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. >

/pdf/petri-nets-properties-analysis-and-applications-43jwyjdxr0.pdf

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

Natural Computing (cf., e.g., [12,13]) is concerned with human-designed computing inspired by nature as well as with computation taking place in nature, i.e., it investigates models, computational techniques, and computational technologies inspired by nature as well as it investigates, in terms of information processing, phenomena/processes taking place in nature.

/pdf/processes-inspired-by-the-functioning-of-living-cells-1t5n0sggxg.pdf

Processes Inspired by the Functioning of Living Cells: Natural Computing Approach

In the context of graph transformation we look at the operation of switching, which can be viewed as a method for realizing global transformations of (group-labelled) graphs through local transformations of the vertices. 

In case vertices are given an identity, various relatively efficient algorithms exist for deciding whether a graph can be switched so that it contains some other graph, the query graph, as an induced subgraph. However, when considering graphs up to isomorphism, we immediately run into the graph isomorphism problem for which no efficient solution is known. Surprisingly enough however, in some cases the decision process can be simplified by transforming the query graph into a "smaller" graph without changing the answer. The main lesson learned is that the size of the query graph is not the dominating factor, but its cycle rank. 

Although a number of our results hold specifically for undirected, unlabelled graphs, we propose a more general framework and give many positive and negative results for more general cases, where the graphs are labelled with elements of a (finitely generated abelian) group.

The Embedding Problem for Switching Classes of Graphs

Proceedings of the REX Workshop on Sematics: Foundations and Applications

On erasing in EOL forms

We can only speculate about the significance of the extraordinary modifications in the structure of micronuclear genes in stichotrichous ciliates that have occurred during evolution However, it is clear the presence of IESs and MDSs, and particularly the scrambling of MDSs in micronuclear genes, requires spectacular manipulations of DNA sequences whenever cells mate and then develop new macronuclei These DNA manipulations are massive, consisting of the excision of more than 100,000 IESs and reordering of many thousands of MDSs Major progress in understanding this intricate DNA processing has been made by studying the nucleotide sequences in micronuclear genes The excision of IESs and the unscrambling and joining of MDSs are referred to as gene assembly In this chapter we postulate three molecular operations based on the pairs of repeats in the ends of MDSs to accomplish the assembling of genes after cell mating In the description of these three operations the pairs of repeats are called pointers because they point the way for MDS joining

Grzegorz Rozenberg

Papers

Processes Inspired by the Functioning of Living Cells: Natural Computing Approach

The Embedding Problem for Switching Classes of Graphs

Proceedings of the REX Workshop on Sematics: Foundations and Applications

On erasing in EOL forms

Molecular Operations for Gene Assembly