Modelling and simulating in systems biology: an approach based on multi-agent systems

Systems Biology is an innovative way of doing biology recently raised in bio-informatics contexts, characterised by the study of biological systems as complex systems with a strong focus on the system level and on the interaction dimension. In other words, the objective is to understand biological systems as a whole, putting on the foreground not only the study of the individual parts as standalone parts, but also of their interaction and of the global properties that emerge at the system level by means of the interaction among the parts. This thesis focuses on the adoption of multi-agent systems (MAS) as a suitable paradigm for Systems Biology, for developing models and simulation of complex biological systems. Multi-agent system have been recently introduced in informatics context as a suitabe paradigm for modelling and engineering complex systems. Roughly speaking, a MAS can be conceived as a set of autonomous and interacting entities, called agents, situated in some kind of nvironment, where they fruitfully interact and coordinate so as to obtain a coherent global system behaviour. The claim of this work is that the general properties of MAS make them an effective approach for modelling and building simulations of complex biological systems, following the methodological principles identified by Systems Biology. In particular, the thesis focuses on cell populations as biological systems. In order to support the claim, the thesis introduces and describes (i) a MAS-based model conceived for modelling the dynamics of systems of cells interacting inside cell environment called niches. (ii) a computational tool, developed for implementing the models and executing the simulations. The tool is meant to work as a kind of virtual laboratory, on top of which kinds of virtual experiments can be performed, characterised by the definition and execution of specific models implemented as MASs, so as to support the validation, falsification and improvement of the models through the observation and analysis of the simulations. A hematopoietic stem cell system is taken as reference case study for formulating a specific model and executing virtual experiments.

Mobile TuCSoN: theoretical and technological requirements for TuCSoN's porting over Android mobile devices

Communication and coordination are two key-aspects in open distributed agent system, being both responsible for the system’s behaviour integrity. An infrastructure capable to handling these issues, like TuCSoN, should to be able to exploit modern technologies and tools provided by fast software engineering contexts. Thesis aims to demonstrate TuCSoN infrastructure’s abilities to cope new possibilities, hardware and software, offered by mobile technology. The scenarios are going to configure, are related to the distributed nature of multi-agent systems where an agent should be located and runned just on a mobile device. We deal new mobile technology frontiers concerned with smartphones using Android operating system by Google. Analysis and deployment of a distributed agent-based system so described go first to impact with quality and quantity considerations about available resources. Engineering issue at the base of our research is to use TuCSoN against to reduced memory and computing capability of a smartphone, without the loss of functionality, efficiency and integrity for the infrastructure. Thesis work is organized on two fronts simultaneously: the former is the rationalization process of the available hardware and software resources, the latter, totally orthogonal, is the adaptation and optimization process about TuCSoN architecture for an ad-hoc client side release.

Tecnologie e framework per la programmazione multi-agente

Negli ultimi anni le tecnologie informatiche sono state al centro di uno sviluppo esponenziale. Fra le incalcolabili innovazioni presentate, ha preso sempre più campo il paradigma per la programmazione ad agenti, che permette la realizzazione di sistemi software complessi, i quali, nell'informatica moderna, ricoprono un ruolo di fondamentale importanza. Questi sistemi, denominati autonomi, mostrano caratteristiche interessanti per scenari dinamici; essi infatti devono essere robusti e resistenti, in grado di adattarsi al contesto ambientale e quindi reagire a determinate modifiche che si verificano nell'ambiente, comportandosi di conseguenza. Indicano perciò la pro-attività dell'entità presa in considerazione. In questa tesi saranno spiegate queste tipologie di sistemi, introdotte le loro caratteristiche e mostrate le loro potenzialità. Tali caratteristiche permettono di responsabilizzare i soggetti, rendendo il sistema auto-organizzato, con una migliore scalabilità e modularità, riducendo quindi le elevate esigenze di calcolo. L'organizzazione di questo documento prevede i primi capitoli atti a introdurre il mondo dei sistemi autonomi, partendo dalle definizioni di autonomia e di agenti software, concludendo con i sistemi multi-agenti, allo scopo di permettere al lettore una comprensione adatta ed esaustiva. I successivi capitoli riguardano le fasi di progettazione delle entità prese in esame, le loro forme di standardizzazione e i modelli che possono adottare, tra i quali il più conosciuto, il modello BDI. Ne seguono due diverse metodologie per l'ingegneria del software orientata agli agenti. Si conclude con la presentazione dello stato dell'arte degli ambienti di sviluppo conosciuti, contenente un'esauriente introduzione ad ognuno di essi ed una visione nel mondo del lavoro del loro apporto negli applicativi in commercio. Infine la tesi terminerà con un capitolo di conclusioni e di riflessioni sui possibili aspetti futuri.

Synthesis in millireactor system and stability of intermediates for the functionalization of imidazole

This Master thesis presents the results obtained in the curricular traineeship, carried out within the laboratories of the Department of Chemistry of the University of Bergen, during the Erasmus period, and within the Department of Industrial Chemistry of the University of Bologna. The project followed in Bergen concerned the synthesis of key intermediates used for the functionalization of the backbone of imidazole, using N,N'- diiodo-5,5-dimethylhydantoin (“DIH”) as an iodinating agent, and employing an innovative kind of chemical reactor: the “Multijet Oscillating Disc Millireactor” (MJOD Reactor). Afterwards, the work performed in Bologna consisted in verifying the stability in solution of the above mentioned N,N'-diiodo-5,5-dimethylhydantoin utilising spectrophotometric techniques and High Performance Liquid Chromatography analyses (HPLC).