Automatic Distributed Code Generation from Formal Models of Asynchronous Concurrent Processes

International audienceFormal process languages inheriting the concurrency and communication features of process algebras are convenient formalisms to model distributed applications, especially when they are equipped with formal verification tools (e.g., model-checkers) to help hunting for bugs early in the development process. However, even starting from a fully verified formal model, bugs are likely to be introduced while translating (generally by hand) the concurrent model —which relies on high-level and expressive communication primitives— into the distributed implementation —which often relies on low-level communication primitives. In this paper, we present DLC, a compiler that enables distributed code to be generated from models written in a formal process language called LNT, which is equipped with a rich verification toolbox named CADP. The generated code can be either executed in an autonomous way (i.e., without requiring additional code to be defined by the user), or connected to external software through user-modifiable C functions. We present an experiment where DLC generates a distributed implementation from the LNT model of the Raft consensus algorithm

Génération automatique d'implémentation distribuée à partir de modèles formels de processus concurrents asynchrones

LNT is a recent formal specification language, based on process algebras, where several concurrent asynchronous processes can interact by multiway rendezvous (i.e., involving two or more processes), with data exchange. The CADP (Construction and Analysis of Distributed Processes) toolbox offers several techniques related to state space exploration, like model checking, to formally verify an LNT specification. This thesis introduces a distributed implementation generation method, starting from an LNT formal model of a parallel composition of processes. Taking advantage of CADP, we developed the new DLC (Distributed LNT Compiler) tool, which is able to generate, from an LNT specification, a distributed implementation in C that can be deployed on several distinct machines linked by a network. In order to handle multiway rendezvous with data exchange between distant processes in a correct and efficient manner, we designed a synchronization protocol that gathers different approaches suggested in the past. We set up a verification method for this kind of protocol, which, using LNT and CADP, can detect livelocks or deadlocks due to the protocol, and also check that the protocol leads to valid interactions with respect to a given specification. This method allowed us to identify possible deadlocks in a protocol from the literature, and to verify the good behavior of our own protocol. We also designed a mechanism that enables the final user, by embedding user-defined C procedures into the implementation, to set up interactions between the generated implementation and other systems in the environment. Finally, we used the new consensus algorithm Raft as a case study, in particular to measure the performances of an implementation generated by DLC.LNT est un langage formel de spécification récent, basé sur les algèbres de processus, où plusieurs processus concurrents et asynchrones peuvent interagir par rendez-vous multiple, c'est-à-dire à deux ou plus, avec échange de données. La boite à outils CADP (Construction and Analysis of Distributed Processes) offre plusieurs techniques relatives à l'exploration d'espace d'états, comme le model checking, pour vérifier formellement une spécification LNT. Cette thèse présente une méthode de génération d'implémentation distribuée à partir d'un modèle formel LNT décrivant une composition parallèle de processus. En s'appuyant sur CADP, nous avons mis au point le nouvel outil DLC (Distributed LNT Compiler), capable de générer, à partir d'une spécification LNT, une implémentation distribuée en C qui peut ensuite être déployée sur plusieurs machines distinctes reliées par un réseau. Pour implémenter de manière correcte et efficace les rendez-vous multiples avec échange de données entre processus distants, nous avons élaboré un protocole de synchronisation qui regroupe différentes approches proposées par le passé. Nous avons mis au point une méthode de vérification de ce type de protocole qui, en utilisant LNT et CADP, permet de détecter des boucles infinies ou des interblocages dus au protocole, et de vérifier que le protocole réalise des rendez-vous cohérents par rapport à une spécification donnée. Cette méthode nous a permis d'identifier de possibles interblocages dans un protocole de la littérature, et de vérifier le bon comportement de notre propre protocole. Nous avons aussi développé un mécanisme qui permet, en embarquant au sein d'une implémentation des procédures C librement définies par l'utilisateur, de mettre en place des interactions entre une implémentation générée et d'autres systèmes de son environnement. Enfin, nous avons appliqué DLC au nouvel algorithme de consensus Raft, qui nous sert de cas d'étude, notamment pour mesurer les performances d'une implémentation générée par DLC

Génération automatique d'implémentation distribuée à partir de modèles formels de processus concurrents asynchrones

LNT is a recent formal specification language, based on process algebras, where several concurrent asynchronous processes can interact by multiway rendezvous (i.e., involving two or more processes), with data exchange. The CADP (Construction and Analysis of Distributed Processes) toolbox offers several techniques related to state space exploration, like model checking, to formally verify an LNT specification. This thesis introduces a distributed implementation generation method, starting from an LNT formal model of a parallel composition of processes. Taking advantage of CADP, we developed the new DLC (Distributed LNT Compiler) tool, which is able to generate, from an LNT specification, a distributed implementation in C that can be deployed on several distinct machines linked by a network. In order to handle multiway rendezvous with data exchange between distant processes in a correct and efficient manner, we designed a synchronization protocol that gathers different approaches suggested in the past. We set up a verification method for this kind of protocol, which, using LNT and CADP, can detect livelocks or deadlocks due to the protocol, and also check that the protocol leads to valid interactions with respect to a given specification. This method allowed us to identify possible deadlocks in a protocol from the literature, and to verify the good behavior of our own protocol. We also designed a mechanism that enables the final user, by embedding user-defined C procedures into the implementation, to set up interactions between the generated implementation and other systems in the environment. Finally, we used the new consensus algorithm Raft as a case study, in particular to measure the performances of an implementation generated by DLC.LNT est un langage formel de spécification récent, basé sur les algèbres de processus, où plusieurs processus concurrents et asynchrones peuvent interagir par rendez-vous multiple, c'est-à-dire à deux ou plus, avec échange de données. La boite à outils CADP (Construction and Analysis of Distributed Processes) offre plusieurs techniques relatives à l'exploration d'espace d'états, comme le model checking, pour vérifier formellement une spécification LNT. Cette thèse présente une méthode de génération d'implémentation distribuée à partir d'un modèle formel LNT décrivant une composition parallèle de processus. En s'appuyant sur CADP, nous avons mis au point le nouvel outil DLC (Distributed LNT Compiler), capable de générer, à partir d'une spécification LNT, une implémentation distribuée en C qui peut ensuite être déployée sur plusieurs machines distinctes reliées par un réseau. Pour implémenter de manière correcte et efficace les rendez-vous multiples avec échange de données entre processus distants, nous avons élaboré un protocole de synchronisation qui regroupe différentes approches proposées par le passé. Nous avons mis au point une méthode de vérification de ce type de protocole qui, en utilisant LNT et CADP, permet de détecter des boucles infinies ou des interblocages dus au protocole, et de vérifier que le protocole réalise des rendez-vous cohérents par rapport à une spécification donnée. Cette méthode nous a permis d'identifier de possibles interblocages dans un protocole de la littérature, et de vérifier le bon comportement de notre propre protocole. Nous avons aussi développé un mécanisme qui permet, en embarquant au sein d'une implémentation des procédures C librement définies par l'utilisateur, de mettre en place des interactions entre une implémentation générée et d'autres systèmes de son environnement. Enfin, nous avons appliqué DLC au nouvel algorithme de consensus Raft, qui nous sert de cas d'étude, notamment pour mesurer les performances d'une implémentation générée par DLC

A MODEL FOR PREDICTING THE PERFORMANCE OF IP VIDEOCONFERENCING

With the incorporation of free desktop videoconferencing (DVC) software on the majority of the world's PCs, over the recent years, there has, inevitably, been considerable interest in using DVC over the Internet. The growing popularity of DVC increases the need for multimedia quality assessment. However, the task of predicting the perceived multimedia quality over the Internet Protocol (IP) networks is complicated by the fact that the audio and video streams are susceptible to unique impairments due to the unpredictable nature of IP networks, different types of task scenarios, different levels of complexity, and other related factors. To date, a standard consensus to define the IP media Quality of Service (QoS) has yet to be implemented. The thesis addresses this problem by investigating a new approach to assess the quality of audio, video, and audiovisual overall as perceived in low cost DVC systems. The main aim of the thesis is to investigate current methods used to assess the perceived IP media quality, and then propose a model which will predict the quality of audiovisual experience from prevailing network parameters. This thesis investigates the effects of various traffic conditions, such as, packet loss, jitter, and delay and other factors that may influence end user acceptance, when low cost DVC is used over the Internet. It also investigates the interaction effects between the audio and video media, and the issues involving the lip sychronisation error. The thesis provides the empirical evidence that the subjective mean opinion score (MOS) of the perceived multimedia quality is unaffected by lip synchronisation error in low cost DVC systems. The data-gathering approach that is advocated in this thesis involves both field and laboratory trials to enable the comparisons of results between classroom-based experiments and real-world environments to be made, and to provide actual real-world confirmation of the bench tests. The subjective test method was employed since it has been proven to be more robust and suitable for the research studies, as compared to objective testing techniques. The MOS results, and the number of observations obtained, have enabled a set of criteria to be established that can be used to determine the acceptable QoS for given network conditions and task scenarios. Based upon these comprehensive findings, the final contribution of the thesis is the proposal of a new adaptive architecture method that is intended to enable the performance of IP based DVC of a particular session to be predicted for a given network condition

The co-regulation of the mucus associated molecules intelectin, resistin like molecule beta and beta galactoside alpha 2-3 sialyltransferase in a T helper cell type 2 reponse

Increased mucin production and goblet cell hyperplasia are common features o f parasitic and allergic disease in man and animals. A protective role for mucus has been suggested in gastro-intestinal parasitic infections in rodents. The mucus associated molecules intelectin (ITLN), resistin like molecule beta (RELMP) and beta galactoside alpha 2-3 sialyltransferase (SIAT4C) are upregulated in nematode infections known to induce a typical T helper cell type 2 (Th2) response in mice. In the present work, it was hypothesised that these three mucus-associated molecules were co-regulated by Th2 cytokines and that their upregulation was part o f a typical anti-parasite response in other species. Sheep were chosen as a model because o f the economic importance o f both respiratory and gastrointestinal tract parasitic infections in sheep.Culture o f a human colonic carcimoma cell line with either interleukin 4 (IL-4) or 1L-13 confirmed the upregulation o f ITLN and RELMP in a Th2 environment but failed to show co-regulation with SIAT4C. O f the T hl or Th2 cytokines examined only IFNy was found to have a significant effect on expression o f SIAT4C transcript. ITLN transcript and protein were demonstrated in sheep tissue and furthermore three different ITLNs (sITLN l, sITLN2, sITLN3) which had a differential tissue distribution were cloned and sequenced. SIAT4C was shown to be widely expressed in sheep tissues and the full sequence was deduced from expressed sequence tags, and confirmed. There was no evidence o f expression o f RELMP in sheep tissues examined.sITLN transcripts were shown to be upregulated in response to IL-4 in an ex vivosheep tracheal explant culture model whilst sheep (s) SIAT4C was significantly downregulated in the same model. However, despite differential regulation by IL-4 ex vivo, in a sheep model o f infection with the abomasal nematode, Teladorsagicicircumcmcta, known to induce a Th2 biased response, sITLN transcripts and protein and sSIAT4C transcript were upregulated in response to a challenge infection.Furthermore, slTLNl and sITLN2 were shown to upregulate at an earlier time point post challenge in previously infected (immune) compared to naive yearling sheep and lambs and significant upregulation o f sSIAT4C transcript was seen in previously infected challenged but not naive challenged sheep and lambs. In conclusion, whilst regulation o f sITLNs and sSIAT4C transcript expression in the mucosa may differ, these molecules may have an important role to play in the mucosal immune response to parasitic infections in sheep

Design nanostruktur založených na klastrových sloučeninách bóru ve vodných roztocích

Náplní této disertační práce bylo studium roztokového chování klastrových sloučenin bóru a jejich interakce s polymery, s důrazem na pochopení zákonitostí vedoucích k tvorbě příslušných nano-struktur. Kromě polymerního systému obsahujícího o-karboran, byl výzkum zaměřen zejména na chování kobalt bis(dikarbollidového) aniontu (COSAN). Hlavní myšlenkou bylo pochopit některé dosud nejasné aspekty micelizace COSANu v souladu s dlouhodobými badatelskými plány v naší skupině. Z toho důvodu byla provedena detailní kalorimetrická studie, která umožnila kromě dalších termodynamických parametrů stanovit hodnotu agregačního čísla solí COSANu při koncentracích blízkých kritické micelární koncentrace (KMK), což je obtížně dostupné pomocí jiných experimentálních technik. Použití acetonitrilu jako příměsi ve vodném roztoku COSANu se ukázalo jako velmi účinný prostředek pro získání alespoň přibližné představy o vnitřní struktuře micel COSANu, což je z experimentálního hlediska jinak velmi obtížné. Z provedených fyzikálně chemických experimentů plyne, že C-H skupiny COSANu pravděpodobně směřují dovnitř nano-agregátů. Dále byla studována solubilizace COSANu v micelách s hydrofobním jádrem a polyelektrolytovou slupkou, kde byl použit COSAN jako modelové léčivo kombinující elektrostatický náboj s hydrofobním...Thesis The main objective of this thesis is the study of boron cluster compounds in solution, their interaction with polymers and the formation of nanostructures. Most of the work was focused around cobalt bis(dicarbollide) (COSAN) but the incorporation of carborane into polymers was also studied. The idea was to close the knowledge gap around the way COSAN aggregates and continue the line of the laboratory in leading this topic. Therefore, we performed in-depth analysis of isothermal titration calorimetry curves to determine the aggregation number at concentrations around the critical micellar concentration (CMC). Thus, the aggregation number obtained was an improvement over previous data obtained a much higher concentration. The use of acetonitrile as a cosolvent in the micellization process helped formulate a model describing how C-H bonds in the COSAN micelles are directed towards the inside of the micelle. Furthermore, COSAN was used as a model drug for loading nanocarriers composed of hydrophobic core and charged corona. The importance of this work relies on the creation of guidelines for drug loading into similar polymeric vectors in order to determine how the nanocarrier will be affected. With the help of coarse-grained simulations, we determined that changes in the hydrophobicity of the...Katedra fyzikální a makromol. chemieDepartment of Physical and Macromolecular ChemistryPřírodovědecká fakultaFaculty of Scienc

The Role of Spanins in Phage Lysis

The work described in this dissertation addresses how spanins function during phage lysis, focusing on the 2CS system of phage lambda, in which Rz and Rz1 are the prototype i-spanin (inner membrane subunit) and o-spanin (OM lipoprotein subunits) of the spanin complex. Results obtained from genetic and biochemical approaches found that there must be at least one homodimerizing intermolecular disulfide bond near the heterotypic interface. The covalent linkage of spanin homodimers was found to be mediated by the host Dsb system, the first time that this system has been shown to catalyze the formation of intermolecular disulfide bonds. Genetic and biochemical studies with the paradigm phage T4 revealed striking differences in the requirements for position and disulfide bond formation in the PseT.3/PseT.2 2CS system, presumably reflecting the separated architecture of the T4 spanin genes. Mutational analysis using an extensive collection of Rz and Rz1 mutants highlighted important domains and motifs of Rz and Rz1 that are required for function. A method has been developed to isolate intragenic and intergenic suppressors for these mutants, which should allow future studies to interrogate interacting interface between the different domains of spanin subunits. In addition, it was found that the spanin complex, in the absence of holin function, can cause rapid lysis of a host mutant that is compromised for peptidoglycan biosynthesis, suggesting that spanin function is regulated by the meshwork of intact peptidoglycan. Furthermore, we developed a spheroplast method to test the model proposed for spanin function: that the last step of lysis is fusion between the IM and OM. The method is based on the fusogenic properties of the spanin subunits externalized on the outer surface of the cytoplasmic membranes of spheroplasts. The unambiguous result was that the lambda 2CS subunits supported efficient, spheroplast fusion, and that spanin missense mutations that abrogate lysis in vivo also blocked the spheroplast fusion activity. These results suggest the last step in lysis of the Gram-negative host is OM disruption by fusion with the IM