Parameterised Multiparty Session Types

For many application-level distributed protocols and parallel algorithms, the set of participants, the number of messages or the interaction structure are only known at run-time. This paper proposes a dependent type theory for multiparty sessions which can statically guarantee type-safe, deadlock-free multiparty interactions among processes whose specifications are parameterised by indices. We use the primitive recursion operator from G\"odel's System T to express a wide range of communication patterns while keeping type checking decidable. To type individual distributed processes, a parameterised global type is projected onto a generic generator which represents a class of all possible end-point types. We prove the termination of the type-checking algorithm in the full system with both multiparty session types and recursive types. We illustrate our type theory through non-trivial programming and verification examples taken from parallel algorithms and Web services usecases.Comment: LMCS 201

Multiparty compatibility in communicating automata: characterisation and synthesis of global session types

Multiparty session types are a type system that can ensure the safety and liveness of distributed peers via the global specification of their interactions. To construct a global specification from a set of distributed uncontrolled behaviours, this paper explores the problem of fully characterising multiparty session types in terms of communicating automata. We equip global and local session types with labelled transition systems (LTSs) that faithfully represent asynchronous communications through unbounded buffered channels. Using the equivalence between the two LTSs, we identify a class of communicating automata that exactly correspond to the projected local types. We exhibit an algorithm to synthesise a global type from a collection of communicating automata. The key property of our findings is the notion of multiparty compatibility which non-trivially extends the duality condition for binary session types

Behavioral types in programming languages

A recent trend in programming language research is to use behav- ioral type theory to ensure various correctness properties of large- scale, communication-intensive systems. Behavioral types encompass concepts such as interfaces, communication protocols, contracts, and choreography. The successful application of behavioral types requires a solid understanding of several practical aspects, from their represen- tation in a concrete programming language, to their integration with other programming constructs such as methods and functions, to de- sign and monitoring methodologies that take behaviors into account. This survey provides an overview of the state of the art of these aspects, which we summarize as the pragmatics of behavioral types

The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes

Of all biochemically characterized metabolic reactions formalized by the IUBMB, over one out of four have yet to be associated with a nucleic or protein sequence, i.e. are sequence-orphan enzymatic activities. Few bioinformatics annotation tools are able to propose candidate genes for such activities by exploiting context-dependent rather than sequence-dependent data, and none are readily accessible and propose result integration across multiple genomes. Here, we present CanOE (Candidate genes for Orphan Enzymes), a four-step bioinformatics strategy that proposes ranked candidate genes for sequence-orphan enzymatic activities (or orphan enzymes for short). The first step locates “genomic metabolons”, i.e. groups of co-localized genes coding proteins catalyzing reactions linked by shared metabolites, in one genome at a time. These metabolons can be particularly helpful for aiding bioanalysts to visualize relevant metabolic data. In the second step, they are used to generate candidate associations between un-annotated genes and gene-less reactions. The third step integrates these gene-reaction associations over several genomes using gene families, and summarizes the strength of family-reaction associations by several scores. In the final step, these scores are used to rank members of gene families which are proposed for metabolic reactions. These associations are of particular interest when the metabolic reaction is a sequence-orphan enzymatic activity. Our strategy found over 60,000 genomic metabolons in more than 1,000 prokaryote organisms from the MicroScope platform, generating candidate genes for many metabolic reactions, of which more than 70 distinct orphan reactions. A computational validation of the approach is discussed. Finally, we present a case study on the anaerobic allantoin degradation pathway in Escherichia coli K-12

Alignement Multiple de Données Génomiques et Post-Génomiques : Approches Algorithmiques

Multiple alignment of biological networks is used to extract functional information from high-throughput data represented by graphs. This data can be protein-protein interactions, metabolic pathways or even the gene layout on a chromosome. We start by giving a precise formalism, based on the notions of layered datagraph and alignment multigraph (MGA), which defines local multiple alignments in the datagraph, allowing for example the tuning of the topology conservation between networks. Next, we present a new algorithm that builds and partitions the MGA ''on the fly", which allows us to deal with alignment of numerous biological networks. In a second part, we extend the formalism to be able to recover alignments - which we call ''partial" - when there are missing nodes on some networks. We explain the algorithms we have designed to compute those alignments, and then we give some improvements and some variants tailored to deal with specific biological problems.L'alignement multiple de réseaux biologiques a pour objectif d'extraire des informations fonctionnelles des données haut-débit représentées sous forme de graphes. Ceci concerne, par exemple, les données d'interaction protéines-protéines, les données métaboliques ou même les données génomiques. Dans un premier temps nous proposons un formalisme précis, qui s'appuie sur les notions de graphe de données stratifié et de multigraphe d'alignement (MGA), et qui définit les alignements multiples locaux en autorisant notamment un réglage de la conservation de la topologie entre les réseaux. Nous présentons ensuite un algorithme de construction et partitionnement ''à la volée" du MGA, qui permet de traiter de façon efficace l'alignement de nombreux réseaux biologiques. Dans un second temps, nous étendons le formalisme pour parvenir à retrouver des alignements - que nous qualifions de ''partiels" - lorsqu'il y a des noeuds manquants sur certains réseaux. Nous détaillons les algorithmes associés, puis nous proposons différentes améliorations, et des variantes adaptées à des problèmes biologiques particuliers

A Protocol Compiler for Secure Sessions in ML

Distributed applications can be structured using sessions that specify flows of messages between roles. We design a small specific language to declare sessions. We then build a compiler, called s2ml, that transforms these declarations down to ML modules securely implementing the sessions. Every run of a well-typed program executing a session through its generated module is guaranteed to follow the session specification, despite any low-level attempt by coalitions of remote peers to deviate from their roles. We detail the inner workings of our compiler, along with our design choices, and illustrate the usage of s2ml with two examples: a simple remote procedure call session, and a complex session for a conference management system

Étude thermodynamique de sels fondus a anion polyatomique

The abundance of data obtained by measuring the specific heat under constant pressure, the sound velocity and the expansivity provides a rich source of empirical information with which one can develop a thermodynamic study of molten salts with polyatomic anions. When applied to molten alkali sulphates, chromates, molybdates and tungstates, this approach reveals their high compactness as characterized by a low coefficient of compressibility (from 1 to 2 × 10 -10 Pa-1), a small free volume (from 1 to 3 Å3), a high internal pressure (about 0.2 × 1010 Pa) and a high specific heat at a constant volume (from 40 to 47 cal mol-1 K-1). The properties studied have been analyzed in relation to a coefficient characterizing the geometry of the ions of each salt.Les mesures conjointes de la chaleur spécifique à pression constante Cp, de la vitesse du son u et du coefficient de dilatation α mènent à un ensemble de données dont la richesse permet une approche satisfaisante, tant macroscopique que microscopique, du milieu étudié. L'application de cette méthode aux sulfates, chromates, molybdates et tungstates alcalins fondus a permis de montrer la grande compacité de ces sels caractérisée par un faible coefficient de compressibilité (de 1 à 2 ×10-1 Pa-1), un faible volume libre (de 1 à 3 Å3), une forte pression interne (de l'ordre de 0,2 x 1010 Pa) et une chaleur spécifique à volume constant élevée (de 40 à 47 cal mol-1 K-1). L'ensemble des propriétés étudiées est analysé en fonction d'un facteur caractéristique de la géométrie des ions constituant les sels

Complément à l'étude thermodynamique de sels fondus à anion polyatomique

By using recent measurements, either original or found in the literature, alkali nitrates are shown to exhibit a rather high compactness marked by a low coefficient of compressibility (from 2 to 3 × 10-10 Pa -1), a small free volume (from 0.8 to 2.2 Å3) and a high internal pressure (about 0.1 x 1010 Pa). Their heat capacity at constant volume goes from 26 to 30 cal mol-1 K-1. They behave in the same way as salts involving tetrahedral polyanions do.L'exploitation de quelques mesures récentes, soit originales soit relevées dans la littérature, montre que les nitrates alcalins fondus présentent une assez grande compacité caractérisée par un faible coefficient de compressibilité (2 à 3 x 10-10 Pa-1), un faible volume libre (0,8 à 2,2 Å3) et une forte pression interne (0,1 x 10+10 Pa). Leur chaleur spécifique à volume constant varie de 26 à 30 cal mol -1 K-1. Leur comportement est voisin des sels à polyanion tétraédrique

Parameterised Multiparty Session Types

For many application-level distributed protocols and parallel algorithms, the set of participants, the number of messages or the interaction structure are only known at run-time. This paper proposes a dependent type theory for multiparty sessions which can statically guarantee type-safe, deadlock-free multiparty interactions among processes whose specifications are parameterised by indices. We use the primitive recursion operator from G\"odel's System T to express a wide range of communication patterns while keeping type checking decidable. To type individual distributed processes, a parameterised global type is projected onto a generic generator which represents a class of all possible end-point types. We prove the termination of the type-checking algorithm in the full system with both multiparty session types and recursive types. We illustrate our type theory through non-trivial programming and verification examples taken from parallel algorithms and Web services usecases