Design and implementation of bioinformatics tools for large scale genome annotation

The continuous increase of genome sequencing projects produced a huge amount of data in the last 10 years: currently more than 600 prokaryotic and 80 eukaryotic genomes are fully sequenced and publically available. However the sole sequencing process of a genome is able to determine just raw nucleotide sequences. This is only the first step of the genome annotation process that will deal with the issue of assigning biological information to each sequence. The annotation process is done at each different level of the biological information processing mechanism, from DNA to protein, and cannot be accomplished only by in vitro analysis procedures resulting extremely expensive and time consuming when applied at a this large scale level. Thus, in silico methods need to be used to accomplish the task. The aim of this work was the implementation of predictive computational methods to allow a fast, reliable, and automated annotation of genomes and proteins starting from aminoacidic sequences. The first part of the work was focused on the implementation of a new machine learning based method for the prediction of the subcellular localization of soluble eukaryotic proteins. The method is called BaCelLo, and was developed in 2006. The main peculiarity of the method is to be independent from biases present in the training dataset, which causes the over‐prediction of the most represented examples in all the other available predictors developed so far. This important result was achieved by a modification, made by myself, to the standard Support Vector Machine (SVM) algorithm with the creation of the so called Balanced SVM. BaCelLo is able to predict the most important subcellular localizations in eukaryotic cells and three, kingdom‐specific, predictors were implemented. In two extensive comparisons, carried out in 2006 and 2008, BaCelLo reported to outperform all the currently available state‐of‐the‐art methods for this prediction task. BaCelLo was subsequently used to completely annotate 5 eukaryotic genomes, by integrating it in a pipeline of predictors developed at the Bologna Biocomputing group by Dr. Pier Luigi Martelli and Dr. Piero Fariselli. An online database, called eSLDB, was developed by integrating, for each aminoacidic sequence extracted from the genome, the predicted subcellular localization merged with experimental and similarity‐based annotations. In the second part of the work a new, machine learning based, method was implemented for the prediction of GPI‐anchored proteins. Basically the method is able to efficiently predict from the raw aminoacidic sequence both the presence of the GPI‐anchor (by means of an SVM), and the position in the sequence of the post‐translational modification event, the so called ω‐site (by means of an Hidden Markov Model (HMM)). The method is called GPIPE and reported to greatly enhance the prediction performances of GPI‐anchored proteins over all the previously developed methods. GPIPE was able to predict up to 88% of the experimentally annotated GPI‐anchored proteins by maintaining a rate of false positive prediction as low as 0.1%. GPIPE was used to completely annotate 81 eukaryotic genomes, and more than 15000 putative GPI‐anchored proteins were predicted, 561 of which are found in H. sapiens. In average 1% of a proteome is predicted as GPI‐anchored. A statistical analysis was performed onto the composition of the regions surrounding the ω‐site that allowed the definition of specific aminoacidic abundances in the different considered regions. Furthermore the hypothesis that compositional biases are present among the four major eukaryotic kingdoms, proposed in literature, was tested and rejected. All the developed predictors and databases are freely available at: BaCelLo http://gpcr.biocomp.unibo.it/bacello eSLDB http://gpcr.biocomp.unibo.it/esldb GPIPE http://gpcr.biocomp.unibo.it/gpipe

Interactions between normative systems and software cognitive agents. A formalization in temporal modal defeasible logic and its implementation

Sustainable computer systems require some flexibility to adapt to environmental unpredictable changes. A solution lies in autonomous software agents which can adapt autonomously to their environments. Though autonomy allows agents to decide which behavior to adopt, a disadvantage is a lack of control, and as a side effect even untrustworthiness: we want to keep some control over such autonomous agents. How to control autonomous agents while respecting their autonomy? A solution is to regulate agents’ behavior by norms. The normative paradigm makes it possible to control autonomous agents while respecting their autonomy, limiting untrustworthiness and augmenting system compliance. It can also facilitate the design of the system, for example, by regulating the coordination among agents. However, an autonomous agent will follow norms or violate them in some conditions. What are the conditions in which a norm is binding upon an agent? While autonomy is regarded as the driving force behind the normative paradigm, cognitive agents provide a basis for modeling the bindingness of norms. In order to cope with the complexity of the modeling of cognitive agents and normative bindingness, we adopt an intentional stance. Since agents are embedded into a dynamic environment, things may not pass at the same instant. Accordingly, our cognitive model is extended to account for some temporal aspects. Special attention is given to the temporal peculiarities of the legal domain such as, among others, the time in force and the time in efficacy of provisions. Some types of normative modifications are also discussed in the framework. It is noteworthy that our temporal account of legal reasoning is integrated to our commonsense temporal account of cognition. As our intention is to build sustainable reasoning systems running unpredictable environment, we adopt a declarative representation of knowledge. A declarative representation of norms will make it easier to update their system representation, thus facilitating system maintenance; and to improve system transparency, thus easing system governance. Since agents are bounded and are embedded into unpredictable environments, and since conflicts may appear amongst mental states and norms, agent reasoning has to be defeasible, i.e. new pieces of information can invalidate formerly derivable conclusions. In this dissertation, our model is formalized into a non-monotonic logic, namely into a temporal modal defeasible logic, in order to account for the interactions between normative systems and software cognitive agents.

Sviluppo di un sistema miniaturizzato per il controllo real-time di assetto di nano e microsatelliti

Microsatelliti e nanosatelliti, come ad esempio i Cubesat, sono carenti di sistemi integrati di controllo d’assetto e di manovra orbitale. Lo scopo di questa tesi è stato quello di realizzare un sistema compatibile con Cubesat di una unità, completo di attuatori magnetici e attuatori meccanici, comprendente tutti i sensori e l’elettronica necessaria per il suo funzionamento, creando un dispositivo totalmente indipendente dal veicolo su cui è installato, capace di funzionare sia autonomamente che ricevendo comandi da terra. Nella tesi sono descritte le campagne di simulazioni numeriche effettuate per validare le scelte tecnologiche effettuate, le fasi di sviluppo dell’elettronica e della meccanica, i test sui prototipi realizzati e il funzionamento del sistema finale. Una integrazione così estrema dei componenti può implicare delle interferenze tra un dispositivo e l’altro, come nel caso dei magnetotorquer e dei magnetometri. Sono stati quindi studiati e valutati gli effetti della loro interazione, verificandone l’entità e la validità del progetto. Poiché i componenti utilizzati sono tutti di basso costo e di derivazione terrestre, è stata effettuata una breve introduzione teorica agli effetti dell’ambiente spaziale sull’elettronica, per poi descrivere un sistema fault-tolerant basato su nuove teorie costruttive. Questo sistema è stato realizzato e testato, verificando così la possibilità di realizzare un controller affidabile e resistente all’ambiente spaziale per il sistema di controllo d’assetto. Sono state infine analizzate alcune possibili versioni avanzate del sistema, delineandone i principali aspetti progettuali, come ad esempio l’integrazione di GPS e l’implementazione di funzioni di determinazione d’assetto sfruttando i sensori presenti a bordo.

Cache-aware development of high integrity real-time systems

Cost, performance and availability considerations are forcing even the most conservative high-integrity embedded real-time systems industry to migrate from simple hardware processors to ones equipped with caches and other acceleration features. This migration disrupts the practices and solutions that industry had developed and consolidated over the years to perform timing analysis. Industry that are confident with the efficiency/effectiveness of their verification and validation processes for old-generation processors, do not have sufficient insight on the effects of the migration to cache-equipped processors. Caches are perceived as an additional source of complexity, which has potential for shattering the guarantees of cost- and schedule-constrained qualification of their systems. The current industrial approach to timing analysis is ill-equipped to cope with the variability incurred by caches. Conversely, the application of advanced WCET analysis techniques on real-world industrial software, developed without analysability in mind, is hardly feasible. We propose a development approach aimed at minimising the cache jitters, as well as at enabling the application of advanced WCET analysis techniques to industrial systems. Our approach builds on:(i) identification of those software constructs that may impede or complicate timing analysis in industrial-scale systems; (ii) elaboration of practical means, under the model-driven engineering (MDE) paradigm, to enforce the automated generation of software that is analyzable by construction; (iii) implementation of a layout optimisation method to remove cache jitters stemming from the software layout in memory, with the intent of facilitating incremental software development, which is of high strategic interest to industry. The integration of those constituents in a structured approach to timing analysis achieves two interesting properties: the resulting software is analysable from the earliest releases onwards - as opposed to becoming so only when the system is final - and more easily amenable to advanced timing analysis by construction, regardless of the system scale and complexity.

Hardware/Software Design of Dynamic Real-Time Schedulers for Embedded Multiprocessor Systems

The new generation of multicore processors opens new perspectives for the design of embedded systems. Multiprocessing, however, poses new challenges to the scheduling of real-time applications, in which the ever-increasing computational demands are constantly flanked by the need of meeting critical time constraints. Many research works have contributed to this field introducing new advanced scheduling algorithms. However, despite many of these works have solidly demonstrated their effectiveness, the actual support for multiprocessor real-time scheduling offered by current operating systems is still very limited. This dissertation deals with implementative aspects of real-time schedulers in modern embedded multiprocessor systems. The first contribution is represented by an open-source scheduling framework, which is capable of realizing complex multiprocessor scheduling policies, such as G-EDF, on conventional operating systems exploiting only their native scheduler from user-space. A set of experimental evaluations compare the proposed solution to other research projects that pursue the same goals by means of kernel modifications, highlighting comparable scheduling performances. The principles that underpin the operation of the framework, originally designed for symmetric multiprocessors, have been further extended first to asymmetric ones, which are subjected to major restrictions such as the lack of support for task migrations, and later to re-programmable hardware architectures (FPGAs). In the latter case, this work introduces a scheduling accelerator, which offloads most of the scheduling operations to the hardware and exhibits extremely low scheduling jitter. The realization of a portable scheduling framework presented many interesting software challenges. One of these has been represented by timekeeping. In this regard, a further contribution is represented by a novel data structure, called addressable binary heap (ABH). Such ABH, which is conceptually a pointer-based implementation of a binary heap, shows very interesting average and worst-case performances when addressing the problem of tick-less timekeeping of high-resolution timers.

Ground penetrating radar early-time technique for soil electromagnetic parameters estimation

In recent years, thanks to the technological advances, electromagnetic methods for non-invasive shallow subsurface characterization have been increasingly used in many areas of environmental and geoscience applications. Among all the geophysical electromagnetic methods, the Ground Penetrating Radar (GPR) has received unprecedented attention over the last few decades due to its capability to obtain, spatially and temporally, high-resolution electromagnetic parameter information thanks to its versatility, its handling, its non-invasive nature, its high resolving power, and its fast implementation. The main focus of this thesis is to perform a dielectric site characterization in an efficient and accurate way studying in-depth a physical phenomenon behind a recent developed GPR approach, the so-called early-time technique, which infers the electrical properties of the soil in the proximity of the antennas. In particular, the early-time approach is based on the amplitude analysis of the early-time portion of the GPR waveform using a fixed-offset ground-coupled antenna configuration where the separation between the transmitting and receiving antenna is on the order of the dominant pulse-wavelength. Amplitude information can be extracted from the early-time signal through complex trace analysis, computing the instantaneous-amplitude attributes over a selected time-duration of the early-time signal. Basically, if the acquired GPR signals are considered to represent the real part of a complex trace, and the imaginary part is the quadrature component obtained by applying a Hilbert transform to the GPR trace, the amplitude envelope is the absolute value of the resulting complex trace (also known as the instantaneous-amplitude). Analysing laboratory information, numerical simulations and natural field conditions, and summarising the overall results embodied in this thesis, it is possible to suggest the early-time GPR technique as an effective method to estimate physical properties of the soil in a fast and non-invasive way.

Operating System Contribution to Composable Timing Behaviour in High-Integrity Real-Time Systems

The development of High-Integrity Real-Time Systems has a high footprint in terms of human, material and schedule costs. Factoring functional, reusable logic in the application favors incremental development and contains costs. Yet, achieving incrementality in the timing behavior is a much harder problem. Complex features at all levels of the execution stack, aimed to boost average-case performance, exhibit timing behavior highly dependent on execution history, which wrecks time composability and incrementaility with it. Our goal here is to restitute time composability to the execution stack, working bottom up across it. We first characterize time composability without making assumptions on the system architecture or the software deployment to it. Later, we focus on the role played by the real-time operating system in our pursuit. Initially we consider single-core processors and, becoming less permissive on the admissible hardware features, we devise solutions that restore a convincing degree of time composability. To show what can be done for real, we developed TiCOS, an ARINC-compliant kernel, and re-designed ORK+, a kernel for Ada Ravenscar runtimes. In that work, we added support for limited-preemption to ORK+, an absolute premiere in the landscape of real-word kernels. Our implementation allows resource sharing to co-exist with limited-preemptive scheduling, which extends state of the art. We then turn our attention to multicore architectures, first considering partitioned systems, for which we achieve results close to those obtained for single-core processors. Subsequently, we shy away from the over-provision of those systems and consider less restrictive uses of homogeneous multiprocessors, where the scheduling algorithm is key to high schedulable utilization. To that end we single out RUN, a promising baseline, and extend it to SPRINT, which supports sporadic task sets, hence matches real-world industrial needs better. To corroborate our results we present findings from real-world case studies from avionic industry.