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.

Le strategie di internazionalizzazione delle imprese distrettuali: un'analisi comparata di tre diversi sistemi locali di produzione in Emilia Romagna

Since the Nineties, the process of globalization has caused a sharp increase in the real and financial integration of the worldwide economy, reducing the obstacles to international trade and minimizing the cost of transaction. The entrance of foreign firms in the domestic market has deeply modified the competitive situation of Italian enterprises, which have been forced to change their strategies in order to cope with those of the new competitors. In this scenario, internationalization is no longer one of the different strategic options available for the firm, but it becomes a forced choice to maintain or acquire a competitive advantage sustainable over time. Internationalization strategies of SMEs, however, are hindered by the shortage of financial resources and entrepreneurial skills, therefore this kind of firms tends toward light forms of foreign expansion, like export and subcontracting. Despite this, many studies have demonstrated that the district localisation increases the firms’ productivity and innovative capacity, so their competiveness both at a domestic and international level. The majority of these empirical contributions has focused mainly on the analysis of commercial flows, confirming that district enterprises reach a superior international performance compared to their external competitors. On the contrary, only few works have tried to evaluate the existence of a district effect on the firms’ ability to invest abroad, but the obtained results are not straightforward. One of the reason of these conclusions is that the phenomena has been analysed without taking into account the differences existing between districts in terms of enterprises’ dimension, diffusion of industrial groups and, above all, the sector of productive specialization, because the technological content of production could improve the innovativeness of district firms, allowing them to adopt advanced forms of internationalisation as foreign direct investments (FDI). The aim of the thesis is to further investigate the district effect on internationalisation, trough an econometric analysis of the international strategies carried out by firms localised in three different local system of production characterised by different technological specialization.

La cooperazione agroalimentare associata in Italia: dimensioni, caratteristiche e comportamenti, con focalizzazione sull'impresa cooperativa orientata all'export

La tesi compie un'analisi sul ruolo della cooperazione nei mercati esteri, focalizzandosi, da un lato, sullo studio dei flussi di export nei settori dell'agroalimentare caratterizzati da una forte presenza cooperativa e, dall'altro, sulle caratteristiche di struttura ed i comportamenti delle imprese cooperative esportatrici e non esportatrici. A tal fine è stata realizzata un'indagine diretta che ha coinvolto un campione di 516 cooperative agroalimentari, delle quali 162 esportatrici e 354 non esportatrici. Sulla base dei risultati dell'indagine è stato possibile analizzare le caratteristiche strutturali ed i comportamenti delle cooperative non esportatrici ed esportatrici, focalizzandosi successivamente sulle modalità  di accesso al mercato estero delle cooperative esportatrici ed infine approfondendo le motivazioni che ostacolano l'export nelle cooperative non esportatrici.

International Agricultural Trade under Regulatory Asymmetry: An Economic Analysis of SME Export Behavior

Over the last three decades, international agricultural trade has grown significantly. Technological advances in transportation logistics and storage have created opportunities to ship anything almost anywhere. Bilateral and multilateral trade agreements have also opened new pathways to an increasingly global market place. Yet, international agricultural trade is often constrained by differences in regulatory regimes. The impact of “regulatory asymmetry” is particularly acute for small and medium sized enterprises (SMEs) that lack resources and expertise to successfully operate in markets that have substantially different regulatory structures. As governments seek to encourage the development of SMEs, policy makers often confront the critical question of what ultimately motivates SME export behavior. Specifically, there is considerable interest in understanding how SMEs confront the challenges of regulatory asymmetry. Neoclassical models of the firm generally emphasize expected profit maximization under uncertainty, however these approaches do not adequately explain the entrepreneurial decision under regulatory asymmetry. Behavioral theories of the firm offer a far richer understanding of decision making by taking into account aspirations and adaptive performance in risky environments. This paper develops an analytical framework for decision making of a single agent. Considering risk, uncertainty and opportunity cost, the analysis focuses on the export behavior response of an SME in a situation of regulatory asymmetry. Drawing on the experience of fruit processor in Muzaffarpur, India, who must consider different regulatory environments when shipping fruit treated with sulfur dioxide, the study dissects the firm-level decision using @Risk, a Monte Carlo computational tool.

Export Supply Chain Organization and Food Safety and Quality Standards: a case study of the Moroccan Fruit and Vegetable Sector

Agri-food supply chains extend beyond national boundaries, partially facilitated by a policy environment that encourages more liberal international trade. Rising concentration within the downstream sector has driven a shift towards “buyer-driven” global value chains (GVCs) extending internationally with global sourcing and the emergence of multinational key economic players that compete with increase emphasis on product quality attributes. Agri-food systems are thus increasingly governed by a range of inter-related public and private standards, both of which are becoming a priori mandatory, especially in supply chains for high-value and quality-differentiated agri-food products and tend to strongly affect upstream agricultural practices, firms’ internal organization and strategic behaviour and to shape the food chain organization. Notably, increasing attention has been given to the impact of SPS measures on agri-food trade and notably on developing countries’ export performance. Food and agricultural trade is the vital link in the mutual dependency of the global trade system and developing countries. Hence, developing countries derive a substantial portion of their income from food and agricultural trade. In Morocco, fruit and vegetable (especially fresh) are the primary agricultural export. Because of the labor intensity, this sector (especially citrus and tomato) is particularly important in terms of income and employment generation, especially for the female laborers hired in the farms and packing houses. Hence, the emergence of agricultural and agrifood product safety issues and the subsequent tightening of market requirements have challenged mutual gains due to the lack of technical and financial capacities of most developing countries.

A new global wheat marketmodel (GLOWMM) for the analysis of wheat export prices

Food commodity prices fluctuations have important impacts on poverty and food insecurity across the world. Conventional models have not provided a complete picture of recent price spikes in agricultural commodity markets, while there is an urgent need for appropriate policy responses. Perhaps new approaches are needed in order to better understand international spill-overs, the feedback between the real and the financial sectors and also the link between food and energy prices. In this paper, we present results from a new worldwide dynamic model that provides short and long-run impulse responses of wheat international prices to various real shocks.

Silk Fibroin: a biopolymer platform for innovative pharmaceutical formulation and biomedical devices.

The protein silk fibroin (SF) from the silkworm Bombyx mori is a FDA-approved biomaterial used over centuries as sutures wire. Importantly, several evidences highlighted the potential of silk biomaterials obtained by using so-called regenerated silk fibroin (RSF) in biomedicine, tissue engineering and drug delivery. Indeed, by a water-based protocol, it is possible to obtain protein water-solution, by extraction and purification of fibroin from silk fibres. Notably, RSF can be processed in a variety of biomaterials forms used in biomedical and technological fields, displaying remarkable properties such as biocompatibility, controllable biodegradability, optical transparency, mechanical robustness. Moreover, RSF biomaterials can be doped and/or chemical functionalized with drugs, optically active molecules, growth factors and/or chemicals In this view, activities of my PhD research program were focused to standardize the process of extraction and purification of protein to get the best physical and chemical characteristics. The analysis of the chemo-physical properties of the fibroin involved both the RSF water-solution and the protein processed in film. Chemo-physical properties have been studied through: vibrational (FT-IR and Raman-FT) and optical (absorption and emission UV-VIS) spectroscopy, nuclear magnetic resonance (1H and 13C NMR), thermal analysis and thermo-gravimetric scan (DSC and TGA). In the last year of my PhD, activities were focused to study and define innovative methods of functionalization of the silk fibroin solution and films. Indeed, research program was the application of different methods of manufacturing approaches of the films of fibroin without the use of harsh treatments and organic solvents. New approaches to doping and chemical functionalization of the silk fibroin were studied. Two different methods have been identified: 1) biodoping that consists in the doping of fibroin with optically active molecules through the addition of fluorescent molecules in the standard diet used for the breeding of silkworms; 2) chemical functionalization via silylation.