Web services and workflow management for biological resources

BACKGORUND: The completion of the Human Genome Project has resulted in large quantities of biological data which are proving difficult to manage and integrate effectively. There is a need for a system that is able to automate accesses to remote sites and to "understand" the information that it is managing in order to link data properly. Workflow management systems combined with Web Services are promising Information and Communication Technologies (ICT) tools. Some have already been proposed and are being increasingly applied to the biomedical domain, especially as many biology-related Web Services are now becoming available. Information on biological resources and on genomic sequences mutations are two examples of very specialized datasets that are useful for specific research domains. RESULTS: The architecture of a system that is able to access and execute predefined workflows is presented in this paper. Web Services allowing access to the IARC TP53 Mutation Database and CABRI catalogues of biological resources have been implemented and are available on-line. Example workflows which retrieve data from these Web Services have also been created and are available on-line. CONCLUSION: We present a general architecture and some building blocks for the implementation of a system that is able to remotely execute workflows of biomedical interest and show how this approach can effectively produce useful outputs. The further development and implementation of Web Services allowing access to an exhaustive set of biomedical databases and the creation of effective and useful workflows will improve the automation of in-silico analysis

Biowep: a workflow enactment portal for bioinformatics applications

<p>Abstract</p> <p>Background</p> <p>The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS), can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing.</p> <p>Results</p> <p>We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved.</p> <p>Conclusion</p> <p>We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical databases and analysis software and the creation of effective workflows can significantly improve automation of in-silico analysis. Biowep is available for interested researchers as a reference portal. They are invited to submit their workflows to the workflow repository. Biowep is further being developed in the sphere of the Laboratory of Interdisciplinary Technologies in Bioinformatics – LITBIO.</p

Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society

The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan. This Editorial provides a brief overview of the Conference topics and introduces the peer-reviewed manuscripts accepted for publication in this Supplement

Preservation, Characterization and Exploitation of Microbial Biodiversity: The Perspective of the Italian Network of Culture Collections

Microorganisms represent most of the biodiversity of living organisms in every ecological habitat. They have profound effects on the functioning of any ecosystem, and therefore on the health of our planet and of human beings. Moreover, microorganisms are the main protagonists in food, medical and biotech industries, and have several environmental applications. Accordingly, the characterization and preservation of microbial biodiversity are essential not only for the maintenance of natural ecosystems but also for research purposes and biotechnological exploitation. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are crucial for the safeguarding and circulation of biological resources, as well as for the progress of life sciences. This review deals with the expertise and services of CCs, in particular concerning preservation and characterization of microbial resources, by pointing to the advanced approaches applied to investigate a huge reservoir of microorganisms. Data sharing and web services as well as the tight interconnection between CCs and the biotechnological industry are highlighted. In addition, guidelines and regulations related to quality management systems (QMSs), biosafety and biosecurity issues are discussed according to the perspectives of CCs and mBRCs

Integração de serviços para extracção de conhecimento

Mestrado em Engenharia de Computadores e TelemáticaCom a descoberta do genoma humano completa, uma enorme quantidade de dados foi gerada, criando grandes desafios na compreensão do valor de toda esta informação. Este cenário trouxe a necessidade de novas ferramentas para extracção automática de informação de bases de dados biológicas. Esta dissertação apresenta um sistema web baseado em princípios Web2.0 desenhado para agregar serviços e dados, melhorando a extracção de conhecimento de bases de dados biológicas. A arquitectura segue uma aproximação ágil e nova, usando fluxos de informação, que podem ser construidos dinamicamente pelo utilizador. O workflow permite a criação de protocolos de obtenção de informação específicos, permitindo que o utilizador aceda a recursos distribuídos numa interface única e centralizada. ABSTRACT: With the advent of human genome disclosure an enormous quantity of data was generated putting great challenges in understanding the value of all this data. This scenario has risen the necessity to have new tools for automatic extraction of knowledge from biological databases. This dissertation presents a web system based on web2.0 principles designed to aggregate services and data and to enhance knowledge extraction from biological databases. The architecture follows a new and agile solution using workflows which may be dynamically built by the user. The workflow allows building specific protocols for information retrieval enabling the user to access distributed resources in a centralized and unique interface

Distributed Web Service Coordination for Collaboration Applications and Biological Workflows

In this dissertation work, we have investigated the main research thrust of decentralized coordination of workflows over web services. To address distributed workflow coordination, first we have developed “Web Coordination Bonds” as a capable set of dependency modeling primitives that enable each web service to manage its own dependencies. Web bond primitives are as powerful as extended Petri nets and have sufficient modeling and expressive capabilities to model workflow dependencies. We have designed and prototyped our “Web Service Coordination Management Middleware” (WSCMM) system that enhances current web services infrastructure to accommodate web bond enabled web services. Finally, based on core concepts of web coordination bonds and WSCMM, we have developed the “BondFlow” system that allows easy configuration distributed coordination of workflows. The footprint of the BonFlow runtime is 24KB and the additional third party software packages, SOAP client and XML parser, account for 115KB

Composição de serviços para aplicações biomédicas

Doutoramento em Engenharia InformáticaA exigente inovação na área das aplicações biomédicas tem guiado a evolução das tecnologias de informação nas últimas décadas. Os desafios associados a uma gestão, integração, análise e interpretação eficientes dos dados provenientes das mais modernas tecnologias de hardware e software requerem um esforço concertado. Desde hardware para sequenciação de genes a registos electrónicos de paciente, passando por pesquisa de fármacos, a possibilidade de explorar com precisão os dados destes ambientes é vital para a compreensão da saúde humana. Esta tese engloba a discussão e o desenvolvimento de melhores estratégias informáticas para ultrapassar estes desafios, principalmente no contexto da composição de serviços, incluindo técnicas flexíveis de integração de dados, como warehousing ou federação, e técnicas avançadas de interoperabilidade, como serviços web ou LinkedData. A composição de serviços é apresentada como um ideal genérico, direcionado para a integração de dados e para a interoperabilidade de software. Relativamente a esta última, esta investigação debruçou-se sobre o campo da farmacovigilância, no contexto do projeto Europeu EU-ADR. As contribuições para este projeto, um novo standard de interoperabilidade e um motor de execução de workflows, sustentam a sucesso da EU-ADR Web Platform, uma plataforma para realizar estudos avançados de farmacovigilância. No contexto do projeto Europeu GEN2PHEN, esta investigação visou ultrapassar os desafios associados à integração de dados distribuídos e heterogéneos no campo do varíoma humano. Foi criada uma nova solução, WAVe - Web Analyses of the Variome, que fornece uma coleção rica de dados de variação genética através de uma interface Web inovadora e de uma API avançada. O desenvolvimento destas estratégias evidenciou duas oportunidades claras na área de software biomédico: melhorar o processo de implementação de software através do recurso a técnicas de desenvolvimento rápidas e aperfeiçoar a qualidade e disponibilidade dos dados através da adopção do paradigma de web semântica. A plataforma COEUS atravessa as fronteiras de integração e interoperabilidade, fornecendo metodologias para a aquisição e tradução flexíveis de dados, bem como uma camada de serviços interoperáveis para explorar semanticamente os dados agregados. Combinando as técnicas de desenvolvimento rápidas com a riqueza da perspectiva "Semantic Web in a box", a plataforma COEUS é uma aproximação pioneira, permitindo o desenvolvimento da próxima geração de aplicações biomédicas.The demand for innovation in the biomedical software domain has been an information technologies evolution driver over the last decades. The challenges associated with the effective management, integration, analyses and interpretation of the wealth of life sciences information stemming from modern hardware and software technologies require concerted efforts. From gene sequencing hardware to pharmacology research up to patient electronic health records, the ability to accurately explore data from these environments is vital to further improve our understanding of human health. This thesis encloses the discussion on building better informatics strategies to address these challenges, primarily in the context of service composition, including warehousing and federation strategies for resource integration, as well as web services or LinkedData for software interoperability. Service composition is introduced as a general principle, geared towards data integration and software interoperability. Concerning the latter, this research covers the service composition requirements within the pharmacovigilance field, namely on the European EU-ADR project. The contributions to this area, the definition of a new interoperability standard and the creation of a new workflow-wrapping engine, are behind the successful construction of the EUADR Web Platform, a workspace for delivering advanced pharmacovigilance studies. In the context of the European GEN2PHEN project, this research tackles the challenges associated with the integration of heterogeneous and distributed data in the human variome field. For this matter, a new lightweight solution was created: WAVe, Web Analysis of the Variome, provides a rich collection of genetic variation data through an innovative portal and an advanced API. The development of the strategies underlying these products highlighted clear opportunities in the biomedical software field: enhancing the software implementation process with rapid application development approaches and improving the quality and availability of data with the adoption of the Semantic Web paradigm. COEUS crosses the boundaries of integration and interoperability as it provides a framework for the flexible acquisition and translation of data into a semantic knowledge base, as well as a comprehensive set of interoperability services, from REST to LinkedData, to fully exploit gathered data semantically. By combining the lightness of rapid application development strategies with the richness of its "Semantic Web in a box" approach, COEUS is a pioneering framework to enhance the development of the next generation of biomedical applications

Aggregation of biological knowledge for immunological and virological applications

Ph.DDOCTOR OF PHILOSOPH