Splicing Systems from Past to Future: Old and New Challenges

A splicing system is a formal model of a recombinant behaviour of sets of double stranded DNA molecules when acted on by restriction enzymes and ligase. In this survey we will concentrate on a specific behaviour of a type of splicing systems, introduced by P\u{a}un and subsequently developed by many researchers in both linear and circular case of splicing definition. In particular, we will present recent results on this topic and how they stimulate new challenging investigations.Comment: Appeared in: Discrete Mathematics and Computer Science. Papers in Memoriam Alexandru Mateescu (1952-2005). The Publishing House of the Romanian Academy, 2014. arXiv admin note: text overlap with arXiv:1112.4897 by other author

Splicing representations of strictly locally testable languages

AbstractThe relationship between the family SH of simple splicing languages, which was recently introduced by Mateescu et al. and the family SLT of strictly locally testable languages is clarified by establishing an ascending hierarchy of families {SiH: i⩾ − 1} of splicing languages for which SH = S1H and the union of the families is the family SLT. A procedure is given which, for an arbitrary regular language L, determines whether L is in SLT and, when L is in SLT, specifies constructively the smallest family in the hierarchy to which L belongs. Examples are given of sets of restriction enzymes for which the action on DNA molecules is naturally represented by splicing systems of the types discussed

Accepting splicing systems with permitting and forbidding words

Abstract: In this paper we propose a generalization of the accepting splicingsystems introduced in Mitrana et al. (Theor Comput Sci 411:2414?2422,2010). More precisely, the input word is accepted as soon as a permittingword is obtained provided that no forbidding word has been obtained sofar, otherwise it is rejected. Note that in the new variant of acceptingsplicing system the input word is rejected if either no permitting word isever generated (like in Mitrana et al. in Theor Comput Sci 411:2414?2422,2010) or a forbidding word has been generated and no permitting wordhad been generated before. We investigate the computational power ofthe new variants of accepting splicing systems and the interrelationshipsamong them. We show that the new condition strictly increases thecomputational power of accepting splicing systems. Although there areregular languages that cannot be accepted by any of the splicing systemsconsidered here, the new variants can accept non-regular and even non-context-free languages, a situation that is not very common in the case of(extended) finite splicing systems without additional restrictions. We alsoshow that the smallest class of languages out of the four classes definedby accepting splicing systems is strictly included in the class of context-free languages. Solutions to a few decidability problems are immediatelyderived from the proof of this result

Developments from enquiries into the learnability of the pattern languages from positive data

AbstractThe pattern languages are languages that are generated from patterns, and were first proposed by Angluin as a non-trivial class that is inferable from positive data [D. Angluin, Finding patterns common to a set of strings, Journal of Computer and System Sciences 21 (1980) 46–62; D. Angluin, Inductive inference of formal languages from positive data, Information and Control 45 (1980) 117–135]. In this paper we chronologize some results that developed from the investigations on the inferability of the pattern languages from positive data

The Converge programming language.

This paper details the Converge programming language, a new dynamically typed imperative programming language capable of compile-time meta-programming, and with an extendable syntax. Although Converge has been designed with the aim of implementing different model transformation approaches as embedded DSL’s in mind, it is also a General Purpose Language (GPL), albeit one with unusually powerful features. The motivation for a new approach to implementing model transformation approaches is simple: existing languages, and their associated tool-chains, lead to long and costly implementation cycles for model transformation approaches. The justification for creating a new language, rather than altering an existing one, is far less obvious— it is reasonable to suggest that, given the vast number of programming languages already in existence, one of them should present itself as a likely candidate for modification. There are two reasons why a new language is necessary to meet the aims of this paper. Firstly, in order to meet its aims, Converge contains a blend of features unique amongst programming languages; some fundamental design choices have been necessary to make these features coalesce, and imposing such choices retrospectively on an existing language would almost certainly lead to untidy results and backwards compatibility issues. Secondly, my personal experience strongly suggests that the complexity of modern languages implementations (when such implementations are available) can make adding new features a significant challenge. In short, I assert that it is easier in the context of model transformations to start with a fresh canvass than to alter an existing language. This paper comes in three main parts. The first part documents the basics of the Converge language itself;. The second part details Converge’s compile-time metaprogramming and syntax extension facilities, including a section detailing suggestions for how some of Converge’s novel features could be added to similar languages. The third part of this paper explains Converge’s syntax extension facility, and documents a user extension which allows simple UML-esque modelling languages to be embedded within Converge. As well as being a practical demonstration of Converge’s features, this facility is used extensively throughout the remainder of the paper

Finite Models of Splicing and Their Complexity

Durante las dos últimas décadas ha surgido una colaboración estrecha entre informáticos, bioquímicos y biólogos moleculares, que ha dado lugar a la investigación en un área conocida como la computación biomolecular. El trabajo en esta tesis pertenece a este área, y estudia un modelo de cómputo llamado sistema de empalme (splicing system). El empalme es el modelo formal del corte y de la recombinación de las moléculas de ADN bajo la influencia de las enzimas de la restricción.Esta tesis presenta el trabajo original en el campo de los sistemas de empalme, que, como ya indica el título, se puede dividir en dos partes. La primera parte introduce y estudia nuevos modelos finitos de empalme. La segunda investiga aspectos de complejidad (tanto computacional como descripcional) de los sistema de empalme. La principal contribución de la primera parte es que pone en duda la asunción general que una definición finita, más realista de sistemas de empalme es necesariamente débil desde un punto de vista computacional. Estudiamos varios modelos alternativos y demostramos que en muchos casos tienen más poder computacional. La segunda parte de la tesis explora otro territorio. El modelo de empalme se ha estudiado mucho respecto a su poder computacional, pero las consideraciones de complejidad no se han tratado apenas. Introducimos una noción de la complejidad temporal y espacial para los sistemas de empalme. Estas definiciones son utilizadas para definir y para caracterizar las clases de complejidad para los sistemas de empalme. Entre otros resultados, presentamos unas caracterizaciones exactas de las clases de empalme en términos de clases de máquina de Turing conocidas. Después, usando una nueva variante de sistemas de empalme, que acepta lenguajes en lugar de generarlos, demostramos que los sistemas de empalme se pueden usar para resolver problemas. Por último, definimos medidas de complejidad descriptional para los sistemas de empalme. Demostramos que en este respecto los sistemas de empalme finitos tienen buenas propiedades comparadosOver the last two decades, a tight collaboration has emerged between computer scientists, biochemists and molecular biologists, which has spurred research into an area known as DNAComputing (also biomolecular computing). The work in this thesis belongs to this field, and studies a computational model called splicing system. Splicing is the formal model of the cutting and recombination of DNA molecules under the influence of restriction enzymes.This thesis presents original work in the field of splicing systems, which, as the title already indicates, can be roughly divided into two parts: 'Finite models of splicing' on the onehand and 'their complexity' on the other. The main contribution of the first part is that it challenges the general assumption that a finite, more realistic definition of splicing is necessarily weal from a computational point of view. We propose and study various alternative models and show that in most cases they have more computational power, often reaching computational completeness. The second part explores other territory. Splicing research has been mainly focused on computational power, but complexity considerations have hardly been addressed. Here we introduce notions of time and space complexity for splicing systems. These definitions are used to characterize splicing complexity classes in terms of well known Turing machine classes. Then, using a new accepting variant of splicing systems, we show that they can also be used as problem solvers. Finally, we study descriptional complexity. We define measures of descriptional complexity for splicing systems and show that for representing regular languages they have good properties with respect to finite automata, especially in the accepting variant

Self-Assembly: Lightweight Language Extension and Datatype Generic Programming, All-in-One!

In this paper we show a general mechanism, called self-assembly, for lightweight language extensions (LLEs). LLEs allow users to define generic operations or properties that operate over a large class of types. With LLEs it is possible, for example, for users to define their own Java-style automatic serialization mechanism; or implement simple forms of custom pluggable type system extensions like an immutability checker. However unlike language built-in mechanisms (such as Java serialization), LLEs are user-definable, multi-purpose (they can be used to define various forms of generic functionality), and highly customizable and extensible. The key idea, inspired by existing datatype-generic programming approaches, is to provide programmers with a generic mechanism for providing automatic implementations of type classes. We implemented our technique as a library, \sselfassembly, for Scala, and evaluated its practicality by migrating a full-featured industrial-strength serialization framework, Scala/Pickling, keeping the same published performance numbers while reducing the code size for type class instance generation by 56%