7 research outputs found
An Abstract Machine for the Stochastic Bioambient calculus
AbstractThis paper presents an abstract machine for the stochastic bioambient calculus. The abstract machine is proved sound and complete with respect to a novel stochastic semantics, and is also shown to preserve the reduction probabilities of the calculus. The machine is implemented as an extension to an existing simulator for stochastic pi-calculus
Stochastic Simulation of Process Calculi for Biology
Biological systems typically involve large numbers of components with
complex, highly parallel interactions and intrinsic stochasticity. To model
this complexity, numerous programming languages based on process calculi have
been developed, many of which are expressive enough to generate unbounded
numbers of molecular species and reactions. As a result of this expressiveness,
such calculi cannot rely on standard reaction-based simulation methods, which
require fixed numbers of species and reactions. Rather than implementing custom
stochastic simulation algorithms for each process calculus, we propose to use a
generic abstract machine that can be instantiated to a range of process calculi
and a range of reaction-based simulation algorithms. The abstract machine
functions as a just-in-time compiler, which dynamically updates the set of
possible reactions and chooses the next reaction in an iterative cycle. In this
short paper we give a brief summary of the generic abstract machine, and show
how it can be instantiated with the stochastic simulation algorithm known as
Gillespie's Direct Method. We also discuss the wider implications of such an
abstract machine, and outline how it can be used to simulate multiple calculi
simultaneously within a common framework.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005
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
Dynamic Compartments in the Imperative Pi Calculus
International audienceDynamic compartments with mutable configurations and variable volumes are of basic interest for the stochastic modeling of biochemistry in cells. We propose a new language to express dynamic compartments that we call the imperative π-calculus. It is obtained from the attributed π-calculus by adding imperative assignment operations to a global store. Previous approaches to dynamic compartments are improved in flexibility or efficiency. This is illustrated by an appropriate model of osmosis and a correct encoding of BioAmbients
Continuous-time temporal logic specification and verification for nonlinear biological systems in uncertain contexts
In this thesis we introduce a complete framework for modelling and verification of biological systems in uncertain contexts based on the bond-calculus process algebra and
the LBUC spatio-temporal logic. The bond-calculus is a biological process algebra which
captures complex patterns of interaction based on affinity patterns, a novel communication
mechanism using pattern matching to express multiway interaction affinities and general
kinetic laws, whilst retaining an agent-centric modelling style for biomolecular species.
The bond-calculus is equipped with a novel continuous semantics which maps models to
systems of Ordinary Differential Equations (ODEs) in a compositional way.
We then extend the bond-calculus to handle uncertain models, featuring interval uncertainties in their species concentrations and reaction rate parameters. Our semantics is also
extended to handle uncertainty in every aspect of a model, producing non-deterministic
continuous systems whose behaviour depends either on time-independent uncertain parameters and initial conditions, corresponding to our partial knowledge of the system at
hand, or time-varying uncertain inputs, corresponding to genuine variability in a system’s
behaviour based on environmental factors.
This language is then coupled with the LBUC spatio-temporal logic which combines
Signal Temporal Logic (STL) temporal operators with an uncertain context operator
which quantifies over an uncertain context model describing the range of environments
over which a property must hold. We develop model-checking procedures for STL and
LBUC properties based on verified signal monitoring over flowpipes produced by the
Flow* verified integrator, including the technique of masking which directs monitoring for
atomic propositions to time regions relevant to the overall verification problem at hand.
This allows us to monitor many interesting nested contextual properties and frequently
reduces monitoring costs by an order of magnitude. Finally, we explore the technique
of contextual signal monitoring which can use a single Flow* flowpipe representing a
functional dependency to complete a whole tree of signals corresponding to different
uncertain contexts. This allows us to produce refined monitoring results over the whole
space and to explore the variation in system behaviour in different contexts