Building Problem Solving Environments with Application Web Service Toolkits

Application portals, or Problem Solving Environments (PSEs), provide user environments that simplify access and integrate various distributed computational services for scientists working on particular classes of problems. Specific application portals are typically built on common sets of core services, so reusability of these services is a key problem in PSE development. In this paper we address the reusability problem by presenting a set of core services built using the Web services model and application metadata services that can be used to build science application front ends out of these core services

MOSE': A grid-enabled software platform to solve geoprocessing problems

Grid computing has emerged as an important new field in the distributed computing arena. It focus on intensive resource sharing, innovative applications, and in some cases, high-performance orientation. This paper describes how grids technologies can be used to develop an infrastructure for developing geoprocessing applications. We present the MOS`E system, a grid-enabled problem solving environment (PSE) able to support the activities that concern the modelling and simulation of spatio-temporal phenomena for analyzing and managing the identification and the mitigation of natural disasters like floods, wildfires, landslides, etc. MOSE' takes advantages of the standardized resource access and workflow support for loosely coupled software components provided by the web/grid services technologies

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

Development of a grid service for multi-objective design optimisation

The emerging grid technology is receiving great attention from researchers and applications that need computational and data capabilities to enhance performance and efficiency. Multi-Objective Design Optimisation (MODO) is computationally and data challenging. The challenges become even more with the emergence of evolutionary computing (EC) techniques which produce multiple solutions in a single simulation run. Other challenges are the complexity in mathematical models and multidisciplinary involvement of experts, thus making MODO collaborative and interactive in nature. These challenges call for a problem solving environment (P SE) that can provide computational and optimisation resources to MODO experts as services. Current PSEs provide only the technical specifications of the services which is used by programmers and do not have service specifications for designers that use the system to support design optimisation as services. There is need for PSEs to have service specification document that describes how the services are provided to the end users. Additionally, providing MODO resources as services enabled designers to share resources that they do not have through service subscription. The aim of this research is to develop specifications and architecture of a grid service for MODO. The specifications provide the service use cases that are used to build MODO services. A service specification document is proposed and this enables service providers to follow a process for providing services to end users. In this research, literature was reviewed and industry survey conducted. This was followed by the design, development, case study and validation. The research studied related PSEs in literature and industry to come up with a service specification document that captures the process for grid service definition. This specification was used to develop a framework for MODO applications. An architecture based on this framework was proposed and implemented as DECGrid (Decision Engineering Centre Grid) prototype. Three real-life case studies were used to validate the prototype. The results obtained compared favourably with the results in literature. Different scenarios for using the services among distributed design experts demonstrated the computational synergy and efficiency in collaboration. The mathematical model building service and optimisation service enabled designers to collaboratively build models using the collaboration service. This helps designers without optimisation knowledge to perform optimisation. The key contributions in this research are the service specifications that support MODO, the framework developed which provides the process for definining the services and the architecture used to implement the framework. The key limitations of the research are the use of only engineering design optimisation case studies and the prototype is not tested in industry.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Building web service ontologies

Harmelen, F.A.H. van [Promotor]Stuckenschmidt, H. [Copromotor

Acta Universitatis Sapientiae - Electrical and Mechanical Engineering

Series Electrical and Mechanical Engineering publishes original papers and surveys in various fields of Electrical and Mechanical Engineering

Service Oriented Mobile Computing

La diffusione di concetti quali Pervasive e Mobile Computing introduce nell'ambito dei sistemi distribuiti due aspetti fondamentali: la mobilità dell'utente e l'interazione con l'ambiente circostante, favorite anche dal crescente utilizzo di dispositivi mobili dotati di connettività wireless come prodotti di consumo. Per estendere le funzionalità introdotte nell'ambito dei sistemi distribuiti dalle Architetture Orientate ai Servizi (SOA) e dal paradigma peer-to-peer anche a dispositivi dalle risorse limitate (in termini di capacità computazionale, memoria e batteria), è necessario disporre di un middleware leggero e progettato tenendo in considerazione tali caratteristiche. In questa tesi viene presentato NAM (Networked Autonomic Machine), un formalismo che descrive in modo esaustivo un sistema di questo tipo; si tratta di un modello teorico per la definizione di entità hardware e software in grado di condividere le proprie risorse in modo completamente altruistico. In particolare, il lavoro si concentra sulla definizione e gestione di un determinato tipo di risorse, i servizi, che possono essere offerti ed utilizzati da dispositivi mobili, mediante meccanismi di composizione e migrazione. NSAM (Networked Service-oriented Autonomic Machine) è una specializzazione di NAM per la condivisione di servizi in una rete peer-to-peer, ed è basato su tre concetti fondamentali: schemi di overlay, composizione dinamica di servizi e auto-configurazione dei peer. Nella tesi vengono presentate anche diverse attività applicative, che fanno riferimento all'utilizzo di due middleware sviluppati dal gruppo di Sistemi Distribuiti (DSG) dell'Università di Parma: SP2A (Service Oriented Peer-to-peer Architecture), framework per lo sviluppo di applicazioni distribuite attraverso la condivisione di risorse in una rete peer-to-peer, e Jxta-Soap che consente la condivisione di Web Services in una rete peer-to-peer JXTA. Le applicazioni realizzate spaziano dall'ambito della logistica, alla creazione di comunità per l'e-learning, all'Ambient Intelligence alla gestione delle emergenze, ed hanno come denominatore comune la creazione di reti eterogenee e la condivisione di risorse anche tra dispositivi mobili. Viene inoltre messo in evidenza come tali applicazioni possano essere ottimizzate mediante l'introduzione del framework NAM descritto, per consentire la condivisione di diversi tipi di risorse in modo efficiente e proattivo