that employ output of functional molecules or phenotypes.

Protein output for DNA computing

Continuing the work begun in [14], we consider contextual grammars (as introduced in [6] with linguistic motivation) with parallel derivations, in which the whole current string participates to a derivation step in the sense that it is splitted into substrings to which contexts are adjoined in a parallel manner. The generative power of such grammars is investigated, when the parallelism is total or partial, and when the selection of contexts is limited to strings in sets of a given type (finite, regular etc.) Then we consider the languages consisting of strings which cannot be further derived (we call them blocking languages). Some open problems are also formulated.

Grzegorz Rozenberg

Papers

Subset languages of petri nets part ii: closure properties

Gene Assembly in Ciliates: Molecular operations

Step semantics of boolean nets

Protein output for DNA computing

Contextual grammars: parallelism and blocking of derivation