Enabling computationally intensive bioinformatics applications on the Grid platform

Bioinformatics is a recent and emerging discipline which aims at studying biological problems through computational approaches. Most branches of bioinformatics such as Genomics, Proteomics and Molecular Dynamics are particularly computationally intensive, requiring huge amount of computational resources for running algorithms of everincreasing complexity over data of everincreasing size. In the search for computational power, the EGEE Grid platform, world's largest community of interconnected clusters load balanced as a whole, seems particularly promising and is considered the new hope for satisfying the everincreasing computational requirements of bioinformatics, as well as physics and other computational sciences. The EGEE platform, however, is rather new and not yet free of problems. In addition, specific requirements of bioinformatics need to be addressed in order to use this new platform effectively for bioinformatics tasks. In my three years' Ph.D. work I addressed numerous aspects of this Grid platform, with particular attention to those needed by the bioinformatics domain. I hence created three major frameworks, Vnas, GridDBManager and SETest, plus an additional smaller standalone solution, to enhance the support for bioinformatics applications in the Grid environment and to reduce the effort needed to create new applications, additionally addressing numerous existing Grid issues and performing a series of optimizations. The Vnas framework is an advanced system for the submission and monitoring of Grid jobs that provides an abstraction with reliability over the Grid platform. In addition, Vnas greatly simplifies the development of new Grid applications by providing a callback system to simplify the creation of arbitrarily complex multistage computational pipelines and provides an abstracted virtual sandbox which bypasses Grid limitations. Vnas also reduces the usage of Grid bandwidth and storage resources by transparently detecting equality of virtual sandbox files based on content, across different submissions, even when performed by different users. BGBlast, evolution of the earlier project GridBlast, now provides a Grid Database Manager (GridDBManager) component for managing and automatically updating biological flatfile databases in the Grid environment. GridDBManager sports very novel features such as an adaptive replication algorithm that constantly optimizes the number of replicas of the managed databases in the Grid environment, balancing between response times (performances) and storage costs according to a programmed cost formula. GridDBManager also provides a very optimized automated management for older versions of the databases based on reverse delta files, which reduces the storage costs required to keep such older versions available in the Grid environment by two orders of magnitude. The SETest framework provides a way to the user to test and regressiontest Python applications completely scattered with side effects (this is a common case with Grid computational pipelines), which could not easily be tested using the more standard methods of unit testing or test cases. The technique is based on a new concept of datasets containing invocations and results of filtered calls. The framework hence significantly accelerates the development of new applications and computational pipelines for the Grid environment, and the efforts required for maintenance. An analysis of the impact of these solutions will be provided in this thesis. This Ph.D. work originated various publications in journals and conference proceedings as reported in the Appendix. Also, I orally presented my work at numerous international conferences related to Grid and bioinformatics.

Enabling Blocks for Integrated CMOS UWB Transceivers

The last decades have seen an unrivaled growth and diffusion of mobile telecommunications. Several standards have been developed to this purposes, from GSM mobile phone communications to WLAN IEEE 802.11, providing different services for the the transmission of signals ranging from voice to high data rate digital communications and Digital Video Broadcasting (DVB). In this wide research and market field, this thesis focuses on Ultra Wideband (UWB) communications, an emerging technology for providing very high data rate transmissions over very short distances. In particular the presented research deals with the circuit design of enabling blocks for MB-OFDM UWB CMOS single-chip transceivers, namely the frequency synthesizer and the transmission mixer and power amplifier. First we discuss three different models for the simulation of chargepump phase-locked loops, namely the continuous time s-domain and discrete time z-domain approximations and the exact semi-analytical time-domain model. The limitations of the two approximated models are analyzed in terms of error in the computed settling time as a function of loop parameters, deriving practical conditions under which the different models are reliable for fast settling PLLs up to fourth order. Besides, a phase noise analysis method based upon the time-domain model is introduced and compared to the results obtained by means of the s-domain model. We compare the three models over the simulation of a fast switching PLL to be integrated in a frequency synthesizer for WiMedia MB-OFDM UWB systems. In the second part, the theoretical analysis is applied to the design of a 60mW 3.4 to 9.2GHz 12 Bands frequency synthesizer for MB-OFDM UWB based on two wide-band PLLs. The design is presented and discussed up to layout level. A test chip has been implemented in TSMC CMOS 90nm technology, measured data is provided. The functionality of the circuit is proved and specifications are met with state-of-the-art area occupation and power consumption. The last part of the thesis deals with the design of a transmission mixer and a power amplifier for MB-OFDM UWB band group 1. The design has been carried on up to layout level in ST Microlectronics 65nm CMOS technology. Main characteristics of the systems are the wideband behavior (1.6 GHz of bandwidth) and the constant behavior over process parameters, temperature and supply voltage thanks to the design of dedicated adaptive biasing circuits.

Enabling Techniques and Algorithms for Integrated Communication and Navigation Satellite Systems

This thesis presents the outcomes of my Ph.D. course in telecommunications engineering. The focus of my research has been on Global Navigation Satellite Systems (GNSS) and in particular on the design of aiding schemes operating both at position and physical level and the evaluation of their feasibility and advantages. Assistance techniques at the position level are considered to enhance receiver availability in challenging scenarios where satellite visibility is limited. Novel positioning techniques relying on peer-to-peer interaction and exchange of information are thus introduced. More specifically two different techniques are proposed: the Pseudorange Sharing Algorithm (PSA), based on the exchange of GNSS data, that allows to obtain coarse positioning where the user has scarce satellite visibility, and the Hybrid approach, which also permits to improve the accuracy of the positioning solution. At the physical level, aiding schemes are investigated to improve the receiver’s ability to synchronize with satellite signals. An innovative code acquisition strategy for dual-band receivers, the Cross-Band Aiding (CBA) technique, is introduced to speed-up initial synchronization by exploiting the exchange of time references between the two bands. In addition vector configurations for code tracking are analyzed and their feedback generation process thoroughly investigated.

Enabling a direct path from end-user specifications to executable protocols in a biology laboratory environment

Biomedical analyses are becoming increasingly complex, with respect to both the type of the data to be produced and the procedures to be executed. This trend is expected to continue in the future. The development of information and protocol management systems that can sustain this challenge is therefore becoming an essential enabling factor for all actors in the field. The use of custom-built solutions that require the biology domain expert to acquire or procure software engineering expertise in the development of the laboratory infrastructure is not fully satisfactory because it incurs undesirable mutual knowledge dependencies between the two camps. We propose instead an infrastructure concept that enables the domain experts to express laboratory protocols using proper domain knowledge, free from the incidence and mediation of the software implementation artefacts. In the system that we propose this is made possible by basing the modelling language on an authoritative domain specific ontology and then using modern model-driven architecture technology to transform the user models in software artefacts ready for execution in a multi-agent based execution platform specialized for biomedical laboratories.