Simulating bacterial transcription and translation in a stochastic pi-calculus

International audienceStochastic simulation of genetic networks based on models in the stochastic pi-calculus is a promising recent approach. This paper contributes an extensible model of the central mechanisms of gene ex- pression i.e. transcription and translation, at the prototypical instance of bacteria. We reach extensibility through object-oriented abstractions, that are expressible in a stochastic π-calculus with pattern guarded inputs. We illustrate our generic model by simulating the effect of translational bursting in bacterial gene expression

Rewriting Modulo \beta in the \lambda\Pi-Calculus Modulo

The lambda-Pi-calculus Modulo is a variant of the lambda-calculus with dependent types where beta-conversion is extended with user-defined rewrite rules. It is an expressive logical framework and has been used to encode logics and type systems in a shallow way. Basic properties such as subject reduction or uniqueness of types do not hold in general in the lambda-Pi-calculus Modulo. However, they hold if the rewrite system generated by the rewrite rules together with beta-reduction is confluent. But this is too restrictive. To handle the case where non confluence comes from the interference between the beta-reduction and rewrite rules with lambda-abstraction on their left-hand side, we introduce a notion of rewriting modulo beta for the lambda-Pi-calculus Modulo. We prove that confluence of rewriting modulo beta is enough to ensure subject reduction and uniqueness of types. We achieve our goal by encoding the lambda-Pi-calculus Modulo into Higher-Order Rewrite System (HRS). As a consequence, we also make the confluence results for HRSs available for the lambda-Pi-calculus Modulo.Comment: In Proceedings LFMTP 2015, arXiv:1507.0759

A type system for components

In modern distributed systems, dynamic reconfiguration, i.e., changing at runtime the communication pattern of a program, is chal- lenging. Generally, it is difficult to guarantee that such modifications will not disrupt ongoing computations. In a previous paper, a solution to this problem was proposed by extending the object-oriented language ABS with a component model allowing the programmer to: i) perform up- dates on objects by means of communication ports and their rebinding; and ii) precisely specify when such updates can safely occur in an object by means of critical sections. However, improper rebind operations could still occur and lead to runtime errors. The present paper introduces a type system for this component model that extends the ABS type system with the notion of ports and a precise analysis that statically enforces that no object will attempt illegal rebinding

Implementing Session Centered Calculi

Recently, specific attention has been devoted to the development of service oriented process calculi. Besides the foundational aspects, it is also interesting to have prototype implementations for them in order to assess usability and to minimize the gap between theory and practice. Typically, these implementations are done in Java taking advantage of its mechanisms supporting network applications. However, most of the recurrent features of service oriented applications are re-implemented from scratch. In this paper we show how to implement a service oriented calculus, CaSPiS (Calculus of Services with Pipelines and Sessions) using the Java framework IMC, where recurrent mechanisms for network applications are already provided. By using the session oriented and pattern matching communication mechanisms provided by IMC, it is relatively simple to implement in Java all CaSPiS abstractions and thus to easily write the implementation in Java of a CaSPiS process

Learning the Semantics of Manipulation Action

In this paper we present a formal computational framework for modeling manipulation actions. The introduced formalism leads to semantics of manipulation action and has applications to both observing and understanding human manipulation actions as well as executing them with a robotic mechanism (e.g. a humanoid robot). It is based on a Combinatory Categorial Grammar. The goal of the introduced framework is to: (1) represent manipulation actions with both syntax and semantic parts, where the semantic part employs $\lambda$-calculus; (2) enable a probabilistic semantic parsing schema to learn the $\lambda$-calculus representation of manipulation action from an annotated action corpus of videos; (3) use (1) and (2) to develop a system that visually observes manipulation actions and understands their meaning while it can reason beyond observations using propositional logic and axiom schemata. The experiments conducted on a public available large manipulation action dataset validate the theoretical framework and our implementation

Canonical Abstract Syntax Trees

This paper presents Gom, a language for describing abstract syntax trees and generating a Java implementation for those trees. Gom includes features allowing the user to specify and modify the interface of the data structure. These features provide in particular the capability to maintain the internal representation of data in canonical form with respect to a rewrite system. This explicitly guarantees that the client program only manipulates normal forms for this rewrite system, a feature which is only implicitly used in many implementations