262 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
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
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
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
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
A formal semantics for Molecular Interaction Maps
In the present work, we describe a possible formal semantics for Molecular Interaction Maps (MIMs), which are standard diagrams, used by biologists to depict interactions at molecular level within a cell environment. First we describe MIM notation in details, then we describe the Calculi of Looping Sequences (CLS), a family of formal languages which models biological systems, whose semantics is a transition systems. Finally, we give a possible formal semantics in CLS for MIMs
Development of a stochastic simulator for biological systems based on Calculus of Looping Sequences.
Molecular Biology produces a huge amount of data concerning the behavior of the
single constituents of living organisms. Nevertheless, this reductionism view is not
sucient to gain a deep comprehension of how such components interact together
at the system level, generating the set of complex behavior we observe in nature.
This is the main motivation of the rising of one of the most interesting and recent
applications of computer science: Computational Systems Biology, a new science
integrating experimental activity and mathematical modeling in order to study the
organization principles and the dynamic behavior of biological systems.
Among the formalisms that either have been applied to or have been inspired by
biological systems there are automata based models, rewrite systems, and process
calculi.
Here we consider a formalism based on term rewriting called Calculus of Looping
Sequences (CLS) aimed to model chemical and biological systems. In order to quantitatively
simulate biological systems a stochastic extension of CLS has been developed;
it allows to express rule schemata with the simplicity of notation of term
rewriting and has some semantic means which are common in process calculi.
In this thesis we carry out the study of the implementation of a stochastic simulator
for the CLS formalism. We propose an extension of Gillespie's stochastic
simulation algorithm that handles rule schemata with rate functions, and we present
an efficient bottom-up, pre-processing based, CLS pattern matching algorithm.
A simulator implementing the ideas introduced in this thesis, has been developed
in F#, a multi-paradigm programming language for .NET framework modeled on
OCaml. Although F# is a research project, still under continuous development,
it has a product quality performance. It merges seamlessly the object oriented,
the functional and the imperative programming paradigms, allowing to exploit the
performance, the portability and the tools of .NET framework
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
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