Formalizing languages for service oriented computing

Service Oriented Computing is a new programming paradigm for addressing distributed system design issues. Services are autonomous computational entities which can be dynamically discovered and composed in order to form more complex systems able to achieve different kinds of task. E-government, e-business and e-science are some examples of the IT areas where Service Oriented Computing will be exploited in the next years. At present, the most credited Service Oriented Computing technology is that of Web Services, whose specifications are enriched day by day by industrial consortia without following a precise and rigorous approach. This PhD thesis aims, on the one hand, at modelling Service Oriented Computing in a formal way in order to precisely define the main concepts it is based upon and, on the other hand, at defining a new approach, called bipolar approach, for addressing system design issues by synergically exploiting choreography and orchestration languages related by means of a mathematical relation called conformance. Choreography allows us to describe systems of services from a global view point whereas orchestration supplies a means for addressing such an issue from a local perspective. In this work we present SOCK, a process algebra based language inspired by the Web Service orchestration language WS-BPEL which catches the essentials of Service Oriented Computing. From the definition of SOCK we will able to define a general model for dealing with Service Oriented Computing where services and systems of services are related to the design of finite state automata and process algebra concurrent systems, respectively. Furthermore, we introduce a formal language for dealing with choreography. Such a language is equipped with a formal semantics and it forms, together with a subset of the SOCK calculus, the bipolar framework. Finally, we present JOLIE which is a Java implentation of a subset of the SOCK calculus and it is part of the bipolar framework we intend to promote.

'We deliberately set high demands for the gold standard'… Inclusive and exclusive pronouns in two social science cultures

[EN] This study analyses the use of inclusive and exclusive pronominal signals in English and Spanish research articles and investigates whether there are differences between the two languages in terms of pronominal signals frequency and usage.

Tool for biomedical signals processing

[ES]Educational tool for training biomedical engineers in the biomedical signals processing field has been developed. It is software for simulation and study of the results obtained in biomedical signals when different signals processing techniques are applied. The tool has been implemented on a graphical user interface to facilitate the use.

Analysis of ion channel stochastic signals for biosensing

In biological world, life of cells is guaranteed by their ability to sense and to respond to a large variety of internal and external stimuli. In particular, excitable cells, like muscle or nerve cells, produce quick depolarizations in response to electrical, mechanical or chemical stimuli: this means that they can change their internal potential through a quick exchange of ions between cytoplasm and the external environment. This can be done thanks to the presence of ion channels, proteins that span the lipid bilayer and act like switches, allowing ionic current to flow opening and shutting in a stochastic way. For a particular class of ion channels, ligand-gated ion channels, the gating processes is strongly influenced by binding between receptive sites located on the channel surface and specific target molecules. These channels, inserted in biomimetic membranes and in presence of a proper electronic system for acquiring and elaborating the electrical signal, could give us the possibility of detecting and quantifying concentrations of specific molecules in complex mixtures from ionic currents across the membrane; in this thesis work, this possibility is investigated. In particular, it reports a description of experiments focused on the creation and the characterization of artificial lipid membranes, the reconstitution of ion channels and the analysis of their electrical and statistical properties. Moreover, after a chapter about the basis of the modelling of the kinetic behaviour of ligand gated ion channels, a possible approach for the estimation of the target molecule concentration, based on a statistical analysis of the ion channel open probability, is proposed. The fifth chapter contains a description of the kinetic characterisation of a ligand gated ion channel: the homomeric α2 isoform of the glycine receptor. It involved both experimental acquisitions and signal analysis. The last chapter represents the conclusions of this thesis, with some remark on the effective performance that may be achieved using ligand gated ion channels as sensing elements.

Expressiveness of Concurrent Languages

The aim of this thesis is to go through different approaches for proving expressiveness properties in several concurrent languages. We analyse four different calculi exploiting for each one a different technique. We begin with the analysis of a synchronous language, we explore the expressiveness of a fragment of CCS! (a variant of Milner's CCS where replication is considered instead of recursion) w.r.t. the existence of faithful encodings (i.e. encodings that respect the behaviour of the encoded model without introducing unnecessary computations) of models of computability strictly less expressive than Turing Machines. Namely, grammars of types 1,2 and 3 in the Chomsky Hierarchy. We then move to asynchronous languages and we study full abstraction for two Linda-like languages. Linda can be considered as the asynchronous version of CCS plus a shared memory (a multiset of elements) that is used for storing messages. After having defined a denotational semantics based on traces, we obtain fully abstract semantics for both languages by using suitable abstractions in order to identify different traces which do not correspond to different behaviours. Since the ability of one of the two variants considered of recognising multiple occurrences of messages in the store (which accounts for an increase of expressiveness) reflects in a less complex abstraction, we then study other languages where multiplicity plays a fundamental role. We consider the language CHR (Constraint Handling Rules) a language which uses multi-headed (guarded) rules. We prove that multiple heads augment the expressive power of the language. Indeed we show that if we restrict to rules where the head contains at most n atoms we could generate a hierarchy of languages with increasing expressiveness (i.e. the CHR language allowing at most n atoms in the heads is more expressive than the language allowing at most m atoms, with m

A core calculus for the analysis and implementation of biologically inspired languages

The application of Concurrency Theory to Systems Biology is in its earliest stage of progress. The metaphor of cells as computing systems by Regev and Shapiro opened the employment of concurrent languages for the modelling of biological systems. Their peculiar characteristics led to the design of many bio-inspired formalisms which achieve higher faithfulness and specificity. In this thesis we present pi@, an extremely simple and conservative extension of the pi-calculus representing a keystone in this respect, thanks to its expressiveness capabilities. The pi@ calculus is obtained by the addition of polyadic synchronisation and priority to the pi-calculus, in order to achieve compartment semantics and atomicity of complex operations respectively. In its direct application to biological modelling, the stochastic variant of the calculus, Spi@, is shown able to model consistently several phenomena such as formation of molecular complexes, hierarchical subdivision of the system into compartments, inter-compartment reactions, dynamic reorganisation of compartment structure consistent with volume variation. The pivotal role of pi@ is evidenced by its capability of encoding in a compositional way several bio-inspired formalisms, so that it represents the optimal core of a framework for the analysis and implementation of bio-inspired languages. In this respect, the encodings of BioAmbients, Brane Calculi and a variant of P Systems in pi@ are formalised. The conciseness of their translation in pi@ allows their indirect comparison by means of their encodings. Furthermore it provides a ready-to-run implementation of minimal effort whose correctness is granted by the correctness of the respective encoding functions. Further important results of general validity are stated on the expressive power of priority. Several impossibility results are described, which clearly state the superior expressiveness of prioritised languages and the problems arising in the attempt of providing their parallel implementation. To this aim, a new setting in distributed computing (the last man standing problem) is singled out and exploited to prove the impossibility of providing a purely parallel implementation of priority by means of point-to-point or broadcast communication.

Expressiveness in biologically inspired languages

A very recent and exciting new area of research is the application of Concurrency Theory tools to formalize and analyze biological systems and one of the most promising approach comes from the process algebras (process calculi). A process calculus is a formal language that allows to describe concurrent systems and comes with well-established techniques for quantitative and qualitative analysis. Biological systems can be regarded as concurrent systems and therefore modeled by means of process calculi. In this thesis we focus on the process calculi approach to the modeling of biological systems and investigate, mostly from a theoretical point of view, several promising bio-inspired formalisms: Brane Calculi and k-calculus family. We provide several expressiveness results mostly by means of comparisons between calculi. We provide a lower bound to the computational power of the non Turing complete MDB Brane Calculi by showing an encoding of a simple P-System into MDB. We address the issue of local implementation within the k-calculus family: whether n-way rewrites can be simulated by binary interactions only. A solution introducing divergence is provided and we prove a deterministic solution preserving the termination property is not possible. We use the symmetric leader election problem to test synchronization capabilities within the k-calculus family. Several fragments of the original k-calculus are considered and we prove an impossibility result about encoding n-way synchronization into (n-1)-way synchronization. A similar impossibility result is obtained in a pure computer science context. We introduce CCSn, an extension of CCS with multiple input prefixes and show, using the dining philosophers problem, that there is no reasonable encoding of CCS(n+1) into CCSn.

Theoretical and implementation aspects in the mechanization of the metatheory of programming languages

Interactive theorem provers are tools designed for the certification of formal proofs developed by means of man-machine collaboration. Formal proofs obtained in this way cover a large variety of logical theories, ranging from the branches of mainstream mathematics, to the field of software verification. The border between these two worlds is marked by results in theoretical computer science and proofs related to the metatheory of programming languages. This last field, which is an obvious application of interactive theorem proving, poses nonetheless a serious challenge to the users of such tools, due both to the particularly structured way in which these proofs are constructed, and to difficulties related to the management of notions typical of programming languages like variable binding. This thesis is composed of two parts, discussing our experience in the development of the Matita interactive theorem prover and its use in the mechanization of the metatheory of programming languages. More specifically, part I covers: - the results of our effort in providing a better framework for the development of tactics for Matita, in order to make their implementation and debugging easier, also resulting in a much clearer code; - a discussion of the implementation of two tactics, providing infrastructure for the unification of constructor forms and the inversion of inductive predicates; we point out interactions between induction and inversion and provide an advancement over the state of the art. In the second part of the thesis, we focus on aspects related to the formalization of programming languages. We describe two works of ours: - a discussion of basic issues we encountered in our formalizations of part 1A of the Poplmark challenge, where we apply the extended inversion principles we implemented for Matita; - a formalization of an algebraic logical framework, posing more complex challenges, including multiple binding and a form of hereditary substitution; this work adopts, for the encoding of binding, an extension of Masahiko Sato's canonical locally named representation we designed during our visit to the Laboratory for Foundations of Computer Science at the University of Edinburgh, under the supervision of Randy Pollack.

Comparison of EEG signals from epilepsy patients with Bump modeling

Background: l’epilessia è una malattia cerebrale che colpisce oggigiorno circa l’1% della popolazione mondiale e causa, a chi ne soffre, convulsioni ricorrenti e improvvise che danneggiano la vita quotidiana del paziente. Le convulsioni sono degli eventi che bloccano istantaneamente la normale attività cerebrale; inoltre differiscono tra i pazienti e, perciò, non esiste un trattamento comune generalizzato. Solitamente, medici neurologi somministrano farmaci, e, in rari casi, l’epilessia è trattata con operazioni neurochirurgiche. Tuttavia, le operazioni hanno effetti positivi nel ridurre le crisi, ma raramente riescono a eliminarle del tutto. Negli ultimi anni, nel campo della ricerca scientifica è stato provato che il segnale EEG contiene informazioni utili per diagnosticare l'arrivo di un attacco epilettico. Inoltre, diversi algoritmi automatici sono stati sviluppati per rilevare automaticamente le crisi epilettiche. Scopo: lo scopo finale di questa ricerca è l'applicabilità e l'affidabilità di un dispositivo automatico portatile in grado di rilevare le convulsioni e utilizzabile come sistema di monitoraggio. L’analisi condotta in questo progetto, è eseguita con tecniche di misure classiche e avanzate, in modo tale da provare tecnicamente l’affidabilità di un tale sistema. La comparazione è stata eseguita sui segnali elettroencefalografici utilizzando due diversi sistemi di acquisizione EEG: il metodo standard utilizzato nelle cliniche e il nuovo dispositivo portatile. Metodi: è necessaria una solida validazione dei segnali EEG registrati con il nuovo dispositivo. I segnali saranno trattati con tecniche classiche e avanzate. Dopo le operazioni di pulizia e allineamento, verrà utilizzato un nuovo metodo di rappresentazione e confronto di segnali : Bump model. In questa tesi il metodo citato verrà ampiamente descritto, testato, validato e adattato alle esigenze del progetto. Questo modello è definito come un approccio economico per la mappatura spazio-frequenziale di wavelet; in particolare, saranno presenti solo gli eventi con un’alta quantità di energia. Risultati: il modello Bump è stato implementato come toolbox su MATLAB dallo sviluppatore F. Vialatte, e migliorato dall’Autore per l’utilizzo di registrazioni EEG da sistemi diversi. Il metodo è validato con segnali artificiali al fine di garantire l’affidabilità, inoltre, è utilizzato su segnali EEG processati e allineati, che contengono eventi epilettici. Questo serve per rilevare la somiglianza dei due sistemi di acquisizione. Conclusioni: i risultati visivi garantiscono la somiglianza tra i due sistemi, questa differenza la si può notare specialmente comparando i grafici di attività background EEG e quelli di artefatti o eventi epilettici. Bump model è uno strumento affidabile per questa applicazione, e potrebbe essere utilizzato anche per lavori futuri (ad esempio utilizzare il metodo di Sincronicità Eventi Stocas- tici SES) o differenti applicazioni, così come le informazioni estratte dai Bump model potrebbero servire come input per misure di sincronicità, dalle quali estrarre utili risultati.