94 research outputs found
Membrane Systems and Petri Net Synthesis
Automated synthesis from behavioural specifications is an attractive and
powerful way of constructing concurrent systems. Here we focus on the problem
of synthesising a membrane system from a behavioural specification given in the
form of a transition system which specifies the desired state space of the
system to be constructed. We demonstrate how a Petri net solution to this
problem, based on the notion of region of a transition system, yields a method
of automated synthesis of membrane systems from state spaces.Comment: In Proceedings MeCBIC 2012, arXiv:1211.347
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
Modelling Cell Cycle using Different Levels of Representation
Understanding the behaviour of biological systems requires a complex setting
of in vitro and in vivo experiments, which attracts high costs in terms of time
and resources. The use of mathematical models allows researchers to perform
computerised simulations of biological systems, which are called in silico
experiments, to attain important insights and predictions about the system
behaviour with a considerably lower cost. Computer visualisation is an
important part of this approach, since it provides a realistic representation
of the system behaviour. We define a formal methodology to model biological
systems using different levels of representation: a purely formal
representation, which we call molecular level, models the biochemical dynamics
of the system; visualisation-oriented representations, which we call visual
levels, provide views of the biological system at a higher level of
organisation and are equipped with the necessary spatial information to
generate the appropriate visualisation. We choose Spatial CLS, a formal
language belonging to the class of Calculi of Looping Sequences, as the
formalism for modelling all representation levels. We illustrate our approach
using the budding yeast cell cycle as a case study
Generalized Communicating P Systems Working in Fair Sequential Model
In this article we consider a new derivation mode for generalized
communicating P systems (GCPS) corresponding to the functioning of population
protocols (PP) and based on the sequential derivation mode and a fairness
condition. We show that PP can be seen as a particular variant of GCPS. We also
consider a particular stochastic evolution satisfying the fairness condition
and obtain that it corresponds to the run of a Gillespie's SSA. This permits to
further describe the dynamics of GCPS by a system of ODEs when the population
size goes to the infinity.Comment: Presented at MeCBIC 201
Modeling and evolving biochemical networks: insights into communication and computation from the biological domain
This paper is concerned with the modeling and evolving
of Cell Signaling Networks (CSNs) in silico. CSNs are
complex biochemical networks responsible for the coordination of cellular activities. We examine the possibility to computationally evolve and simulate Artificial Cell Signaling Networks (ACSNs) by means of Evolutionary Computation techniques. From a practical point of view, realizing and evolving ACSNs may provide novel computational paradigms for a variety of application areas. For example, understanding some inherent properties of CSNs such as crosstalk may be of interest: A potential benefit of engineering crosstalking systems is that it allows the modification of a specific process according to the state of other processes in the system. This is clearly necessary in order to achieve complex control tasks. This work may also contribute to the biological understanding of the origins and evolution of real CSNs. An introduction to CSNs is first
provided, in which we describe the potential applications
of modeling and evolving these biochemical networks in
silico. We then review the different classes of techniques to model CSNs, this is followed by a presentation of two alternative approaches employed to evolve CSNs within the
ESIGNET project. Results obtained with these methods
are summarized and discussed
Qualitative modelling and analysis of regulations in multi-cellular systems using Petri nets and topological collections
In this paper, we aim at modelling and analyzing the regulation processes in
multi-cellular biological systems, in particular tissues.
The modelling framework is based on interconnected logical regulatory
networks a la Rene Thomas equipped with information about their spatial
relationships. The semantics of such models is expressed through colored Petri
nets to implement regulation rules, combined with topological collections to
implement the spatial information.
Some constraints are put on the the representation of spatial information in
order to preserve the possibility of an enumerative and exhaustive state space
exploration.
This paper presents the modelling framework, its semantics, as well as a
prototype implementation that allowed preliminary experimentation on some
applications.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005
Dependencies and Simultaneity in Membrane Systems
Membrane system computations proceed in a synchronous fashion: at each step
all the applicable rules are actually applied. Hence each step depends on the
previous one. This coarse view can be refined by looking at the dependencies
among rule occurrences, by recording, for an object, which was the a rule that
produced it and subsequently (in a later step), which was the a rule that
consumed it. In this paper we propose a way to look also at the other main
ingredient in membrane system computations, namely the simultaneity in the rule
applications. This is achieved using zero-safe nets that allows to synchronize
transitions, i.e., rule occurrences. Zero-safe nets can be unfolded into
occurrence nets in a classical way, and to this unfolding an event structure
can be associated. The capability of capturing simultaneity of zero-safe nets
is transferred on the level of event structure by adding a way to express which
events occur simultaneously
- …