Gerenciamento de workflows científicos em bioinformática
Resumo
A proliferação de dados e ferramentas de bioinformática originou diversos desafios: como entender e organizar esses recursos, como compartilhar e reusar experimentos bem sucedidos, e como prover interoperabilidade entre dados e ferramentas de diferentes locais e utilizados por usuários com perfis distintos. Várias soluções vem sendo propostas para estes problemas, geralmente para alguns aspectos específicos, envolvendo freqüentemente o uso de workflows científicos. A solução oferecida pela tese também é centrada em workflows científicos, mas cobre todos os pontos levantados, contribuindo assim para dar um apoio integrado aos usuários. A infra-estrutura proposta permite projetar, reusar, validar, compartilhar e documentar experimentos de bioinformática.
Referências
Andrew et al, P. (2006). Presenting Windows Workflow Foundation. SAMS Publishing.
Barga, R. and Digiampietri, L. (2006a). Automatic generation of workflow provenance. In Provenance and Annotation of Data International Provenance and Annotation Workshop (IPAW), volume 4145 of Lecture Notes in Computer Science. Springer.
Barga, R. and Digiampietri, L. (2006b). Redux - First provenance challenge. [link] (as of 2007-04-04).
SBC 2008 39 Barga, R. and Digiampietri, L. (2007). Automatic capture and efficient storage of escience experiment provenance. Concurrency and Computation: Practice and Experience. DOI: 10.1002/cpe.1235.
Bausch, W., Pautasso, C., Schaeppi, R., and Alonso, G. (2001). Bioopera: Cluster-aware computing. In Proceeding of the the 4th IEEE International Conference on Cluster Computing (Cluster), pages 90–94.
Buttler, D., Coleman, M., Critchlow, T., Fileto, R., Han, W., Pu, C., Rocco, D., and Xiong, L. (2002). Querying multiple bioinformatics information sources: can semantic web research help? ACM SIGMOD Record, 31(4):56–64.
Cavalcanti, M., Targino, R., Baiao, F., Rössle, S., Bisch, P., Pires, P., Campos, M., and Mattoso, M. (2005). Managing structural genomic workflows using Web services. Data & Knowledge Engineering, 53(1):45–74.
Digiampietri, L., Medeiros, C., and Setubal, J. (2005). A framework based in Web services orchestration bioinformatics workflow management. Genetics and Molecular Research, 4(3):535–542.
Digiampietri, L., Medeiros, C., Setubal, J., and Barga, R. (2007a). Traceability Mechanisms for Bioinformatics Scientific Workflows. In Proceedings of the AAAI2007’s Workshop on Semantic e-Science (SeS07), pages 26–33, Vancouver, Canada.
Digiampietri, L., Pérez-Alcazar, J., and Medeiros, C. (2007b). AI Planning in Web Services Composition: a review of current approaches and a new solution. In VI ENIA - Proceedings of the XXVII Brazilian Computer Society Conference (CSBC2007).
Digiampietri, L., Pérez-Alcázar, J., and Medeiros, C. (2007c). An ontology-based framework for bioinformatics workflows. International Journal of Bioinformatics Research and Applications, 3(3):268–285.
Digiampietri, L., Setubal, J. C., and Medeiros, C. B. (2006). Bioinformatics scientific workflows: combining databases, AI and Web services. In Proceedings of V Workshop de Teses e Dissertaes em Bancos de Dados (WTDBD), pages 2–9.
First Provenance Challenge. First Provenance Challenge. [link] (as of 2006-11-13).
Long, D. and Fox, M. (2003). The 3rd International Planning Competition: Results and Analysis. Journal of Artificial Intelligence Research, 20:1–59.
Medeiros, C., Perez-Alcazar, J., Digiampietri, L., Pastorello, G., Santanche, A., Torres, R., Madeira, E., and Bacarin, E. (2005). WOODSS and the Web: Annotating and Reusing Scientific Workflows. ACM SIGMOD Record, 34(3):18–23.
Seffino, L., Medeiros, C., Rocha, J., and Yi, B. (1999). WOODSS - A Spatial Decision Support System based on Workflows. Decision Support Systems, 27(1-2):105–123.
The myGrid Consortium. myGrid: Middleware for in silico experiments in biology. [link] (as of 2008-02-02).
Wainer, J., Weske, M., Vossen, G., and Medeiros, C. (1996). Scientific Workflow Systems. In The NSF Workshop on Workflow and Process Automation Information Systems.
Barga, R. and Digiampietri, L. (2006a). Automatic generation of workflow provenance. In Provenance and Annotation of Data International Provenance and Annotation Workshop (IPAW), volume 4145 of Lecture Notes in Computer Science. Springer.
Barga, R. and Digiampietri, L. (2006b). Redux - First provenance challenge. [link] (as of 2007-04-04).
SBC 2008 39 Barga, R. and Digiampietri, L. (2007). Automatic capture and efficient storage of escience experiment provenance. Concurrency and Computation: Practice and Experience. DOI: 10.1002/cpe.1235.
Bausch, W., Pautasso, C., Schaeppi, R., and Alonso, G. (2001). Bioopera: Cluster-aware computing. In Proceeding of the the 4th IEEE International Conference on Cluster Computing (Cluster), pages 90–94.
Buttler, D., Coleman, M., Critchlow, T., Fileto, R., Han, W., Pu, C., Rocco, D., and Xiong, L. (2002). Querying multiple bioinformatics information sources: can semantic web research help? ACM SIGMOD Record, 31(4):56–64.
Cavalcanti, M., Targino, R., Baiao, F., Rössle, S., Bisch, P., Pires, P., Campos, M., and Mattoso, M. (2005). Managing structural genomic workflows using Web services. Data & Knowledge Engineering, 53(1):45–74.
Digiampietri, L., Medeiros, C., and Setubal, J. (2005). A framework based in Web services orchestration bioinformatics workflow management. Genetics and Molecular Research, 4(3):535–542.
Digiampietri, L., Medeiros, C., Setubal, J., and Barga, R. (2007a). Traceability Mechanisms for Bioinformatics Scientific Workflows. In Proceedings of the AAAI2007’s Workshop on Semantic e-Science (SeS07), pages 26–33, Vancouver, Canada.
Digiampietri, L., Pérez-Alcazar, J., and Medeiros, C. (2007b). AI Planning in Web Services Composition: a review of current approaches and a new solution. In VI ENIA - Proceedings of the XXVII Brazilian Computer Society Conference (CSBC2007).
Digiampietri, L., Pérez-Alcázar, J., and Medeiros, C. (2007c). An ontology-based framework for bioinformatics workflows. International Journal of Bioinformatics Research and Applications, 3(3):268–285.
Digiampietri, L., Setubal, J. C., and Medeiros, C. B. (2006). Bioinformatics scientific workflows: combining databases, AI and Web services. In Proceedings of V Workshop de Teses e Dissertaes em Bancos de Dados (WTDBD), pages 2–9.
First Provenance Challenge. First Provenance Challenge. [link] (as of 2006-11-13).
Long, D. and Fox, M. (2003). The 3rd International Planning Competition: Results and Analysis. Journal of Artificial Intelligence Research, 20:1–59.
Medeiros, C., Perez-Alcazar, J., Digiampietri, L., Pastorello, G., Santanche, A., Torres, R., Madeira, E., and Bacarin, E. (2005). WOODSS and the Web: Annotating and Reusing Scientific Workflows. ACM SIGMOD Record, 34(3):18–23.
Seffino, L., Medeiros, C., Rocha, J., and Yi, B. (1999). WOODSS - A Spatial Decision Support System based on Workflows. Decision Support Systems, 27(1-2):105–123.
The myGrid Consortium. myGrid: Middleware for in silico experiments in biology. [link] (as of 2008-02-02).
Wainer, J., Weske, M., Vossen, G., and Medeiros, C. (1996). Scientific Workflow Systems. In The NSF Workshop on Workflow and Process Automation Information Systems.
Publicado
12/07/2008
Como Citar
DIGIAMPIETRI, Luciano Antonio; SETUBAL, João Carlos; MEDEIROS, Claudia Bauzer.
Gerenciamento de workflows científicos em bioinformática. In: CONCURSO DE TESES E DISSERTAÇÕES (CTD), 21. , 2008, Belém/PA.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2008
.
p. 33-40.
ISSN 2763-8820.
