Type Directed Semantics for the Calculus of Looping Sequences

The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules. Here we enrich this calculus with a type discipline which preserves some biological properties deriving from the requirement of certain elements, and the repellency of others. In particular, the type system guarantees the soundness of the application of reduction rules with respect to the elements which are required (all requirements must be satisfied) and to the elements which are excluded (two elements which repel each other cannot occur in the same compartment). As an example, we model the possible interactions (and compatibility) of different blood types with different antigens. The type system does not allow transfusion with incompatible blood types

Types for BioAmbients

The BioAmbients calculus is a process algebra suitable for representing compartmentalization, molecular localization and movements between compartments. In this paper we enrich this calculus with a static type system classifying each ambient with group types specifying the kind of compartments in which the ambient can stay. The type system ensures that, in a well-typed process, ambients cannot be nested in a way that violates the type hierarchy. Exploiting the information given by the group types, we also extend the operational semantics of BioAmbients with rules signalling errors that may derive from undesired ambients' moves (i.e. merging incompatible tissues). Thus, the signal of errors can help the modeller to detect and locate unwanted situations that may arise in a biological system, and give practical hints on how to avoid the undesired behaviour

Topological Calculus of Looping Sequences

Il Calculus of Looping Sequences (CLS) permette la descrizione dei sistemi biologici e della loro evoluzione. Nell'ambito del lavoro di tesi e' stata sviluppata una estensione del CLS, chiamata Topological CLS (TCLS), dove ad ogni oggetto del sistema biologico sono associate una precisa posizione e dimensione nello spazio. Gli oggetti possono muoversi autonomamente e l'applicabilita' delle regole di riscrittura, che modellano le reazioni tra gli elementi, puo' essere determinata dalle posizioni degli oggetti coinvolti. Infine, alle regole di riscrittura e' associato un parametro che ne specifica la velocita' di reazione. Il Topological CLS e' stato quindi utilizzato per modellare due esempi di sistemi biologici: il processo di mitosi e il quorum-sensing

12th International Workshop on Termination (WST 2012) : WST 2012, February 19–23, 2012, Obergurgl, Austria / ed. by Georg Moser

This volume contains the proceedings of the 12th International Workshop on Termination (WST 2012), to be held February 19–23, 2012 in Obergurgl, Austria. The goal of the Workshop on Termination is to be a venue for presentation and discussion of all topics in and around termination. In this way, the workshop tries to bridge the gaps between different communities interested and active in research in and around termination. The 12th International Workshop on Termination in Obergurgl continues the successful workshops held in St. Andrews (1993), La Bresse (1995), Ede (1997), Dagstuhl (1999), Utrecht (2001), Valencia (2003), Aachen (2004), Seattle (2006), Paris (2007), Leipzig (2009), and Edinburgh (2010). The 12th International Workshop on Termination did welcome contributions on all aspects of termination and complexity analysis. Contributions from the imperative, constraint, functional, and logic programming communities, and papers investigating applications of complexity or termination (for example in program transformation or theorem proving) were particularly welcome. We did receive 18 submissions which all were accepted. Each paper was assigned two reviewers. In addition to these 18 contributed talks, WST 2012, hosts three invited talks by Alexander Krauss, Martin Hofmann, and Fausto Spoto

Probabilistic call by push value

We introduce a probabilistic extension of Levy's Call-By-Push-Value. This extension consists simply in adding a " flipping coin " boolean closed atomic expression. This language can be understood as a major generalization of Scott's PCF encompassing both call-by-name and call-by-value and featuring recursive (possibly lazy) data types. We interpret the language in the previously introduced denotational model of probabilistic coherence spaces, a categorical model of full classical Linear Logic, interpreting data types as coalgebras for the resource comonad. We prove adequacy and full abstraction, generalizing earlier results to a much more realistic and powerful programming language

Strategic programming on graph rewriting systems

We describe a strategy language to control the application of graph rewriting rules, and show how this language can be used to write high-level declarative programs in several application areas. This language is part of a graph-based programming tool built within the port-graph transformation and visualisation environment PORGY.Comment: In Proceedings IWS 2010, arXiv:1012.533

A Calculus for Molecular Interaction Maps

Molecular Interaction Maps are a graphical formalism used by biologists to describe complex interactions between molecules. We provide a formal description of MIMs using process algebras and determine its computational power

First-order logic with self-reference

We consider an extension of first-order logic with a recursion operator that corresponds to allowing formulas to refer to themselves. We investigate the obtained language under two different systems of semantics, thereby obtaining two closely related but different logics. We provide a natural deduction system that is complete for validities for both of these logics, and we also investigate a range of related basic decision problems. For example, the validity problems of the two-variable fragments of the logics are shown coNexpTime-complete, which is in stark contrast with the high undecidability of two-variable logic extended with least fixed points. We also argue for the naturalness and benefits of the investigated approach to recursion and self-reference by, for example, relating the new logics to Lindstrom's Second Theorem

Innocent strategies as presheaves and interactive equivalences for CCS

Seeking a general framework for reasoning about and comparing programming languages, we derive a new view of Milner's CCS. We construct a category E of plays, and a subcategory V of views. We argue that presheaves on V adequately represent innocent strategies, in the sense of game semantics. We then equip innocent strategies with a simple notion of interaction. This results in an interpretation of CCS. Based on this, we propose a notion of interactive equivalence for innocent strategies, which is close in spirit to Beffara's interpretation of testing equivalences in concurrency theory. In this framework we prove that the analogues of fair and must testing equivalences coincide, while they differ in the standard setting.Comment: In Proceedings ICE 2011, arXiv:1108.014