Bigraphical models for protein and membrane interactions

We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules representing biologically admissible interactions. At the protein level, these bigraphic reactive systems correspond exactly to systems of kappa-calculus. Membrane-level interactions are represented by just two general rules, whose application can be triggered by protein-level interactions in a well-de\"ined and precise way. This framework can be used to compare and merge models at different abstraction levels; in particular, higher-level (e.g. mobility) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. As examples, we formalize in our framework the vesiculation and the phagocytosis processes

A framework for protein and membrane interactions

We introduce the BioBeta Framework, a meta-model for both protein-level and membrane-level interactions of living cells. This formalism aims to provide a formal setting where to encode, compare and merge models at different abstraction levels; in particular, higher-level (e.g. membrane) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. A BioBeta specification provides a protein signature together a set of protein reactions, in the spirit of the kappa-calculus. Moreover, the specification describes when a protein configuration triggers one of the only two membrane interaction allowed, that is "pinch" and "fuse". In this paper we define the syntax and semantics of BioBeta, analyse its properties, give it an interpretation as biobigraphical reactive systems, and discuss its expressivity by comparing with kappa-calculus and modelling significant examples. Notably, BioBeta has been designed after a bigraphical metamodel for the same purposes. Hence, each instance of the calculus corresponds to a bigraphical reactive system, and vice versa (almost). Therefore, we can inherith the rich theory of bigraphs, such as the automatic construction of labelled transition systems and behavioural congruences

An Algebra for Directed Bigraphs

We study the algebraic structure of directed bigraphs, a bigraphical model of computations with locations, connections and resources previously introduced as a unifying generalization of other variants of bigraphs. We give a sound and complete axiomatization of the (pre)category of directed bigraphs. Using this axiomatization, we give an adequate encoding of the Fusion calculus, showing the utility of the added directnes

Controlling resource access in Directed Bigraphs

We study directed bigraph with negative ports, a bigraphical framework for representing models for distributed, concurrent and ubiquitous computing. With respect to previous versions, we add the possibility that components may govern the access to resources, like (web) servers control requests from clients. This framework encompasses many common computational aspects, such as name or channel creation, references, client/server connections, localities, etc, still allowing to derive systematically labelled transition systems whose bisimilarities are congruences. As application examples, we analyse the encodings of client/server communications through firewalls, of (compositional) Petri nets and of chemical reactions

Deriving Barbed Bisimulations for Bigraphical Reactive Systems

We study the definition of a general abstract notion of barbed bisimilarity for reactive systems on bigraphs. More precisely, given a bigraphical reactive system, we define the corresponding barbs from the contextual labels given by the IPO construction, in a general and systematic way. These barbs correspond to observe which names on the interface are actually involved in reactions (and how). As examples, we apply this construction to the (bigraphical representation of the) pi-calculus and of Mobile Ambients, and compare the resulting barbed equivalences with those previously known for these calculi

Controlling resource access in Directed Bigraphs

We study directed bigraph with negative ports, a bigraphical framework for representing models for distributed, concurrent and ubiquitous computing. With respect to previous versions, we add the possibility that components may govern the access to resources, like (web) servers control requests from clients. This framework encompasses many common computational aspects, such as name or channel creation, references, client/server connections, localities, etc, still allowing to derive systematically labelled transition systems whose bisimilarities are congruences. As application examples, we analyse the encodings of client/server communications through firewalls, of (compositional) Petri nets and of chemical reactions

Graph Algebras for Bigraphs

Binding bigraphs are a graphical formalism intended to be a meta-model for mobile, concurrent and communicating systems. In this paper we present an algebra of typed graph terms which correspond precisely to binding bigraphs over a given signature. As particular cases, pure bigraphs and local bigraphs are described by two sublanguages which can be given a simple syntactic characterization. Moreover, we give a formal connection between these languages and Synchronized Hyperedge Replacement algebras and the hierarchical graphs used in Architectural Design Rewriting. This allows to transfer results and constructions among formalisms which have been developed independently, e.g., the systematic definition of congruent bisimulations for SHR graphs via the IPO construction

Primitives for Contract-based Synchronization

We investigate how contracts can be used to regulate the interaction between processes. To do that, we study a variant of the concurrent constraints calculus presented in [1], featuring primitives for multi-party synchronization via contracts. We proceed in two directions. First, we exploit our primitives to model some contract-based interactions. Then, we discuss how several models for concurrency can be expressed through our primitives. In particular, we encode the pi-calculus and graph rewriting.Comment: In Proceedings ICE 2010, arXiv:1010.530

A linear programming approach to general dataflow process network verification and dimensioning

In this paper, we present linear programming-based sufficient conditions, some of them polynomial-time, to establish the liveness and memory boundedness of general dataflow process networks. Furthermore, this approach can be used to obtain safe upper bounds on the size of the channel buffers of such a network.Comment: In Proceedings ICE 2010, arXiv:1010.530