In silico identification of conserved intercoding sequences in Leishmania genomes: Unraveling putative cis-regulatory elements

In silico analyses of Leishmania spp. genome data are a powerful resource to improve the understanding of these pathogens' biology. Trypanosomatids such as Leishmania spp. have their protein-coding genes grouped in long polycistronic units of functionally unrelated genes. The control of gene expression happens by a variety of posttranscriptional mechanisms. The high degree of synteny among Leishmania species is accompanied by highly conserved coding sequences (CDS) and poorly conserved intercoding untranslated sequences. To identify the elements involved in the control of gene expression, we conducted an in silico investigation to find conserved intercoding sequences (CICS) in the genomes of L major, L infantum, and L braziliensis. We used a combination of computational tools, such as Linux-Shell, PERL and R languages, BLAST, MSPcrunch, SSAKE, and Pred-A-Term algorithms to construct a pipeline which was able to: (i) search for conservation in target-regions, (ii) eliminate CICS redundancy and mask repeat elements, (iii) predict the mRNA's extremities, (iv) analyze the distribution of orthologous genes within the generated LeishCICS-clusters, (v) assign GO terms to the LeishCICS-clusters. and (vi) provide statistical support for the gene-enrichment annotation. We associated the LeishCICS-cluster data, generated at the end of the pipeline, with the expression profile oft. donovani genes during promastigote-amastigote differentiation, as previously evaluated by others (GEO accession: GSE21936). A Pearson's correlation coefficient greater than 0.5 was observed for 730 LeishCICS-clusters containing from 2 to 17 genes. The designed computational pipeline is a useful tool and its application identified potential regulatory cis elements and putative regulons in Leishmania. (C) 2012 Elsevier B.V. All rights reserved.

BayGO: Bayesian analysis of ontology term enrichment in microarray data

Abstract Background The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. Results BayGO implements a Bayesian approach to search for enriched terms from microarray data. The R source-code is freely available at http://blasto.iq.usp.br/~tkoide/BayGO in three versions: Linux, which can be easily incorporated into pre-existent pipelines; Windows, to be controlled interactively; and as a web-tool. The software was validated using a bacterial heat shock response dataset, since this stress triggers known system-level responses. Conclusion The Bayesian model accounts for the fact that, eventually, not all the genes from a given category are observable in microarray data due to low intensity signal, quality filters, genes that were not spotted and so on. Moreover, BayGO allows one to measure the statistical association between generic ontology terms and differential expression, instead of working only with the common significance analysis.

Anomalous diffusion evidenced by particle tracking at high frame rates.

Diffusion is a common phenomenon in nature and generally is associated with a system trying to reach a local or a global equilibrium state, as a result of highly irregular individual particle motion. Therefore it is of fundamental importance in physics, chemistry and biology. Particle tracking in complex fluids can reveal important characteristics of its properties. In living cells, we coat the microbead with a peptide (RGD) that binds to integrin receptors at the plasma membrane, which connects to the CSK. This procedure is based on the hypothesis that the microsphere can move only if the structure where it is attached move as well. Then, the observed trajectory of microbeads is a probe of the cytoskeleton (CSK), which is governed by several factors, including thermal diffusion, pressure gradients, and molecular motors. The possibility of separating the trajectories into passive and active diffusion may give information about the viscoelasticity of the cell structure and molecular motors activity. And also we could analyze the motion via generalized Stokes-Einstein relation, avoiding the use of any active techniques. Usually a 12 to 16 Frames Per Second (FPS) system is used to track the microbeads in cell for about 5 minutes. Several factors make this FPS limitation: camera computer communication, light, computer speed for online analysis among others. Here we used a high quality camera and our own software, developed in C++ and Linux, to reach high FPS. Measurements were conducted with samples for 10£ and 20£ objectives. We performed sequentially images with different intervals, all with 2 ¹s exposure. The sequences of intervals are in milliseconds: 4 5 ms (maximum speed) 14, 25, 50 and 100 FPS. Our preliminary results highlight the difference between passive and active diffusion, since the passive diffusion is represented by a Gaussian in the distribution of displacements of the center of mass of individual beads between consecutive frames. However, the active process, or anomalous diffusion, shows as long tails in the distribution of displacements.

Integración de redes de microcontroladores distribuidos basados en bus CAN. Lado microcontrolador

[ES] El principal objetivo de este TFG fue la creación de un protocolo basado en CAN que facilitase la integración de redes de microcontroladores. Dicho protocolo tendría que ser sencillo de usar pero con funcionalidades potentes. Se eligió CAN como base puesto que se trataba de un estándar robusto y ampliamente reconocido. El resultado obtenido fue TouCAN, una librería potente pero amigable al usuario. TouCAN posee dos partes claramente diferenciadas pero estrechamente relacionadas, un lado microcontrolador y un lado supervisor. El lado microncontrolador que es sobre el que versa este TFG, está diseñado sobre Arduino, una tecnología muy en boga actualmente dada la facilidad de desarrollo y a una comunidad entusiasta. El objetivo principal de esta parte es la de interconectar los microcontroladores entre sí mediante el protocolo definido en TouCAN, proporcionando las clases y los métodos necesarios para ello. Por otra parte proporciona una serie de métodos de comunicación por el puerto serie para la interacción con un PC supervisor. El lado supervisor está basado en sistemas UNIX, por lo que es compatible con las diversas distribuciones Linux existentes además de ser fácilmente portables a otros sistemas como Mac OS X. Su principal función es la de servir como supervisor del lado microcontrolador. Conectándose a uno de los nodos maestros es capaz de interactuar con el resto de la red, permitiéndole al usuario comunicarse con sus dispositivos en todo momento. TouCAN tiene el potencial necesario para convertirse en una herramienta libre de amplio uso puesto que es sencillo pero potente, sostenida por una tecnología ampliamente conocida.

Integración de redes de microcontroladores distribuidos basados en bus CAN. Lado supervisor

[ES] El presente TFG tiene por objetivo el desarrollo de una librería que permita al usuario controlar de forma sencilla una red de microcontroladores. Como protocolo de comunicación sobre el que trabajar se ha utilizado el bus CAN, que proporciona una capa para el control de errores, configuración del ancho de banda, gestión de prioridades y protocolo de mensajes. Como resultado al proyecto, se obtiene la librería TouCAN en la cual se establecen dos partes diferenciadas, el lado microcontrolador y el lado supervisor. Cada una de estas partes se desarrollará en un TFG distinto, siendo el lado supervisor el correspondiente a este TFG. El lado microcontrolador se apoyará sobre la plataforma Arduino. En esta parte, se desarrollará la capacidad de conectar diferentes dispositivos de la red de microcontroladores entre sí, definiendo para ello un protocolo de comunicación que permita la realización de comunicaciones síncronas y asíncronas entre los distintos dispositivos de la red. Para dotar al arduino de la capacidad de hacer uso del protocolo bus CAN, se utilizará un Shield destinado a tal fin. El objetivo del supervisor será la integración de la red de microcontroladores con dispositivos de propósito general, tales como un ordenador personal, que permita realizar tareas de control y monitorización de los distintos sistemas empotrados situados en la red. Como sistema operativo utilizado en la elaboración de la librería se utilizó una distribución GNU/Linux. Para la comunicación del dispositivo supervisor con la red de microcontroladores se utilizará el puerto serie disponible en la plataforma Arduino.

Control automatizado de audiencias televisivas

[ES] Actualmente en España existe una única compañía dedicada a la medida de las audiencias televisivas, que realiza mediante la instalación de unos pequeños aparatos en el domicilio de los voluntarios, obteniendo datos de los mismos. Sin embargo, el funcionamiento de estos dispositivos es manual, siendo el usuario el responsable de indicar en todo momento el canal que está espectando y el número de espectadores presentes. Ésto además de una carga, puede suponer una desviación, voluntaria o involuntaria de los datos por parte del usuario. Para mejorar estas funcionalidades, se llevará a cabo un estudio en la aplicación de técnicas de visión por computador en el campo de la medición de audiencias. Durante este estudio se llevará a cabo el desarrollo de un sistema distribuido que permite la captación, análisis y representación de la información obtenida. Este sistema distribuido estará formado por: Una aplicación cliente, encargada de la obtención de los datos sin intervención del usuario a través de técnicas de visión por computador, barajándose las posibilidades de utilizar como base hardware un Smart-T o un mini-pc, sobre los que se ejecutaría un sistema basado en Linux. Esta aplicación se ejecutará, obviamente, en el hogar del usuario. Un servidor, que ejecutará la aplicación encargada de la clasificación y estudio de los datos obtenidos mediante el uso de Bases de Datos, así como su representación a través de una aplicación web para su consulta a través de un navegador.

Desarrollo de un videojuego multiplataforma en Java

[ES] El trabajo consistirá en abordar el desarrollo de un videojuego utilizando el lenguaje de programación Java y una librería especializada en desarrollo de videojuegos. Crearemos un videojuego del género plataformas. Para ello utilizaremos una vista en dos dimensiones, el jugador controlará un personaje humanoide con el que deberá atravesar una serie de niveles. Los niveles estarán agrupados en mundos con distintas temáticas (nieve, espacio, etc.) y en ellos el jugador se encontrará con múltiples obstáculos y enemigos. Los mundos se definen como agrupaciones de diez niveles en las que en el décimo nivel de cada mundo (nivel final) el jugador se enfrenta a un enemigo con una complejidad mayor al resto. Un ejemplo de videojuego de plataformas similar al que se va a desarrollar sería: "Super Mario Bros.". La librería que utilizaremos permite el desarrollo de videojuegos de escritorio y para móviles utilizando el mismo código. Es multiplataforma y soporta Windows, Linux, Mac OS X, Android, iOS, y navegadores con soporte WebGL.

Realizzazione di un modello di router ottico in ambiente open source

Realizzazione di un modello di router ottico in ambiente open source

Sincronizzazione e condivisione di file system tra sistemi operativi

La necessità di sincronizzare i propri dati si presenta in una moltitudine di situazioni, infatti il numero di dispositivi informatici a nostra disposizione è in continua crescita e, all' aumentare del loro numero, cresce l' esigenza di mantenere aggiornate le multiple copie dei dati in essi memorizzati. Vi sono diversi fattori che complicano tale situazione, tra questi la varietà sempre maggiore dei sistemi operativi utilizzati nei diversi dispositivi, si parla di Microsoft Windows, delle tante distribuzioni Linux, di Mac OS X, di Solaris o di altri sistemi operativi UNIX, senza contare i sistemi operativi più orientati al settore mobile come Android. Ogni sistema operativo ha inoltre un modo particolare di gestire i dati, si pensi alla differente gestione dei permessi dei file o alla sensibilità alle maiuscole. Bisogna anche considerare che se gli aggiornamenti dei dati avvenissero soltanto su di uno di questi dispositivi sarebbe richiesta una semplice copia dei dati aggiornati sugli altri dispositivi, ma che non è sempre possibile utilizzare tale approccio. Infatti i dati vengono spesso aggiornati in maniera indipendente in più di un dispositivo, magari nello stesso momento, è pertanto necessario che le applicazioni che si occupano di sincronizzare tali dati riconoscano le situazioni di conflitto, nelle quali gli stessi dati sono stati aggiornati in più di una copia ed in maniera differente, e permettano di risolverle, uniformando lo stato delle repliche. Considerando l' importanza e il valore che possono avere i dati, sia a livello lavorativo che personale, è necessario che tali applicazioni possano garantirne la sicurezza, evitando in ogni caso un loro danneggiamento, perchè sempre più spesso il valore di un dispositivo dipende più dai dati in esso contenuti che dal costo dello hardware. In questa tesi verranno illustrate alcune idee alternative su come possa aver luogo la condivisione e la sincronizzazione di dati tra sistemi operativi diversi, sia nel caso in cui siano installati nello stesso dispositivo che tra dispositivi differenti. La prima parte della tesi descriverà nel dettaglio l' applicativo Unison. Tale applicazione, consente di mantenere sincronizzate tra di loro repliche dei dati, memorizzate in diversi dispositivi che possono anche eseguire sistemi operativi differenti. Unison funziona a livello utente, analizzando separatamente lo stato delle repliche al momento dell' esecuzione, senza cioè mantenere traccia delle operazioni che sono state effettuate sui dati per modificarli dal loro stato precedente a quello attuale. Unison permette la sincronizzazione anche quando i dati siano stati modificati in maniera indipendente su più di un dispositivo, occupandosi di risolvere gli eventuali conflitti che possono verificarsi rispettando la volontà dell' utente. Verranno messe in evidenza le strategie utilizzate dai suoi ideatori per garantire la sicurezza dei dati ad esso affidati e come queste abbiano effetto nelle più diverse condizioni. Verrà poi fornita un' analisi dettagiata di come possa essere utilizzata l' applicazione, fornendo una descrizione accurata delle funzionalità e vari esempi per renderne più chiaro il funzionamento. Nella seconda parte della tesi si descriverà invece come condividere file system tra sistemi operativi diversi all' interno della stessa macchina, si tratta di un approccio diametralmente opposto al precedente, in cui al posto di avere una singola copia dei dati, si manteneva una replica per ogni dispositivo coinvolto. Concentrando l' attenzione sui sistemi operativi Linux e Microsoft Windows verranno descritti approfonditamente gli strumenti utilizzati e illustrate le caratteristiche tecniche sottostanti.

XCSurf: Riprogettazione dell'Interfaccia Utente

Il Progetto XCModel, che da dieci anni si sviluppa e si perfeziona col contributo di varie persone, consente la progettazione di scene 3D e la resa fotorealistica. Esso si appoggia sulle funzionalita' grafiche di X-Window in Linux: si tratta di un ambiente in costante evoluzione, dovuta sia alle continue innovazioni hardware che ai cambiamenti degli standard. XCModel e' composto da vari pacchetti, ognuno dei quali specializzato nel trattare un particolare aspetto della modellazione o della resa (curve, superfici, textures, luci, ...) e che si presentano come applicazioni dotate di una sofisticata interfaccia grafica. Tutte attingono alle funzioni della Libreria XTools, che fornisce numerose primitive grafiche facenti uso delle potenzialita' di X-Window. I recenti cambiamenti nelle specifiche di X-Org, ed in particolare la de- standardizzazione del backing-store, ha obbligato il team di XCModel ad una consistente riprogettazione di XTools e di tutti i pacchetti che su di esso s'appoggiano. S'e' colta l'occasione per un massiccio debugging e per modificare i pacchetti in base alle impressioni emerse nel corso degli anni da parte degli utilizzatori, primi tra tutti gli studenti del corso di Grafica tenuto dal Prof. Giulio Casciola, project-manager di XCModel: questa e' un'ulteriore testimonianza del continuo adattamento e dell'aggiornabilita' del Progetto! Nella fattispecie, ci si occupera' delle modifiche effettuate in particolare al pacchetto XCSurf, finalizzato alla creazione ed alla modifica di curve e superfici 3D da utilizzarsi successivamente per la creazione delle scene: tale pacchetto e' di fatto risultato il pie' avulso dalle specifiche di XTools, il che ha costretto ad un massiccio intervento al codice del programma, ma d'altro canto ha consentito una standardizzazione del pacchetto in linea con gli altri, in particolare ridisegnandone l'interfaccia. Nel primo capitolo si effettuera' una veloce panoramica dell'ambiente XCModel e delle problematiche emerse dai cambiamenti degli standard di X-Window. Il secondo capitolo affrontera' un'ampia analisi dell'hardware, del software e dei paradigmi che caratterizzano la grafica interattiva, e gli ambienti necessari per interagire con essa ed esaminando i vari obiettivi raggiungibili. Infine, il terzo capitolo analizzera' nel dettaglio le modifiche effettuate ai pacchetti di XCModel ed in particolare ad XCSurf per l'adattamento ai nuovi standard, nel rispetto delle politiche e delle linee guida dettate dalla grafica interattiva.

Sistemi riconfigurabili a basso consumo per applicazioni di monitoraggio distribuito

The term Ambient Intelligence (AmI) refers to a vision on the future of the information society where smart, electronic environment are sensitive and responsive to the presence of people and their activities (Context awareness). In an ambient intelligence world, devices work in concert to support people in carrying out their everyday life activities, tasks and rituals in an easy, natural way using information and intelligence that is hidden in the network connecting these devices. This promotes the creation of pervasive environments improving the quality of life of the occupants and enhancing the human experience. AmI stems from the convergence of three key technologies: ubiquitous computing, ubiquitous communication and natural interfaces. Ambient intelligent systems are heterogeneous and require an excellent cooperation between several hardware/software technologies and disciplines, including signal processing, networking and protocols, embedded systems, information management, and distributed algorithms. Since a large amount of fixed and mobile sensors embedded is deployed into the environment, the Wireless Sensor Networks is one of the most relevant enabling technologies for AmI. WSN are complex systems made up of a number of sensor nodes which can be deployed in a target area to sense physical phenomena and communicate with other nodes and base stations. These simple devices typically embed a low power computational unit (microcontrollers, FPGAs etc.), a wireless communication unit, one or more sensors and a some form of energy supply (either batteries or energy scavenger modules). WNS promises of revolutionizing the interactions between the real physical worlds and human beings. Low-cost, low-computational power, low energy consumption and small size are characteristics that must be taken into consideration when designing and dealing with WSNs. To fully exploit the potential of distributed sensing approaches, a set of challengesmust be addressed. Sensor nodes are inherently resource-constrained systems with very low power consumption and small size requirements which enables than to reduce the interference on the physical phenomena sensed and to allow easy and low-cost deployment. They have limited processing speed,storage capacity and communication bandwidth that must be efficiently used to increase the degree of local ”understanding” of the observed phenomena. A particular case of sensor nodes are video sensors. This topic holds strong interest for a wide range of contexts such as military, security, robotics and most recently consumer applications. Vision sensors are extremely effective for medium to long-range sensing because vision provides rich information to human operators. However, image sensors generate a huge amount of data, whichmust be heavily processed before it is transmitted due to the scarce bandwidth capability of radio interfaces. In particular, in video-surveillance, it has been shown that source-side compression is mandatory due to limited bandwidth and delay constraints. Moreover, there is an ample opportunity for performing higher-level processing functions, such as object recognition that has the potential to drastically reduce the required bandwidth (e.g. by transmitting compressed images only when something ‘interesting‘ is detected). The energy cost of image processing must however be carefully minimized. Imaging could play and plays an important role in sensing devices for ambient intelligence. Computer vision can for instance be used for recognising persons and objects and recognising behaviour such as illness and rioting. Having a wireless camera as a camera mote opens the way for distributed scene analysis. More eyes see more than one and a camera system that can observe a scene from multiple directions would be able to overcome occlusion problems and could describe objects in their true 3D appearance. In real-time, these approaches are a recently opened field of research. In this thesis we pay attention to the realities of hardware/software technologies and the design needed to realize systems for distributed monitoring, attempting to propose solutions on open issues and filling the gap between AmI scenarios and hardware reality. The physical implementation of an individual wireless node is constrained by three important metrics which are outlined below. Despite that the design of the sensor network and its sensor nodes is strictly application dependent, a number of constraints should almost always be considered. Among them: • Small form factor to reduce nodes intrusiveness. • Low power consumption to reduce battery size and to extend nodes lifetime. • Low cost for a widespread diffusion. These limitations typically result in the adoption of low power, low cost devices such as low powermicrocontrollers with few kilobytes of RAMand tenth of kilobytes of program memory with whomonly simple data processing algorithms can be implemented. However the overall computational power of the WNS can be very large since the network presents a high degree of parallelism that can be exploited through the adoption of ad-hoc techniques. Furthermore through the fusion of information from the dense mesh of sensors even complex phenomena can be monitored. In this dissertation we present our results in building several AmI applications suitable for a WSN implementation. The work can be divided into two main areas:Low Power Video Sensor Node and Video Processing Alghoritm and Multimodal Surveillance . Low Power Video Sensor Nodes and Video Processing Alghoritms In comparison to scalar sensors, such as temperature, pressure, humidity, velocity, and acceleration sensors, vision sensors generate much higher bandwidth data due to the two-dimensional nature of their pixel array. We have tackled all the constraints listed above and have proposed solutions to overcome the current WSNlimits for Video sensor node. We have designed and developed wireless video sensor nodes focusing on the small size and the flexibility of reuse in different applications. The video nodes target a different design point: the portability (on-board power supply, wireless communication), a scanty power budget (500mW),while still providing a prominent level of intelligence, namely sophisticated classification algorithmand high level of reconfigurability. We developed two different video sensor node: The device architecture of the first one is based on a low-cost low-power FPGA+microcontroller system-on-chip. The second one is based on ARM9 processor. Both systems designed within the above mentioned power envelope could operate in a continuous fashion with Li-Polymer battery pack and solar panel. Novel low power low cost video sensor nodes which, in contrast to sensors that just watch the world, are capable of comprehending the perceived information in order to interpret it locally, are presented. Featuring such intelligence, these nodes would be able to cope with such tasks as recognition of unattended bags in airports, persons carrying potentially dangerous objects, etc.,which normally require a human operator. Vision algorithms for object detection, acquisition like human detection with Support Vector Machine (SVM) classification and abandoned/removed object detection are implemented, described and illustrated on real world data. Multimodal surveillance: In several setup the use of wired video cameras may not be possible. For this reason building an energy efficient wireless vision network for monitoring and surveillance is one of the major efforts in the sensor network community. Energy efficiency for wireless smart camera networks is one of the major efforts in distributed monitoring and surveillance community. For this reason, building an energy efficient wireless vision network for monitoring and surveillance is one of the major efforts in the sensor network community. The Pyroelectric Infra-Red (PIR) sensors have been used to extend the lifetime of a solar-powered video sensor node by providing an energy level dependent trigger to the video camera and the wireless module. Such approach has shown to be able to extend node lifetime and possibly result in continuous operation of the node.Being low-cost, passive (thus low-power) and presenting a limited form factor, PIR sensors are well suited for WSN applications. Moreover techniques to have aggressive power management policies are essential for achieving long-termoperating on standalone distributed cameras needed to improve the power consumption. We have used an adaptive controller like Model Predictive Control (MPC) to help the system to improve the performances outperforming naive power management policies.

Quality of experience in skype video calls

Skype is one of the well-known applications that has guided the evolution of real-time video streaming and has become one of the most used software in everyday life. It provides VoIP audio/video calls as well as messaging chat and file transfer. Many versions are available covering all the principal operating systems like Windows, Macintosh and Linux but also mobile systems. Voice quality decreed Skype success since its birth in 2003 and peer-to-peer architecture has allowed worldwide diffusion. After video call introduction in 2006 Skype became a complete solution to communicate between two or more people. As a primarily video conferencing application, Skype assumes certain characteristics of the delivered video to optimize its perceived quality. However in the last years, and with the recent release of SkypeKit1, many new Skype video-enabled devices came out especially in the mobile world. This forced a change to the traditional recording, streaming and receiving settings allowing for a wide range of network and content dynamics. Video calls are not anymore based on static ‘chatting’ but mobile devices have opened new possibilities and can be used in several scenarios. For instance, lecture streaming or one-to-one mobile video conferences exhibit more dynamics as both caller and callee might be on move. Most of these cases are different from “head&shoulder” only content. Therefore, Skype needs to optimize its video streaming engine to cover more video types. Heterogeneous connections require different behaviors and solutions and Skype must face with this variety to maintain a certain quality independently from connection used. Part of the present work will be focused on analyzing Skype behavior depending on video content. Since Skype protocol is proprietary most of the studies so far have tried to characterize its traffic and to reverse engineer its protocol. However, questions related to the behavior of Skype, especially on quality as perceived by users, remain unanswered. We will study Skype video codecs capabilities and video quality assessment. Another motivation of our work is the design of a mechanism that estimates the perceived cost of network conditions on Skype video delivery. To this extent we will try to assess in an objective way the impact of network impairments on the perceived quality of a Skype video call. Traditional video streaming schemes lack the necessary flexibility and adaptivity that Skype tries to achieve at the edge of a network. Our contribution will lye on a testbed and consequent objective video quality analysis that we will carry out on input videos. We will stream raw video files with Skype via an impaired channel and then we will record it at the receiver side to analyze with objective quality of experience metrics.

Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli

Synthetic Biology is a relatively new discipline, born at the beginning of the New Millennium, that brings the typical engineering approach (abstraction, modularity and standardization) to biotechnology. These principles aim to tame the extreme complexity of the various components and aid the construction of artificial biological systems with specific functions, usually by means of synthetic genetic circuits implemented in bacteria or simple eukaryotes like yeast. The cell becomes a programmable machine and its low-level programming language is made of strings of DNA. This work was performed in collaboration with researchers of the Department of Electrical Engineering of the University of Washington in Seattle and also with a student of the Corso di Laurea Magistrale in Ingegneria Biomedica at the University of Bologna: Marilisa Cortesi. During the collaboration I contributed to a Synthetic Biology project already started in the Klavins Laboratory. In particular, I modeled and subsequently simulated a synthetic genetic circuit that was ideated for the implementation of a multicelled behavior in a growing bacterial microcolony. In the first chapter the foundations of molecular biology are introduced: structure of the nucleic acids, transcription, translation and methods to regulate gene expression. An introduction to Synthetic Biology completes the section. In the second chapter is described the synthetic genetic circuit that was conceived to make spontaneously emerge, from an isogenic microcolony of bacteria, two different groups of cells, termed leaders and followers. The circuit exploits the intrinsic stochasticity of gene expression and intercellular communication via small molecules to break the symmetry in the phenotype of the microcolony. The four modules of the circuit (coin flipper, sender, receiver and follower) and their interactions are then illustrated. In the third chapter is derived the mathematical representation of the various components of the circuit and the several simplifying assumptions are made explicit. Transcription and translation are modeled as a single step and gene expression is function of the intracellular concentration of the various transcription factors that act on the different promoters of the circuit. A list of the various parameters and a justification for their value closes the chapter. In the fourth chapter are described the main characteristics of the gro simulation environment, developed by the Self Organizing Systems Laboratory of the University of Washington. Then, a sensitivity analysis performed to pinpoint the desirable characteristics of the various genetic components is detailed. The sensitivity analysis makes use of a cost function that is based on the fraction of cells in each one of the different possible states at the end of the simulation and the wanted outcome. Thanks to a particular kind of scatter plot, the parameters are ranked. Starting from an initial condition in which all the parameters assume their nominal value, the ranking suggest which parameter to tune in order to reach the goal. Obtaining a microcolony in which almost all the cells are in the follower state and only a few in the leader state seems to be the most difficult task. A small number of leader cells struggle to produce enough signal to turn the rest of the microcolony in the follower state. It is possible to obtain a microcolony in which the majority of cells are followers by increasing as much as possible the production of signal. Reaching the goal of a microcolony that is split in half between leaders and followers is comparatively easy. The best strategy seems to be increasing slightly the production of the enzyme. To end up with a majority of leaders, instead, it is advisable to increase the basal expression of the coin flipper module. At the end of the chapter, a possible future application of the leader election circuit, the spontaneous formation of spatial patterns in a microcolony, is modeled with the finite state machine formalism. The gro simulations provide insights into the genetic components that are needed to implement the behavior. In particular, since both the examples of pattern formation rely on a local version of Leader Election, a short-range communication system is essential. Moreover, new synthetic components that allow to reliably downregulate the growth rate in specific cells without side effects need to be developed. In the appendix are listed the gro code utilized to simulate the model of the circuit, a script in the Python programming language that was used to split the simulations on a Linux cluster and the Matlab code developed to analyze the data.

Applying partial virtualization on ELF binaries through dynamic loaders

The technology of partial virtualization is a revolutionary approach to the world of virtualization. It lies directly in-between full system virtual machines (like QEMU or XEN) and application-related virtual machines (like the JVM or the CLR). The ViewOS project is the flagship of such technique, developed by the Virtual Square laboratory, created to provide an abstract view of the underlying system resources on a per-process basis and work against the principle of the Global View Assumption. Virtual Square provides several different methods to achieve partial virtualization within the ViewOS system, both at user and kernel levels. Each of these approaches have their own advantages and shortcomings. This paper provides an analysis of the different virtualization methods and problems related to both the generic and partial virtualization worlds. This paper is the result of an in-depth study and research for a new technology to be employed to provide partial virtualization based on ELF dynamic binaries. It starts with a mild analysis of currently available virtualization alternatives and then goes on describing the ViewOS system, highlighting its current shortcomings. The vloader project is then proposed as a possible solution to some of these inconveniences with a working proof of concept and examples to outline the potential of such new virtualization technique. By injecting specific code and libraries in the middle of the binary loading mechanism provided by the ELF standard, the vloader project can promote a streamlined and simplified approach to trace system calls. With the advantages outlined in the following paper, this method presents better performance and portability compared to the currently available ViewOS implementations. Furthermore, some of itsdisadvantages are also discussed, along with their possible solutions.

Porting monitor di rete per gestione interfacce su device android.

Il lavoro svolto in questa tesi consiste nell'effettuare il porting del Monitor di rete da Linux ad Android,facente parte di un sistema più complesso conosciuto come ABPS. Il ruolo del monitor è quello di configurare dinamicamente tutte le interfacce di rete disponibili sul dispositivo sul quale lavora,in modo da essere connessi sempre alla miglior rete conosciuta,ad esempio al miglior Access Point nel caso del interfaccia wireless.