The Design of XML-Based Model and Experiment Description Languages for Network Simulation

The Simulation Automation Framework for Experiments (SAFE) is a project created to raise the level of abstraction in network simulation tools and thereby address issues that undermine credibility. SAFE incorporates best practices in network simulationto automate the experimental process and to guide users in the development of sound scientific studies using the popular ns-3 network simulator. My contributions to the SAFE project: the design of two XML-based languages called NEDL (ns-3 Experiment Description Language) and NSTL (ns-3 Script Templating Language), which facilitate the description of experiments and network simulationmodels, respectively. The languages provide a foundation for the construction of better interfaces between the user and the ns-3 simulator. They also provide input to a mechanism which automates the execution of network simulation experiments. Additionally,this thesis demonstrates that one can develop tools to generate ns-3 scripts in Python or C++ automatically from NSTL model descriptions

Automatic Selection of Statistical Model Checkers for Analysis of Biological Models

Statistical Model Checking (SMC) blends the speed of simulation with the rigorous analytical capabilities of model checking, and its success has prompted researchers to implement a number of SMC tools whose availability provides flexibility and fine-tuned control over model analysis. However, each tool has its own practical limitations, and different tools have different requirements and performance characteristics. The performance of different tools may also depend on the specific features of the input model or the type of query to be verified. Consequently, choosing the most suitable tool for verifying any given model requires a significant degree of experience, and in most cases, it is challenging to predict the right one. The aim of our research has been to simplify the model checking process for researchers in biological systems modelling by simplifying and rationalising the model selection process. This has been achieved through delivery of the various key contributions listed below. • We have developed a software component for verification of kernel P (kP) system models, using the NuSMV model checker. We integrated it into a larger software platform (www.kpworkbench.org). • We surveyed five popular SMC tools, comparing their modelling languages, external dependencies, expressibility of specification languages, and performance. To best of our knowledge, this is the first known attempt to categorise the performance of SMC tools based on the commonly used property specifications (property patterns) for model checking. • We have proposed a set of model features which can be used for predicting the fastest SMC for biological model verification, and have shown, moreover, that the proposed features both reduce computation time and increase predictive power. • We used machine learning algorithms for predicting the fastest SMC tool for verification of biological models, and have shown that this approach can successfully predict the fastest SMC tool with over 90% accuracy. • We have developed a software tool, SMC Predictor, that predicts the fastest SMC tool for a given model and property query, and have made this freely available to the wider research community (www.smcpredictor.com). Our results show that using our methodology can generate significant savings in the amount of time and resources required for model verification

Computational Efficiency of P Systems with Symport/Antiport Rules and Membrane Separation

Membrane ssion is a process by which a biological membrane is split into two new ones in such a way that the contents of the initial membrane is separated and distributed between the new membranes. Inspired by this biological phenomenon, membrane separation rules were considered in membrane computing. In this paper we deal with celllike P systems with membrane separation rules that use symport/antiport rules (such systems compute by changing the places of objects with respect to the membranes, and not by changing the objects themselves) as communication rules. Speci cally we study a lower bound on the length of communication rules with respect to the computational e ciency of such kind of membrane systems; that is, their ability to solve computationally hard problems in polynomial time by trading space for time. The main result of this paper is the following: communication rules involving at most three objects is enough to achieve the computational e ciency of P systems with membrane separation. Thus, a polynomial time solution to SAT problem is provided in this computing framework. It is known that only problems in P can be solved in polynomial time by using minimal cooperation in communication rules and membrane separation, so the lower bound of the e ciency obtained is an optimal bound.Ministerio de Economía y Competitividad TIN2012-3743

Image Processing and Simulation Toolboxes of Microscopy Images of Bacterial Cells

Recent advances in microscopy imaging technology have allowed the characterization of the dynamics of cellular processes at the single-cell and single-molecule level. Particularly in bacterial cell studies, and using the E. coli as a case study, these techniques have been used to detect and track internal cell structures such as the Nucleoid and the Cell Wall and fluorescently tagged molecular aggregates such as FtsZ proteins, Min system proteins, inclusion bodies and all the different types of RNA molecules. These studies have been performed with using multi-modal, multi-process, time-lapse microscopy, producing both morphological and functional images. To facilitate the finding of relationships between cellular processes, from small-scale, such as gene expression, to large-scale, such as cell division, an image processing toolbox was implemented with several automatic and/or manual features such as, cell segmentation and tracking, intra-modal and intra-modal image registration, as well as the detection, counting and characterization of several cellular components. Two segmentation algorithms of cellular component were implemented, the first one based on the Gaussian Distribution and the second based on Thresholding and morphological structuring functions. These algorithms were used to perform the segmentation of Nucleoids and to identify the different stages of FtsZ Ring formation (allied with the use of machine learning algorithms), which allowed to understand how the temperature influences the physical properties of the Nucleoid and correlated those properties with the exclusion of protein aggregates from the center of the cell. Another study used the segmentation algorithms to study how the temperature affects the formation of the FtsZ Ring. The validation of the developed image processing methods and techniques has been based on benchmark databases manually produced and curated by experts. When dealing with thousands of cells and hundreds of images, these manually generated datasets can become the biggest cost in a research project. To expedite these studies in terms of time and lower the cost of the manual labour, an image simulation was implemented to generate realistic artificial images. The proposed image simulation toolbox can generate biologically inspired objects that mimic the spatial and temporal organization of bacterial cells and their processes, such as cell growth and division and cell motility, and cell morphology (shape, size and cluster organization). The image simulation toolbox was shown to be useful in the validation of three cell tracking algorithms: Simple Nearest-Neighbour, Nearest-Neighbour with Morphology and DBSCAN cluster identification algorithm. It was shown that the Simple Nearest-Neighbour still performed with great reliability when simulating objects with small velocities, while the other algorithms performed better for higher velocities and when there were larger clusters present

Feasibility study for a numerical aerodynamic simulation facility. Volume 1

A Numerical Aerodynamic Simulation Facility (NASF) was designed for the simulation of fluid flow around three-dimensional bodies, both in wind tunnel environments and in free space. The application of numerical simulation to this field of endeavor promised to yield economies in aerodynamic and aircraft body designs. A model for a NASF/FMP (Flow Model Processor) ensemble using a possible approach to meeting NASF goals is presented. The computer hardware and software are presented, along with the entire design and performance analysis and evaluation

Model-driven dual caching For nomadic service-oriented architecture clients

Mobile devices have evolved over the years from resource constrained devices that supported only the most basic tasks to powerful handheld computing devices. However, the most significant step in the evolution of mobile devices was the introduction of wireless connectivity which enabled them to host applications that require internet connectivity such as email, web browsers and maybe most importantly smart/rich clients. Being able to host smart clients allows the users of mobile devices to seamlessly access the Information Technology (IT) resources of their organizations. One increasingly popular way of enabling access to IT resources is by using Web Services (WS). This trend has been aided by the rapid availability of WS packages/tools, most notably the efforts of the Apache group and Integrated Development Environment (IDE) vendors. But the widespread use of WS raises questions for users of mobile devices such as laptops or PDAs; how and if they can participate in WS. Unlike their “wired” counterparts (desktop computers and servers) they rely on a wireless network that is characterized by low bandwidth and unreliable connectivity.The aim of this thesis is to enable mobile devices to host Web Services consumers. It introduces a Model-Driven Dual Caching (MDDC) approach to overcome problems arising from temporarily loss of connectivity and fluctuations in bandwidth

Algorithms and Software for Biological MP Modeling by Statistical and Optimization Techniques

I sistemi biologici sono gruppi di entit\ue0 biologiche (es. molecole ed organismi), che interagiscono producendo specifiche dinamiche. Questi sistemi sono solitamente caratterizzati da una elevata complessit\ue0 perch\ue8 coinvolgono un elevato numero di componenti con molte interconnessioni. La comprensione dei meccanismi che governano i sistemi biologici e la previsione dei loro comportamenti in condizioni normali e patologiche \ue8 una sfida cruciale della biologia dei sistemi (in inglese detta systems biology), un'area di ricerca al confine tra biologia, medicina, matematica ed informatica. In questa tesi i P sistemi metabolici, detti brevemente sistemi MP, sono stati utilizzati come modello discreto per l'analisi di dinamiche biologiche. Essi sono una classe deterministica dei P sistemi classici, che utilizzano regole di riscrittura per rappresentare le reazioni chimiche e "funzioni di regolazioni di flusso" per regolare la reattivit\ue0 di ciascuna reazione rispetto alla quantita' di sostanze presenti istantaneamente nel sistema. Dopo un excursus sulla letteratura relativa ad alcuni modelli convenzionali (come le equazioni differenziali ed i modelli stocastici proposti da Gillespie) e non-convenzionali (come i P sistemi ed i P sistemi metabolici), saranno presentati i risultati della mia ricerca. Essi riguardano tre argomenti principali: i) l'equivalenza tra sistemi MP e reti di Petri ibride funzionali, ii) le prospettive statistiche e di ottimizzazione nella generazione di sistemi MP a partire da dati sperimentali, iii) lo sviluppo di un laboratorio virtuale chiamato MetaPlab, un software Java basato sui sistemi MP. L'equivalenza tra i sistemi MP e le reti di Petri ibride funzionali \ue8 stata dimostrata per mezzo di due teoremi ed alcuni esperimenti al computer per il caso di studio del meccanismo regolativo del gene operone lac nella pathway glicolitica. Il secondo argomento di ricerca concerne nuovi approcci per la sintesi delle funzioni di regolazione di flusso. La regressione stepwise e le reti neurali sono state impiegate come approssimatori di funzioni, mentre algoritmi di ottimizzazione classici ed evolutivi (es. backpropagation, algoritmi genetici, particle swarm optimization ed algoritmi memetici) sono stati impiegati per l'addestramento dei modelli. Una completo workflow per l'analisi dei dati sperimentali \ue8 stato presentato. Esso gestisce ed indirizza l'intero processo di sintesi delle funzioni di regolazione, dalla preparazione dei dati alla selezione delle variabili, fino alla generazione dei modelli ed alla loro validazione. Le metodologie proposte sono state testate con successo tramite esperimenti al computer sui casi di studio dell'oscillatore mitotico negli embrioni anfibi e del non photochemical quenching (NPQ). L'ultimo tema di ricerca \ue8 infine piu' applicativo e riguarda la progettazione e lo sviluppo di una architettura Java basata su plugin e di una serie di plugin che consentono di automatizzare varie fasi del processo di modellazione con sistemi MP, come la simulazione di dinamiche, la determinazione dei flussi e la generazione delle funzioni di regolazione.Biological systems are groups of biological entities, (e.g., molecules and organisms), that interact together producing specific dynamics. These systems are usually characterized by a high complexity, since they involve a large number of components having many interconnections. Understanding biological system mechanisms, and predicting their behaviors in normal and pathological conditions is a crucial challenge in systems biology, which is a central research area on the border among biology, medicine, mathematics and computer science. In this thesis metabolic P systems, also called MP systems, have been employed as discrete modeling framework for the analysis of biological system dynamics. They are a deterministic class of P systems employing rewriting rules to represent chemical reactions and "flux regulation functions" to tune reactions reactivity according to the amount of substances present in the system. After an excursus on the literature about some conventional (i.e., differential equations, Gillespie's models) and unconventional (i.e., P systems and metabolic P systems) modeling frameworks, the results of my research are presented. They concern three research topics: i) equivalences between MP systems and hybrid functional Petri nets, ii) statistical and optimization perspectives in the generation of MP models from experimental data, iii) development of the virtual laboratory MetaPlab, a Java software based on MP systems. The equivalence between MP systems and hybrid functional Petri nets is proved by two theorems and some in silico experiments for the case study of the lac operon gene regulatory mechanism and glycolytic pathway. The second topic concerns new approaches to the synthesis of flux regulation functions. Stepwise linear regression and neural networks are employed as function approximators, and classical/evolutionary optimization algorithms (e.g., backpropagation, genetic algorithms, particle swarm optimization, memetic algorithms) as learning techniques. A complete pipeline for data analysis is also presented, which addresses the entire process of flux regulation function synthesis, from data preparation to feature selection, model generation and statistical validation. The proposed methodologies have been successfully tested by means of in silico experiments on the mitotic oscillator in early amphibian embryos and the non photochemical quenching (NPQ). The last research topic is more applicative, and pertains the design and development of a Java plugin architecture and several plugins which enable to automatize many tasks related to MP modeling, such as, dynamics computation, flux discovery, and regulation function synthesis

Towards secure computation for people

My research investigates three questions: How do we customize protocols and implementations to account for the unique requirement of each setting and its target community, what are necessary steps that we can take to transition secure computation tools into practice, and how can we promote their adoption for users at large? In this dissertation I present several of my works that address these three questions with a particular focus on one of them. First my work on "Hecate: Abuse Reporting in Secure Messengers with Sealed Sender" designs a customized protocol to protect people from abuse and surveillance in online end to end encrypted messaging. Our key insight is to add pre-processing to asymmetric message franking, where the moderating entity can generate batches of tokens per user during off-peak hours that can later be deposited when reporting abuse. This thesis then demonstrates that by carefully tailoring our cryptographic protocols for real world use cases, we can achieve orders of magnitude improvements over prior works with minimal assumptions over the resources available to people. Second, my work on "Batched Differentially Private Information Retrieval" contributes a novel Private Information Retrieval (PIR) protocol called DP-PIR that is designed to provide high throughput at high query rates. It does so by pushing all public key operations into an offline stage, batching queries from multiple clients via techniques similar to mixnets, and maintain differential privacy guarantees over the access patterns of the database. Finally, I provide three case studies showing that we cannot hope to further the adoption of cryptographic tools in practice without collaborating with the very people we are trying to protect. I discuss a pilot deployment of secure multi-party computation (MPC) that I have done with the Department of Education, deployments of MPC I have done for the Boston Women’s Workforce Council and the Greater Boston Chamber of Commerce, and ongoing work in developing tool chain support for MPC via an automated resource estimation tool called Carousels