Ecological Modelling with the Calculus of Wrapped Compartments

The Calculus of Wrapped Compartments is a framework based on stochastic multiset rewriting in a compartmentalised setting originally developed for the modelling and analysis of biological interactions. In this paper, we propose to use this calculus for the description of ecological systems and we provide the modelling guidelines to encode within the calculus some of the main interactions leading ecosystems evolution. As a case study, we model the distribution of height of Croton wagneri, a shrub constituting the endemic predominant species of the dry ecosystem in southern Ecuador. In particular, we consider the plant at different altitude gradients (i.e. at different temperature conditions), to study how it adapts under the effects of global climate change.Comment: A preliminary version of this paper has been presented in CMC13 (LNCS 7762, pp 358-377, 2013

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

A Calculus of Looping Sequences with Local Rules

In this paper we present a variant of the Calculus of Looping Sequences (CLS for short) with global and local rewrite rules. While global rules, as in CLS, are applied anywhere in a given term, local rules can only be applied in the compartment on which they are defined. Local rules are dynamic: they can be added, moved and erased. We enrich the new calculus with a parallel semantics where a reduction step is lead by any number of global and local rules that could be performed in parallel. A type system is developed to enforce the property that a compartment must contain only local rules with specific features. As a running example we model some interactions happening in a cell starting from its nucleus and moving towards its mitochondria.Comment: In Proceedings DCM 2011, arXiv:1207.682

A Type System for a Stochastic CLS

The Stochastic Calculus of Looping Sequences is suitable to describe the evolution of microbiological systems, taking into account the speed of the described activities. We propose a type system for this calculus that models how the presence of positive and negative catalysers can modify these speeds. We claim that types are the right abstraction in order to represent the interaction between elements without specifying exactly the element positions. Our claim is supported through an example modelling the lactose operon

Approximating Imperfect Cryptography in a Formal Model

We present a formal view of cryptography that overcomes the usual assumptions of formal models for reasoning about security of computer systems, i.e. perfect cryptography and Dolev-Yao adversary model. In our framework, equivalence among formal cryptographic expressions is parameterized by a computational adversary that may exploit weaknesses of the cryptosystem to cryptanalyze ciphertext with a certain probability of success. To validate our approach, we show that in the restricted setting of ideal cryptosystems, for which the probability of guessing information that the Dolev-Yao adversary cannot derive is negligible, the computational adversary is limited to the allowed behaviors of the Dolev-Yao adversary

On Designing Multicore-aware Simulators for Biological Systems

The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to speed it up on multi-core platforms, which pose new challenges for parallelisation techniques. These opportunities are developed in two general families of solutions involving both the single simulation and a bulk of independent simulations (either replicas of derived from parameter sweep). Proposed solutions are tested on the parallelisation of the CWC simulator (Calculus of Wrapped Compartments) that is carried out according to proposed solutions by way of the FastFlow programming framework making possible fast development and efficient execution on multi-cores.Comment: 19 pages + cover pag

Parallel BioScape: A Stochastic and Parallel Language for Mobile and Spatial Interactions

BioScape is a concurrent language motivated by the biological landscapes found at the interface of biology and biomaterials. It has been motivated by the need to model antibacterial surfaces, biofilm formation, and the effect of DNAse in treating and preventing biofilm infections. As its predecessor, SPiM, BioScape has a sequential semantics based on Gillespie's algorithm, and its implementation does not scale beyond 1000 agents. However, in order to model larger and more realistic systems, a semantics that may take advantage of the new multi-core and GPU architectures is needed. This motivates the introduction of parallel semantics, which is the contribution of this paper: Parallel BioScape, an extension with fully parallel semantics.Comment: In Proceedings MeCBIC 2012, arXiv:1211.347

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

Stochastic Calculus of Wrapped Compartments

The Calculus of Wrapped Compartments (CWC) is a variant of the Calculus of Looping Sequences (CLS). While keeping the same expressiveness, CWC strongly simplifies the development of automatic tools for the analysis of biological systems. The main simplification consists in the removal of the sequencing operator, thus lightening the formal treatment of the patterns to be matched in a term (whose complexity in CLS is strongly affected by the variables matching in the sequences). We define a stochastic semantics for this new calculus. As an application we model the interaction between macrophages and apoptotic neutrophils and a mechanism of gene regulation in E.Coli

Stochastic Bigraphs

In this paper we present a stochastic semantics for Bigraphical Reactive Systems. A reduction and a labelled stochastic semantics for bigraphs are defined. As a sanity check, we prove that the two semantics are consistent with each other. We illustrate the expressiveness of the framework with an example of membrane budding in a biological system