Maria Luiza Machado Campos

Monitoring e-business Web services usage through a log based architecture

The emergence of Web services represents a significant advance in the continuing evolution of e-business. In order to fully explore business opportunities provided by this paradigm, it is important to track its utilization. This can be done through the use of logging facilities. However, current Web logging approaches do not contemplate Web services utilization. This paper presents a Web services logging architecture based on SOAP intermediaries that captures comprehensive services usage information, which can be explored to improve B2B and B2C transactions by providing feedback on customer electronic behavior.

Managing structural genomic workflows using web services

In silico scientific experiments encompass multiple combinations of program and data resources. Each resource combination in an execution flow is called a scientific workflow. In bioinformatics environments, program composition is a frequent operation, requiring complex management. A scientist faces many challenges when building an experiment: finding the right program to use, the adequate parameters to tune, managing input/output data, building and reusing workflows. Typically, these workflows are implemented using script languages because of their simplicity, despite their specificity and difficulty of reuse. In contrast, Web service technology was specially conceived to encapsulate and combine programs and data, providing interoperation between applications from different platforms. The Web services approach is superior to scripts with regard to interoperability, scalability and flexibility issues. We have combined metadata support with Web services within a framework that supports scientific workflows. While most works are focused on metadata issues to manage and integrate heterogeneous scientific data sources, in this work we concentrate on metadata support to program management within workflows. We have used this framework with a real structural genomic workflow, showing its viability and evidencing its advantages.

GARSA: genomic analysis resources for sequence annotation

SUMMARY Growth of genome data and analysis possibilities have brought new levels of difficulty for scientists to understand, integrate and deal with all this ever-increasing information. In this scenario, GARSA has been conceived aiming to facilitate the tasks of integrating, analyzing and presenting genomic information from several bioinformatics tools and genomic databases, in a flexible way. GARSA is a user-friendly web-based system designed to analyze genomic data in the context of a pipeline. EST and GGS data can be analyzed using the system since it accepts (1) chromatograms, (2) download of sequences from GenBank, (3) Fasta files stored locally or (4) a combination of all three. Quality evaluation of chromatograms, vector removing and clusterization are easily performed as part of the pipeline. A number of local and customizable Blast and CDD analyses can be performed as well as Interpro, complemented with phylogeny analyses. GARSA is being used for the analyses of Trypanosoma vivax (GSS and EST), Trypanosoma rangeli (GSS, EST and ORESTES), Bothrops jararaca (EST), Piaractus mesopotamicus (EST) and Lutzomyia longipalpis (EST). AVAILABILITY The GARSA system is freely available under GPL license (http://www.biowebdb.org/garsa/). For download requests visit http://www.biowebdb.org/garsa/ or contact Dr Alberto Dávila.

Provenance Services for Distributed Workflows

Scientific experiments using workflows benefit from mechanisms to trace the generation of results. As workflows start to scale it is fundamental to have access to their underlying processes, parameters and data. Particularly in molecular dynamics (MD) simulations, a study of the interatomic interactions in proteins must use distributed high performance computing environments to produce timely results. Scientists trust in experiments produced by gathering distributed partial results may be limited without provenance information. This paper presents a service architecture that captures and stores provenance data from distributed, autonomous, replicated and heterogeneous resources. Such provenance data can be used to trace the history of the distributed execution process. These services can be coupled to workflow management systems. The Kepler system was used as a basis to manage a grid workflow application. Experimental results regarding cluster and grid MD simulations were evaluated using the provenance services architecture.

A survey on metadata for describing and retrieving Internet resources

Metadata, or “information that makes data useful,” have been considered by the database community basically as data in dictionaries used to control database management systems operations. More recently, metadata have been used to describe digital resources available across networks. This paper presents a survey of the state of the art concerning the use and importance of metadata, focusing on different standards and models found in the literature, describing how they serve as a basis for integrating heterogeneous resources on the Web and for developing more sophisticated search mechanisms.

ProtozoaDB: dynamic visualization and exploration of protozoan genomes.

ProtozoaDB (http://www.biowebdb.org/protozoadb) is being developed to initially host both genomics and post-genomics data from Plasmodium falciparum, Entamoeba histolytica, Trypanosoma brucei, T. cruzi and Leishmania major, but will hopefully host other protozoan species as more genomes are sequenced. It is based on the Genomics Unified Schema and offers a modern Web-based interface for user-friendly data visualization and exploration. This database is not intended to duplicate other similar efforts such as GeneDB, PlasmoDB, TcruziDB or even TDRtargets, but to be complementary by providing further analyses with emphasis on distant similarities (HMM-based) and phylogeny-based annotations including orthology analysis. ProtozoaDB will be progressively linked to the above-mentioned databases, focusing in performing a multi-source dynamic combination of information through advanced interoperable Web tools such as Web services. Also, to provide Web services will allow third-party software to retrieve and use data from ProtozoaDB in automated pipelines (workflows) or other interoperable Web technologies, promoting better information reuse and integration. We also expect ProtozoaDB to catalyze the development of local and regional bioinformatics capabilities (research and training), and therefore promote/enhance scientific advancement in developing countries.

Elaboration of use case specifications: an approach based on use case fragments

Use case description has gained a wide acceptance among the many techniques available for information systems requirements specification. However, piecing up all the details required for the production of a high quality use case can be a daunting task, especially for students and novice requirements professionals. This paper presents an approach aiming at reducing the time required for the elaboration of high quality use case specifications. The basis of the approach is to write a use case text using the composition of set of pre-defined fragments, where each fragment represents a recurring set of interactions required to achieve a sub-goal. Each fragment can then be customized to meet use case goals. Since each fragment is coded using the best practices for writing use case steps, both the fragment text and the final use case text will be well composed. We believe that this approach will allow novice requirements professional to write high quality use cases in less time than it would be necessary using the other approaches. Our experience on writing use cases for business information systems using a catalogue of use case fragments suggested that they can be a facilitator in several aspects, not only improving the writing speed, but also leading to standardization and concision of use case specifications.

The Ecobase project: database and web technologies for environmental information systems

A very large number of data sources on environment, energy, and natural resources are available worldwide. Unfortunately, users usually face several problems when they want to search and use relevant information. In the Ecobase project, we address these problems in the context of several environmental applications in Brazil and Europe. We propose a distributed architecture for environmental information systems (EIS) based on the Le Select middleware developed at INRIA. In this paper, we present this architecture and its capabilities, and discuss the lessons learned and open issues.

Using social networks analysis for collaboration and team formation identification

Social networks are sets of links that organize people, groups, and institutions in an equal and democratic way, and around a common purpose [4]. During the formation of such networks, problems can arise, such as elements that concentrate many relationships, very isolated individuals or peripheral members of a network, people who are the only link between two distinct groups, agglomerations of people in isolated points. This can cause a series of communications problems, which ultimately will cause losses to the most important element that flows through social networks: knowledge. Thus it is necessary a series of analysis on social networks so we can monitor possible collaborations and assist in the formation of work teams, this can be done through the concept of balancing social networks developed by us [20], whose main focus is to maintain the social network as cohesive as possible in order to maximize the flow of knowledge. A practical application of these analysis occurred in the project BRINCA (Analysis and Balancing of Scientific Social Networks in Cancer Control). BRINCAs goals are to analyze how members of the Cancer INCT (National Institute of Science and Technology) collaborate and how the scientific knowledge flows amongst the different researchers and institutions. With this project we could perform contextualized analysis (i.e. by relationship type, subject, institution, geographic location, time) and use the metrics of social network analysis to understand and verify how collaboration occurs in a multi-disciplinary, multi-team project. Moreover, we used the criteria of social network analysis to perform the balancing. In addition, some of the analysis made on the scenery of cancer are shown.

Sharing scientific models in environmental applications

Environmental applications have been stimulating the cooperation among scientists from different disciplines. There are many examples where this cooperation takes place through exchanging scientific resources, such as data, programs and mathematical models. Finding the right model to apply in an environmental problem is a difficult task. Usually, this decision is based on previous experience. To facilitate the exchange and dissemination of information we propose a scientific resources architecture, where scientists may share their data, programs and models. We also present a scientific publishing metamodel for scientific resources description. The main goal of the proposed architecture is to provide scientific metadata support to effective model sharing, representing an innovative contribution to environmental applications. Scientific experiments and workflows are also considered as scientific resources that need to be shared. We believe that the proposed scientific publishing metamodel could be naturally extended to include these other scientific resources.