A Process Calculus for Spatially-explicit Ecological Models

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 define the behavior of an individual of a population while, at the second level, we may specify a system as the collection of individuals of various species located in space, moving through their life cycle while changing their location, if they so wish, and interacting with each other in various ways such as preying on each other. Furthermore, we propose a probabilistic temporal logic for reasoning about the behavior of PALPS processes. We illustrate our framework via models of dispersal in metapopulations.Comment: In Proceedings MeCBIC 2012, arXiv:1211.347

An Intuitive Automated Modelling Interface for Systems Biology

We introduce a natural language interface for building stochastic pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and transformation. This language thus allows us to model biochemical systems modularly by describing their dynamics in a narrative-style language, while making amendments, refinements and extensions on the models easy. We demonstrate the language on a model of Fc-gamma receptor phosphorylation during phagocytosis. We provide a tool implementation of the translation into a stochastic pi calculus language, Microsoft Research's SPiM

cJoin: join with communicating transactions

This paper proposes a formal approach to the design and programming of Long Running Transactions (LRT). We exploit techniques from process calculi to define cJoin, which is an extension of the join calculus with few well-disciplined primitives for LRT. Transactions in cJoin are intended to describe the transactional interaction of several partners, under the assumption that any partner executing a transaction may communicate only with other transactional partners. In such case, the transactions run by any party are bound to achieve the same outcome (i.e., all succeed or all fail). Hence, a distinguishing feature of cJoin, called dynamic joinability, is that ongoing transactions can be merged to complete their tasks and when this happens either all succeed or all abort. Additionally, cJoin is based on compensations, i.e., partial executions of transactions are recovered by executing user-defined programs instead of providing automatic roll-back. The expressiveness and generality of cJoin is demonstrated by many examples addressing common programming patterns. The mathematical foundation is accompanied by a prototype language implementation, which is an extension of the jocaml compiler

A flat process calculus for nested membrane interactions

The link-calculus has been recently proposed as a process calculus for representing interactions that are open (i.e. that the number of processes may vary), and multiparty (i.e. that may involve more than two processes). Here, we apply the link-calculus for expressing, possibly hierarchical and non dyadic, biological interactions. In particular, we provide a natural encoding of Cardelli's Brane calculus, a compartment-based calculus, introduced to model the behaviour of nested membranes. Notably, the link-calculus is at, but we can model membranes just as special processes taking part in the biological reaction. Moreover, we give evidence that the link-calculus allows one to directly model biological phenomena at the more appropriate level of abstraction

Flux Analysis in Process Models via Causality

We present an approach for flux analysis in process algebra models of biological systems. We perceive flux as the flow of resources in stochastic simulations. We resort to an established correspondence between event structures, a broadly recognised model of concurrency, and state transitions of process models, seen as Petri nets. We show that we can this way extract the causal resource dependencies in simulations between individual state transitions as partial orders of events. We propose transformations on the partial orders that provide means for further analysis, and introduce a software tool, which implements these ideas. By means of an example of a published model of the Rho GTP-binding proteins, we argue that this approach can provide the substitute for flux analysis techniques on ordinary differential equation models within the stochastic setting of process algebras

Membrane Systems and Time Petri Nets

We investigate the relationship of time Petri nets and di erent variants of membrane systems. First we show that the added feature of \time" in time Petri nets makes it possible to simulate the maximal parallel rule application of membrane systems without introducing maximal parallelism to the Petri net semantics, then we de ne local time P systems and explore how time Petri nets and the computations of local time P systems can be related

Towards Bridging Two Cell-Inspired Models: P Systems and R Systems

We examine, from the point of view of membrane computing, the two basic assumptions of reaction systems, the "threshold" and "no permanence" ones. In certain circumstances (e.g., defining the successful computations by local halting), the second assumption can be incorporated in a transition P system or in a symport/antiport P system without losing the universality. The case of the first postulate remains open: the reaction systems deal, deterministically, with finite sets of symbols, which is not of much interest for computing; three ways to introduce nondeterminism are suggested and left as research topics.Junta de Andalucía P08 – TIC 0420

Run-time Variability with First-class Contexts

Software must be regularly updated to keep up with changing requirements. Unfortunately, to install an update, the system must usually be restarted, which is inconvenient and costly. In this dissertation, we aim at overcoming the need for restart by enabling run-time changes at the programming language level. We argue that the best way to achieve this goal is to improve the support for encapsulation, information hiding and late binding by contextualizing behavior. In our approach, behavioral variations are encapsulated into context objects that alter the behavior of other objects locally. We present three contextual language features that demonstrate our approach. First, we present a feature to evolve software by scoping variations to threads. This way, arbitrary objects can be substituted over time without compromising safety. Second, we present a variant of dynamic proxies that operate by delegation instead of forwarding. The proxies can be used as building blocks to implement contextualization mechanisms from within the language. Third, we contextualize the behavior of objects to intercept exchanges of references between objects. This approach scales information hiding from objects to aggregates. The three language features are supported by formalizations and case studies, showing their soundness and practicality. With these three complementary language features, developers can easily design applications that can accommodate run-time changes