Studies on distributed approaches for large scale multi-criteria protein structure comparison and analysis

Protein Structure Comparison (PSC) is at the core of many important structural biology problems. PSC is used to infer the evolutionary history of distantly related proteins; it can also help in the identification of the biological function of a new protein by comparing it with other proteins whose function has already been annotated; PSC is also a key step in protein structure prediction, because one needs to reliably and efficiently compare tens or hundreds of thousands of decoys (predicted structures) in evaluation of 'native-like' candidates (e.g. Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment). Each of these applications, as well as many others where molecular comparison plays an important role, requires a different notion of similarity, which naturally lead to the Multi-Criteria Protein Structure Comparison (MC-PSC) problem. ProCKSI (www.procksi.org), was the first publicly available server to provide algorithmic solutions for the MC-PSC problem by means of an enhanced structural comparison that relies on the principled application of information fusion to similarity assessments derived from multiple comparison methods (e.g. USM, FAST, MaxCMO, DaliLite, CE and TMAlign). Current MC-PSC works well for moderately sized data sets and it is time consuming as it provides public service to multiple users. Many of the structural bioinformatics applications mentioned above would benefit from the ability to perform, for a dedicated user, thousands or tens of thousands of comparisons through multiple methods in real-time, a capacity beyond our current technology. This research is aimed at the investigation of Grid-styled distributed computing strategies for the solution of the enormous computational challenge inherent in MC-PSC. To this aim a novel distributed algorithm has been designed, implemented and evaluated with different load balancing strategies and selection and configuration of a variety of software tools, services and technologies on different levels of infrastructures ranging from local testbeds to production level eScience infrastructures such as the National Grid Service (NGS). Empirical results of different experiments reporting on the scalability, speedup and efficiency of the overall system are presented and discussed along with the software engineering aspects behind the implementation of a distributed solution to the MC-PSC problem based on a local computer cluster as well as with a GRID implementation. The results lead us to conclude that the combination of better and faster parallel and distributed algorithms with more similarity comparison methods provides an unprecedented advance on protein structure comparison and analysis technology. These advances might facilitate both directed and fortuitous discovery of protein similarities, families, super-families, domains, etc, and also help pave the way to faster and better protein function inference, annotation and protein structure prediction and assessment thus empowering the structural biologist to do a science that he/she would not have done otherwise

Studies on distributed approaches for large scale multi-criteria protein structure comparison and analysis

Protein Structure Comparison (PSC) is at the core of many important structural biology problems. PSC is used to infer the evolutionary history of distantly related proteins; it can also help in the identification of the biological function of a new protein by comparing it with other proteins whose function has already been annotated; PSC is also a key step in protein structure prediction, because one needs to reliably and efficiently compare tens or hundreds of thousands of decoys (predicted structures) in evaluation of 'native-like' candidates (e.g. Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment). Each of these applications, as well as many others where molecular comparison plays an important role, requires a different notion of similarity, which naturally lead to the Multi-Criteria Protein Structure Comparison (MC-PSC) problem. ProCKSI (www.procksi.org), was the first publicly available server to provide algorithmic solutions for the MC-PSC problem by means of an enhanced structural comparison that relies on the principled application of information fusion to similarity assessments derived from multiple comparison methods (e.g. USM, FAST, MaxCMO, DaliLite, CE and TMAlign). Current MC-PSC works well for moderately sized data sets and it is time consuming as it provides public service to multiple users. Many of the structural bioinformatics applications mentioned above would benefit from the ability to perform, for a dedicated user, thousands or tens of thousands of comparisons through multiple methods in real-time, a capacity beyond our current technology. This research is aimed at the investigation of Grid-styled distributed computing strategies for the solution of the enormous computational challenge inherent in MC-PSC. To this aim a novel distributed algorithm has been designed, implemented and evaluated with different load balancing strategies and selection and configuration of a variety of software tools, services and technologies on different levels of infrastructures ranging from local testbeds to production level eScience infrastructures such as the National Grid Service (NGS). Empirical results of different experiments reporting on the scalability, speedup and efficiency of the overall system are presented and discussed along with the software engineering aspects behind the implementation of a distributed solution to the MC-PSC problem based on a local computer cluster as well as with a GRID implementation. The results lead us to conclude that the combination of better and faster parallel and distributed algorithms with more similarity comparison methods provides an unprecedented advance on protein structure comparison and analysis technology. These advances might facilitate both directed and fortuitous discovery of protein similarities, families, super-families, domains, etc, and also help pave the way to faster and better protein function inference, annotation and protein structure prediction and assessment thus empowering the structural biologist to do a science that he/she would not have done otherwise

A Framework for Grid-Enabling Scientific Workflow Systems. Architecture and application case studies on interoperability and heterogeneity in support for Grid workflow automation.

Since the early 2000s, Service Oriented Architectures (SOAs) have played a key role in the development of complex applications within a virtual organization (VO) context. Grids and workflows have emerged as vital technologies for addressing the (SOA) paradigm. Given the variety of Grid middleware, scientific workflow systems and Grid workflows available, bringing the two technologies together in a flexible, reusable and generalized way has been largely overlooked, particularly from a scientific end user perspective. The lack of domain focus in this area has led to a slow uptake of Grid technologies. This thesis aims to design a framework for Grid-enabling workflows, which identifies the essential technological components, how these components fit together in layered architecture and the interactions between them. To produce such a framework, this thesis first investigates the definition of a Grid-workflow architecture and mapping Grid functionality to workflow nodes, focusing on striking a balance between performance, usability and the Grid functionality supported. Next, it presents an examination of framework extensions for supporting various forms of Grid heterogeneity, essential for ii VO based collaboration. Given the complex nature of Grid technologies, the work presented here investigates abstracting Grid based workflows through high-level definitions and resolution using semantic technologies. Finally, this thesis presents a way to resolves abstract Grid workflows using semantic technologies and intelligent, autonomous agents. The frameworks presented in this thesis are tested and evaluated within the context of domain-based case studies defined in the SIMDAT, BRIDGE and ARGUGRID EU funded research projects

Law in the present future : approaching the legal imaginary of smart cities with science (and) fiction

This doctoral research concerns smart cities, describing digital solutions and social issues related to their innovative technologies, adopted models, and major projects around the world. The many perspectives mentioned in it were identified by online tools used for the textual analysis of two databases that were built from relevant publications on the main subject by authors coming from media and academia. Expected legal elements emerged from the applied process, such as privacy, security, transparency, participation, accountability, and governance. A general review was produced on the information available about the public policies of Big Data in the two municipal cases of Rio de Janeiro and Montréal, and their regulation in the Brazilian and Canadian contexts. The combined approaches from science and literature were explored to reflect on the normative concerns represented by the global challenges and local risks brought by urban surveillance, climate change, and other neoliberal conditions. Cyberpunk Science Fiction reveals itself useful for engaging with the shared problems that need to be faced in the present time, all involving democracy. The results achieved reveal that this work was, in fact, about the complex network of practices and senses between (post)modern law and the imaginary of the future.Cette recherche doctorale centrée sur les villes intelligentes met en évidence les solutions numériques et les questionnements sociétaux qui ont trait aux technologies innovantes, ainsi qu’aux principaux modèles et projets développés autour d’elles à travers le monde. Des perspectives multiples en lien avec ces développements ont été identifiées à l’aide d’outils en ligne qui ont permis l’analyse textuelle de deux bases de données comprenant des publications scientifiques et des écrits médiatiques. De ce processus analytique ont émergé des éléments juridiques relatifs aux questions de vie privée, de sécurité, de transparence, de participation, d’imputabilité et de gouvernance. De plus, à partir de ces informations a été réalisée une revue des politiques publiques relatives aux mégadonnées dans les villes de Rio de Janeiro et de Montréal, ainsi que des réglementations nationales du Canada et du Brésil en lien avec ce sujet. Finalement, à travers l’exploration d’écrits scientifiques et fictionnels de la littérature, les principaux enjeux normatifs soulevés localement et mondialement par la surveillance urbaine, les changements climatiques et les politiques néolibérales ont pu être mis à jour. Le courant cyberpunk de la science-fiction s’est avéré particulièrement utile pour révéler les principaux problèmes politiques, en lien avec la préservation de la démocratie, auxquelles sont confrontées nos sociétés présentement. Les résultats de la recherche démontrent finalement la présence d’un réseau de pratiques et de significations entre le droit (post)moderne et les représentations imaginaires du futur