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

Towards robustness in parsing - fuzzifying context-free language recognition the computational complexity of PCGS with regular components prefix and periodic languages of rational w-languages Cantor sets and Dejean's conjecture recent developments in trace theory trace language definable with modular quantifiers finite state recognizability for two-dimensional languages - a brief survey on emptiness and counting for alternating finite automata descriptional and computational complexity measure for distributive generation of languages nondeterminism degrees of context-free languages the membership problem for unordered vector languages transforming a single-valued transducer into a mealy machine.

Developments in language theory ii: at the crossroads of mathematics, computer science and biology

We describe a formal language/notation for DNA molecules that may contain nicks and gaps. The elements of the language, DNA expressions, denote formal DNA molecules. Different DNA expressions may denote the same formal DNA molecule. We analyse the shortest DNA expressions denoting a given formal DNA molecule: what is their length, how are they constructed, how many of them are there, and how can they be characterized.

/pdf/combinatorial-aspects-of-minimal-dna-expressions-8r4gxm5kc8.pdf

Combinatorial aspects of minimal DNA expressions

Gene assembly in ciliates is a life process fascinating from both the biological and the computational points of view. Several formal models of this process have been formulated and investigated, among them a model based on (legal) strings and a model based on (overlap) graphs. The latter is more abstract because the translation of legal strings into overlap graphs is not injective. In this paper we consider and solve the overlap equivalence problem for realistic strings: when do two different realistic legal strings translate into the same overlap graph? Realistic legal strings are legal strings that “really” correspond to genes generated during the gene assembly process.

Formal Properties of Gene Assembly: Equivalence Problem for Overlap Graphs

The intramolecular model for gene assembly in ciliates considers three operations, ld, hi, and dlad that can assemble any gene pattern through folding and recombination: the molecule is folded so that two occurrences of a pointer (short nucleotide sequence) get aligned and then the sequence is rearranged through recombination of pointers. In general, the sequence rearranged by one operation can be arbitrarily long and consist of many coding and non-coding blocks. We consider in this paper some simpler variants of the three operations, where only one coding block is rearranged at a time. We characterize in this paper the gene patterns that can be assembled through these variants. Our characterization is in terms of signed permutations and dependency graphs. Interestingly, we show that simple assemblies possess rather involved properties: a gene pattern may have both successful and unsuccessful assemblies and also more than one successful assembling strategy.

Simple operations for gene assembly

On montre que si K est un langage algebrique dont toute paire iterante forte est degeneree, alors K est un langage rationnel Ce resultat generalise un resultat analogue prouve par Boasson pour les paires iterantes

/pdf/strong-iterative-pairs-and-the-regularity-of-context-free-4k79xpian9.pdf

Grzegorz Rozenberg

Papers

Developments in language theory ii: at the crossroads of mathematics, computer science and biology

Combinatorial aspects of minimal DNA expressions

Formal Properties of Gene Assembly: Equivalence Problem for Overlap Graphs

Simple operations for gene assembly

Strong iterative pairs and the regularity of context-free languages