Related papers: Types for BioAmbients
We propose PALPS, a Process Algebra with Locations for Population Systems. PALPS allows us to produce spatially-explicit, individual-based models and to reason about their behavior. Our calculus has two levels: at the first level we may…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…
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…
This paper deals with the probabilistic behaviours of distributed systems described by a process calculus considering both probabilistic internal choices and nondeterministic external choices. For this calculus we define and study a typing…
The Shape Calculus is a bio-inspired calculus for describing 3D shapes moving in a space. A shape forms a 3D process when combined with a behaviour. Behaviours are specified with a timed CCS-like process algebra using a notion of channel…
The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules. We enrich this calculus with a type discipline to guarantee the soundness of reduction rules with respect…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
We propose a type system for reasoning on protocol conformance and deadlock freedom in networks of processes that communicate through unordered mailboxes. We model these networks in the mailbox calculus, a mild extension of the asynchronous…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…
Ecology studies the interactions between individuals, species and the environment. The ability to predict the dynamics of ecological systems would support the design and monitoring of control strategies and would help to address pressing…
Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…
Multiparty sessions with asynchronous communications and global types play an important role for the modelling of interaction protocols in distributed systems. In designing such calculi the aim is to enforce, by typing, good properties for…
In this paper we extend PALPS, a process calculus proposed for the spatially-explicit individual-based modeling of ecological systems, with the notion of a policy. A policy is an entity for specifying orderings between the different…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
Many biological, physical, and social interactions have a particular dependence on where they take place. In living cells, protein movement between the nucleus and cytoplasm affects cellular response (i.e., proteins must be present in the…
While distributed systems with transfer of processes have become pervasive, methods for reasoning about their behaviour are underdeveloped. In this paper we propose a bisimulation technique for proving behavioural equivalence of such…
In this paper, I present a summary on some works that utilized static analysis techniques for understanding biological systems. Control flow analysis, context dependent analysis, and other techniques were employed to investigate the…
Situation calculus has been widely applied in Artificial Intelligence related fields. This formalism is considered as a dialect of logic programming language and mostly used in dynamic domain modeling. However, type systems are hardly…
Linear type systems need to keep track of how programs use their resources. The standard approach is to use context splits specifying how resources are (disjointly) split across subterms. In this approach, context splits redundantly echo…
Classical approaches like process algebras or labelled transition systems deal with static composition to model non-trivial concurrent or distributed systems; this is not sufficient for systems with dynamic architecture and with variable…