Sviluppo di un'applicazione bioinformatica per la gestione dei dati di antibiotico sensibilità di isolati clinici

Il problema dell'antibiotico-resistenza è un problema di sanità pubblica per affrontare il quale è necessario un sistema di sorveglianza basato sulla raccolta e l'analisi dei dati epidemiologici di laboratorio. Il progetto di dottorato è consistito nello sviluppo di una applicazione web per la gestione di tali dati di antibiotico sensibilità di isolati clinici utilizzabile a livello di ospedale. Si è creata una piattaforma web associata a un database relazionale per avere un’applicazione dinamica che potesse essere aggiornata facilmente inserendo nuovi dati senza dover manualmente modificare le pagine HTML che compongono l’applicazione stessa. E’ stato utilizzato il database open-source MySQL in quanto presenta numerosi vantaggi: estremamente stabile, elevate prestazioni, supportato da una grande comunità online ed inoltre gratuito. Il contenuto dinamico dell’applicazione web deve essere generato da un linguaggio di programmazione tipo “scripting” che automatizzi operazioni di inserimento, modifica, cancellazione, visualizzazione di larghe quantità di dati. E’ stato scelto il PHP, linguaggio open-source sviluppato appositamente per la realizzazione di pagine web dinamiche, perfettamente utilizzabile con il database MySQL. E’ stata definita l’architettura del database creando le tabelle contenenti i dati e le relazioni tra di esse: le anagrafiche, i dati relativi ai campioni, microrganismi isolati e agli antibiogrammi con le categorie interpretative relative al dato antibiotico. Definite tabelle e relazioni del database è stato scritto il codice associato alle funzioni principali: inserimento manuale di antibiogrammi, importazione di antibiogrammi multipli provenienti da file esportati da strumenti automatizzati, modifica/eliminazione degli antibiogrammi precedenti inseriti nel sistema, analisi dei dati presenti nel database con tendenze e andamenti relativi alla prevalenza di specie microbiche e alla chemioresistenza degli stessi, corredate da grafici. Lo sviluppo ha incluso continui test delle funzioni via via implementate usando reali dati clinici e sono stati introdotti appositi controlli e l’introduzione di una semplice e pulita veste grafica.

A communication infrastructure to support knowledge level agents on the web

Agent Communication Languages (ACLs) have been developed to provide a way for agents to communicate with each other supporting cooperation in Multi-Agent Systems. In the past few years many ACLs have been proposed for Multi-Agent Systems, such as KQML and FIPA-ACL. The goal of these languages is to support high-level, human like communication among agents, exploiting Knowledge Level features rather than symbol level ones. Adopting these ACLs, and mainly the FIPA-ACL specifications, many agent platforms and prototypes have been developed. Despite these efforts, an important issue in the research on ACLs is still open and concerns how these languages should deal (at the Knowledge Level) with possible failures of agents. Indeed, the notion of Knowledge Level cannot be straightforwardly extended to a distributed framework such as MASs, because problems concerning communication and concurrency may arise when several Knowledge Level agents interact (for example deadlock or starvation). The main contribution of this Thesis is the design and the implementation of NOWHERE, a platform to support Knowledge Level Agents on the Web. NOWHERE exploits an advanced Agent Communication Language, FT-ACL, which provides high-level fault-tolerant communication primitives and satisfies a set of well defined Knowledge Level programming requirements. NOWHERE is well integrated with current technologies, for example providing full integration for Web services. Supporting different middleware used to send messages, it can be adapted to various scenarios. In this Thesis we present the design and the implementation of the architecture, together with a discussion of the most interesting details and a comparison with other emerging agent platforms. We also present several case studies where we discuss the benefits of programming agents using the NOWHERE architecture, comparing the results with other solutions. Finally, the complete source code of the basic examples can be found in appendix.

One archive, many readings. Personal archives as complex networks in the semantic web

Personal archives are the archives created by individuals for their own purposes. Among these are the library and documentary collections of writers and scholars. It is only recently that archival literature has begun to focus on this category of archives, emphasising how their heterogeneous nature necessitates the conciliation of different approaches to archival description, and calling for a broader understanding of the principle of provenance, recognising that multiple creators, including subsequent researchers, can contribute to shaping personal archives over time by adding new layers of contexts. Despite these advances in the theoretical debate, current architectures for archival representation remain behind. Finding aids privilege a single point of view and do not allow subsequent users to embed their own, potentially conflicting, readings. Using semantic web technologies this study aims to define a conceptual model for writers' archives based on existing and widely adopted models in the cultural heritage and humanities domains. The model developed can be used to represent different types of documents at various levels of analysis, as well as record content and components. It also enables the representation of complex relationships and the incorporation of additional layers of interpretation into the finding aid, transforming it from a static search tool into a dynamic research platform.  The personal archive and library of Giuseppe Raimondi serves as a case study for the creation of an archival knowledge base using the proposed conceptual model. By querying the knowledge graph through SPARQL, the effectiveness of the model is evaluated. The results demonstrate that the model addresses the primary representation challenges identified in archival literature, from both a technological and methodological standpoint. The ultimate goal is to bring the output par excellence of archival science, i.e. the finding aid, more in line with the latest developments in archival thinking.