18 research outputs found
An Approach to the Engineering of Cellular Models Based on P Systems
Living cells assembled into colonies or tissues communicate using complex systems.
These systems consist in the interaction between many molecular species
distributed over many compartments. Among the different cellular processes
used by cells to monitor their environment and respond accordingly, gene regulatory
networks, rather than individual genes, are responsible for the information
processing and orchestration of the appropriate response [16].
In this respect, synthetic biology has emerged recently as a novel discipline
aiming at unravelling the design principles in gene regulatory systems by synthetically
engineering transcriptional networks which perform a specific and prefixed
task [2]. Formal modelling and analysis are key methodologies used in the
field to engineer, assess and compare different genetic designs or devices.
In order to model cellular systems in colonies or tissues one requires a formalism
able to represent the following relevant features:
– Single cells should be described as the elementary units in the system. Nevertheless,
they cannot be represented as homogeneous points as they exhibit
complex structures containing different compartments where specific molecular
species interact according to particular reactions.
– The molecular interactions taking place in cellular systems are inherently
discrete and stochastic processes. This is a key feature of cellular systems
that needs to be taken into account when describing their dynamics [9].
– It has been postulated that gene regulatory networks are organised in a
modular manner in such a way that cellular processes arise from the orchestrated
interactions between different genetic transcriptional units that can
be considered separable modules [1].
– Spatial and geometric information must be represented in the system in
order to describe processes involving pattern formation.
In this work we review recent advances in the use of the computational
paradigm membrane computing or P systems as a formal methodology in synthetic
biology for the specification and analysis on cellular system models according
to the previously presented points
Discrete Solution of Differential Equations by P Metabolic Algorithm
The relationships existing between MP graphs, metabolic P systems, and
ODE systems are investigated. Formal results show that every MP system, once derived
by its MP graph, results in an ODE system whose solution equals, in the limit, the solution
obtained by a non-cooperative MP system that is ODE equivalent to the original one.
The freedom of choice of the ODE equivalent from the original MP system resembles the
same freedom which is left in the choice and optimization of a numerical scheme while
computing the solution of an ODE system
On Modeling Signal Transduction Networks
Signal transduction networks are very complex processes employed by the
living cell to suitably react to environmental stimuli. Qualitative and quantitative computational
models play an increasingly important role in the representation of these
networks and in the search of new insights about these phenomena. In this work we analyze
some graph-based models used to discover qualitative properties of such networks.
In turn, we show that MP systems can naturally extend these graph-based models by
adding some qualitative elements. The case study of integrins activation during the lymphocyte
recruitment, a crucial phenomenon in inflammatory processes, is described, and
a first MP graph for this network is designed. Finally, we discuss some open problems
related to the qualitative modeling of signaling networks
Cellular modelling using P systems and process algebra.
In this paper various molecular chemical interactions are modelled
under different computational paradigms. P systems and -calculus are
used to describe intra-cellular reactions like protein-protein interactions
and gene regulation control
Towards a P Systems Pseudomonas Quorum Sensing Model
Pseudomonas aeruginosa is an opportunistic bacterium that
exploits quorum sensing communication to synchronize individuals in a
colony and this leads to an increase in the effectiveness of its virulence.
In this paper we derived a mechanistic P systems model to describe the
behavior of a single bacterium and we discuss a possible approach, based
on an evolutionary algorithm, to tune its parameters that will allow a
quantitative simulation of the system.Kingdom's Engineering and Physical Sciences Research Council EP/D021847/
A Multiscale Modeling Framework Based on P Systems
Cellular systems present a highly complex organization at
different scales including the molecular, cellular and colony levels. The
complexity at each one of these levels is tightly interrelated. Integrative
systems biology aims to obtain a deeper understanding of cellular systems
by focusing on the systemic and systematic integration of the different
levels of organization in cellular systems.
The different approaches in cellular modeling within systems biology
have been classified into mathematical and computational frameworks.
Specifically, the methodology to develop computational models has been
recently called executable biology since it produces executable algorithms
whose computations resemble the evolution of cellular systems.
In this work we present P systems as a multiscale modeling framework
within executable biology. P system models explicitly specify the
molecular, cellular and colony levels in cellular systems in a relevant and
understandable manner. Molecular species and their structure are represented
by objects or strings, compartmentalization is described using
membrane structures and finally cellular colonies and tissues are modeled
as a collection of interacting individual P systems.
The interactions between the components of cellular systems are described
using rewriting rules. These rules can in turn be grouped together
into modules to characterize specific cellular processes. One of our current
research lines focuses on the design of cell systems biology models
exhibiting a prefixed behavior through the automatic assembly of these
cellular modules. Our approach is equally applicable to synthetic as well
as systems biology.Kingdom's Engineering and Physical Sciences Research Council EP/ E017215/1Biotechnology and Biological Sciences Research Council/United Kingdom BB/F01855X/1Biotechnology and Biological Sciences Research Council/United Kingdom BB/D019613/
A Multiscale Modeling Framework Based on P Systems
Cellular systems present a highly complex organization at
different scales including the molecular, cellular and colony levels. The
complexity at each one of these levels is tightly interrelated. Integrative
systems biology aims to obtain a deeper understanding of cellular systems
by focusing on the systemic and systematic integration of the different
levels of organization in cellular systems.
The different approaches in cellular modeling within systems biology
have been classified into mathematical and computational frameworks.
Specifically, the methodology to develop computational models has been
recently called executable biology since it produces executable algorithms
whose computations resemble the evolution of cellular systems.
In this work we present P systems as a multiscale modeling framework
within executable biology. P system models explicitly specify the
molecular, cellular and colony levels in cellular systems in a relevant and
understandable manner. Molecular species and their structure are represented
by objects or strings, compartmentalization is described using
membrane structures and finally cellular colonies and tissues are modeled
as a collection of interacting individual P systems.
The interactions between the components of cellular systems are described
using rewriting rules. These rules can in turn be grouped together
into modules to characterize specific cellular processes. One of our current
research lines focuses on the design of cell systems biology models
exhibiting a prefixed behavior through the automatic assembly of these
cellular modules. Our approach is equally applicable to synthetic as well
as systems biology.Kingdom's Engineering and Physical Sciences Research Council EP/ E017215/1Biotechnology and Biological Sciences Research Council/United Kingdom BB/F01855X/1Biotechnology and Biological Sciences Research Council/United Kingdom BB/D019613/
Towards Probabilistic Model Checking on P Systems Using PRISM
This paper presents the use of P systems and π-calculus to
model interacting molecular entities and how they are translated into a
probabilistic and symbolic model checker called PRISM.Ministerio de Educación y Ciencia TIN2005-09345-C04-01Junta de Andalucía TIC-58
Membrane Computing as a Modeling Framework. Cellular Systems Case Studies
Membrane computing is a branch of natural computing aiming
to abstract computing models from the structure and functioning of
the living cell, and from the way cells cooperate in tissues, organs, or
other populations of cells. This research area developed very fast, both
at the theoretical level and in what concerns the applications. After a
very short description of the domain, we mention here the main areas
where membrane computing was used as a framework for devising models
(biology and bio-medicine, linguistics, economics, computer science,
etc.), then we discuss in a certain detail the possibility of using membrane
computing as a high level computational modeling framework for
addressing structural and dynamical aspects of cellular systems. We close
with a comprehensive bibliography of membrane computing applications
A Modeling Approach Based on P Systems with Bounded Parallelism
This paper presents a general framework for modelling with
membrane systems that is based on a computational paradigm where
rules have associated a finite set of attributes and a corresponding function.
Attributes and functions are meant to provide those extra features
that allow to define different strategies to run a P system. Such a strategy
relying on a bounded parallelism is presented using an operational
approach and applying it for a case study presenting the basic model of
quorum sensing for Vibrio fischeri bacteria.Ministerio de Ciencia y Tecnología TIN2005-09345-C04-01Junta de Andalucía TIC-58