7 research outputs found
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
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
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
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