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\n\n \n \n \n \n \n Supporting Dynamic Parameter Sweep in Adaptive and User-Steered Workflow.\n \n \n \n\n\n \n Dias, J.; Ogasawara, E.; Oliveira, D.; Porto, F.; Coutinho, A.; and Mattoso, M.\n\n\n \n\n\n\n In
WORKS, of
WORKS '11, pages 31–36, Seattle, WA, USA, 2011. ACM\n
ACM ID: 1645178\n\n
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@inproceedings{dias_supporting_2011,\n\taddress = {Seattle, WA, USA},\n\tseries = {{WORKS} '11},\n\ttitle = {Supporting {Dynamic} {Parameter} {Sweep} in {Adaptive} and {User}-{Steered} {Workflow}},\n\tisbn = {978-1-4503-1100-7},\n\tdoi = {10.1145/2110497.2110502},\n\tbooktitle = {{WORKS}},\n\tpublisher = {ACM},\n\tauthor = {Dias, Jonas and Ogasawara, Eduardo and Oliveira, Daniel and Porto, Fabio and Coutinho, Alvaro and Mattoso, Marta},\n\tyear = {2011},\n\tnote = {ACM ID: 1645178},\n\tkeywords = {Workflow management, design, logistics, management, strategic information systems planning, systems analysis and design, systems development, theory},\n\tpages = {31--36},\n}\n\n
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\n\n \n \n \n \n \n \n SciPhy: A Cloud-Based Workflow for Phylogenetic Analysis of Drug Targets in Protozoan Genomes.\n \n \n \n \n\n\n \n Ocaña, K.; Oliveira, D. d.; Ogasawara, E.; Dávila, A.; Lima, A.; and Mattoso, M.\n\n\n \n\n\n\n In
Advances in Bioinformatics and Computational Biology, of
Lecture Notes in Computer Science, pages 66–70, 2011. Springer\n
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\n\n \n \n Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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@inproceedings{ocana_sciphy:_2011,\n\tseries = {Lecture {Notes} in {Computer} {Science}},\n\ttitle = {{SciPhy}: {A} {Cloud}-{Based} {Workflow} for {Phylogenetic} {Analysis} of {Drug} {Targets} in {Protozoan} {Genomes}},\n\tcopyright = {©2011 Springer-Verlag GmbH Berlin Heidelberg},\n\tisbn = {978-3-642-22824-7 978-3-642-22825-4},\n\tshorttitle = {{SciPhy}},\n\turl = {http://link.springer.com/chapter/10.1007/978-3-642-22825-4_9},\n\tabstract = {Bioinformatics experiments are rapidly evolving with genomic projects that analyze large amounts of data. This fact demands high performance computation and opens up for exploring new approaches to provide better control and performance when running experiments, including Phylogeny/Phylogenomics. We designed a phylogenetic scientific workflow, named SciPhy, to construct phylogenetic trees from a set of drug target enzymes found in protozoan genomes. Our contribution is the development, implementation and test of SciPhy in public cloud computing environments. SciPhy can be used in other Bioinformatics experiments to control a systematic execution with high performance while producing provenance data.},\n\tlanguage = {en},\n\turldate = {2014-03-14},\n\tbooktitle = {Advances in {Bioinformatics} and {Computational} {Biology}},\n\tpublisher = {Springer},\n\tauthor = {Ocaña, Kary and Oliveira, Daniel de and Ogasawara, Eduardo and Dávila, A. and Lima, A. and Mattoso, Marta},\n\tyear = {2011},\n\tkeywords = {Algorithm Analysis and Problem Complexity, Artificial Intelligence (incl. Robotics), Computation by Abstract Devices, Computational Biology/Bioinformatics, Database Management, Pattern Recognition, Phylogeny, Protozoa, Scientific workflow, cloud computing},\n\tpages = {66--70},\n}\n\n
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\n Bioinformatics experiments are rapidly evolving with genomic projects that analyze large amounts of data. This fact demands high performance computation and opens up for exploring new approaches to provide better control and performance when running experiments, including Phylogeny/Phylogenomics. We designed a phylogenetic scientific workflow, named SciPhy, to construct phylogenetic trees from a set of drug target enzymes found in protozoan genomes. Our contribution is the development, implementation and test of SciPhy in public cloud computing environments. SciPhy can be used in other Bioinformatics experiments to control a systematic execution with high performance while producing provenance data.\n
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\n\n \n \n \n \n \n Virtual Partitioning ad-hoc Queries over Distributed XML Databases.\n \n \n \n\n\n \n Rodrigues, C.; Braganholo, V.; and Mattoso, M.\n\n\n \n\n\n\n
Journal of Information and Data Management, 2(3): 495–510. 2011.\n
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\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n
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@article{rodrigues_virtual_2011,\n\ttitle = {Virtual {Partitioning} ad-hoc {Queries} over {Distributed} {XML} {Databases}},\n\tvolume = {2},\n\tissn = {21787107},\n\tnumber = {3},\n\tjournal = {Journal of Information and Data Management},\n\tauthor = {Rodrigues, Carla and Braganholo, Vanessa and Mattoso, Marta},\n\tyear = {2011},\n\tkeywords = {XML, distributed query processing, virtual partitioning},\n\tpages = {495--510},\n}\n\n
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\n\n \n \n \n \n \n Migrating Scientific Experiments to the Cloud.\n \n \n \n\n\n \n Oliveira, D.; Baiao, F.; and Mattoso, M.\n\n\n \n\n\n\n
HPC in the Cloud. March 2011.\n
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@article{oliveira_migrating_2011,\n\ttitle = {Migrating {Scientific} {Experiments} to the {Cloud}},\n\tjournal = {HPC in the Cloud},\n\tauthor = {Oliveira, Daniel and Baiao, Fernanda and Mattoso, Marta},\n\tmonth = mar,\n\tyear = {2011},\n}\n\n
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\n\n \n \n \n \n \n \n Provenance management in Swift.\n \n \n \n \n\n\n \n Gadelha, L. M.; Clifford, B.; Mattoso, M.; Wilde, M.; and Foster, I.\n\n\n \n\n\n\n
Future Generation Computer Systems, 27(6): 775–780. June 2011.\n
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\n\n \n \n Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n
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@article{gadelha_provenance_2011-1,\n\ttitle = {Provenance management in {Swift}},\n\tvolume = {27},\n\tissn = {0167-739X},\n\turl = {http://www.sciencedirect.com/science/article/pii/S0167739X1000083X},\n\tdoi = {16/j.future.2010.05.003},\n\tabstract = {{\\textless}p{\\textgreater}{\\textless}br/{\\textgreater}The Swift parallel scripting language allows for the specification, execution and analysis of large-scale computations in parallel and distributed environments. It incorporates a data model for recording and querying provenance information. In this article we describe these capabilities and evaluate the interoperability with other systems through the use of the Open Provenance Model. We describe Swift's provenance data model and compare it to the Open Provenance Model. We also describe and evaluate activities performed within the Third Provenance Challenge, which consisted of implementing a specific scientific workflow, capturing and recording provenance information of its execution, performing provenance queries, and exchanging provenance information with other systems. Finally, we propose improvements to both the Open Provenance Model and Swift's provenance system.{\\textless}/p{\\textgreater}},\n\tnumber = {6},\n\turldate = {2011-06-04},\n\tjournal = {Future Generation Computer Systems},\n\tauthor = {Gadelha, Luiz M.R. and Clifford, Ben and Mattoso, Marta and Wilde, Michael and Foster, Ian},\n\tmonth = jun,\n\tyear = {2011},\n\tkeywords = {Parallel scripting languages, Scientific workflows, provenance},\n\tpages = {775--780},\n}\n\n
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\n \\textlessp\\textgreater\\textlessbr/\\textgreaterThe Swift parallel scripting language allows for the specification, execution and analysis of large-scale computations in parallel and distributed environments. It incorporates a data model for recording and querying provenance information. In this article we describe these capabilities and evaluate the interoperability with other systems through the use of the Open Provenance Model. We describe Swift's provenance data model and compare it to the Open Provenance Model. We also describe and evaluate activities performed within the Third Provenance Challenge, which consisted of implementing a specific scientific workflow, capturing and recording provenance information of its execution, performing provenance queries, and exchanging provenance information with other systems. Finally, we propose improvements to both the Open Provenance Model and Swift's provenance system.\\textless/p\\textgreater\n
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\n\n \n \n \n \n \n A Performance Evaluation of X-Ray Crystallography Scientific Workflow Using SciCumulus.\n \n \n \n\n\n \n Oliveira, D.; Ocaña, K.; Ogasawara, E.; Dias, J.; Baião, F.; and Mattoso, M.\n\n\n \n\n\n\n In
IEEE International Conference on Cloud Computing (CLOUD), pages 708–715, Washington, D.C., USA, July 2011. IEEE\n
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\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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@inproceedings{oliveira_performance_2011,\n\taddress = {Washington, D.C., USA},\n\ttitle = {A {Performance} {Evaluation} of {X}-{Ray} {Crystallography} {Scientific} {Workflow} {Using} {SciCumulus}},\n\tisbn = {978-1-4577-0836-7},\n\tdoi = {10.1109/CLOUD.2011.99},\n\tabstract = {X-ray crystallography is an important field due to its role in drug discovery and its relevance in bioinformatics experiments of comparative genomics, phylogenomics, evolutionary analysis, ortholog detection, and three-dimensional structure determination. Managing these experiments is a challenging task due to the orchestration of legacy tools and the management of several variations of the same experiment. Workflows can model a coherent flow of activities that are managed by scientific workflow management systems (SWfMS). Due to the huge amount of variations of the workflow to be explored (parameters, input data) it is often necessary to execute X-ray crystallography experiments in High Performance Computing (HPC) environments. Cloud computing is well known for its scalable and elastic HPC model. In this paper, we present a performance evaluation for the X-ray crystallography workflow defined by the PC4 (Provenance Challenge series). The workflow was executed using the SciCumulus middleware at the Amazon EC2 cloud environment. SciCumulus is a layer for SWfMS that offers support for the parallel execution of scientific workflows in cloud environments with provenance mechanisms. Our results reinforce the benefits (total execution time × monetary cost) of parallelizing the X-ray crystallography workflow using SciCumulus. The results show a consistent way to execute X-ray crystallography workflows that need HPC using cloud computing. The evaluated workflow shares features of many scientific workflows and can be applied to other experiments.},\n\tlanguage = {English},\n\tbooktitle = {{IEEE} {International} {Conference} on {Cloud} {Computing} ({CLOUD})},\n\tpublisher = {IEEE},\n\tauthor = {Oliveira, D. and Ocaña, K. and Ogasawara, E. and Dias, Jonas and Baião, F. and Mattoso, M.},\n\tmonth = jul,\n\tyear = {2011},\n\tkeywords = {Amazon EC2 cloud environment, Middleware, Phylogenomics, Reflection, SciCumulus middleware, Scientific workflows, X-ray crystallography, X-ray crystallography scientific workflow, X-ray diffraction, X-ray imaging, bioinformatics, cloud computing, crystallography, drug discovery, evolutionary analysis, execution time, high performance computing, monetary cost, ortholog detection, parallel execution, performance evaluation, provenance challenge series, scalable elastic HPC model, scientific information systems, scientific workflow management system, three-dimensional structure determination, workflow management software},\n\tpages = {708--715},\n}\n\n
\n
\n\n\n
\n X-ray crystallography is an important field due to its role in drug discovery and its relevance in bioinformatics experiments of comparative genomics, phylogenomics, evolutionary analysis, ortholog detection, and three-dimensional structure determination. Managing these experiments is a challenging task due to the orchestration of legacy tools and the management of several variations of the same experiment. Workflows can model a coherent flow of activities that are managed by scientific workflow management systems (SWfMS). Due to the huge amount of variations of the workflow to be explored (parameters, input data) it is often necessary to execute X-ray crystallography experiments in High Performance Computing (HPC) environments. Cloud computing is well known for its scalable and elastic HPC model. In this paper, we present a performance evaluation for the X-ray crystallography workflow defined by the PC4 (Provenance Challenge series). The workflow was executed using the SciCumulus middleware at the Amazon EC2 cloud environment. SciCumulus is a layer for SWfMS that offers support for the parallel execution of scientific workflows in cloud environments with provenance mechanisms. Our results reinforce the benefits (total execution time × monetary cost) of parallelizing the X-ray crystallography workflow using SciCumulus. The results show a consistent way to execute X-ray crystallography workflows that need HPC using cloud computing. The evaluated workflow shares features of many scientific workflows and can be applied to other experiments.\n
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\n\n \n \n \n \n \n Optimizing Phylogenetic Analysis Using SciHmm Cloud-based Scientific Workflow.\n \n \n \n\n\n \n Ocaña, K. A. C. S.; Oliveira, D.; Dias, J.; Ogasawara, E.; and Mattoso, M.\n\n\n \n\n\n\n In
Proceedings of the 7th IEEE International Conference on e-Science (e-Science), pages 190–197, Stockholm, Sweden, December 2011. IEEE\n
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@inproceedings{ocana_optimizing_2011,\n\taddress = {Stockholm, Sweden},\n\ttitle = {Optimizing {Phylogenetic} {Analysis} {Using} {SciHmm} {Cloud}-based {Scientific} {Workflow}},\n\tlanguage = {English},\n\tbooktitle = {Proceedings of the 7th {IEEE} {International} {Conference} on e-{Science} (e-{Science})},\n\tpublisher = {IEEE},\n\tauthor = {Ocaña, Kary A. C. S. and Oliveira, Daniel and Dias, Jonas and Ogasawara, Eduardo and Mattoso, Marta},\n\tmonth = dec,\n\tyear = {2011},\n\tkeywords = {Auditing, Computational modeling, Computers, Distributed databases, Electronic mail, Pedigree, Sketch, authoritative local repository, central server, data models, data-intensive scientific applications, decentralized architecture, distributed, distributed data provenance, lineage, meta data, metadata, monitoring, provenance, provenance management system, provenance records, query formulation, querying, remote hosts, tracking},\n\tpages = {190--197},\n}\n\n
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\n\n \n \n \n \n \n Heurísticas para Controle de Execução de Atividades de Workflows Científicos na Nuvem.\n \n \n \n\n\n \n Costa, F.; Oliveira, D.; and M., M.\n\n\n \n\n\n\n In
Anais do Workshop de Teses e Dissertações em bancos de Dados - SBBD 2011, Florianópolis, SC, Brasil, 2011. Sociedade Brasileira de Computação\n
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@inproceedings{costa_heuristicas_2011,\n\taddress = {Florianópolis, SC, Brasil},\n\ttitle = {Heurísticas para {Controle} de {Execução} de {Atividades} de {Workflows} {Científicos} na {Nuvem}},\n\tbooktitle = {Anais do {Workshop} de {Teses} e {Dissertações} em bancos de {Dados} - {SBBD} 2011},\n\tpublisher = {Sociedade Brasileira de Computação},\n\tauthor = {Costa, Flávio and Oliveira, D. and Mattoso M.},\n\tyear = {2011},\n}\n\n
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\n\n \n \n \n \n \n Challenges in managing implicit and abstract provenance data: experiences with ProvManager.\n \n \n \n\n\n \n Marinho, A.; Mattoso, M.; Werner, C.; Braganholo, V.; and Murta, L.\n\n\n \n\n\n\n In
TaPP, pages 1–6, Crete, Greece, 2011. USENIX Association\n
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@inproceedings{marinho_challenges_2011,\n\taddress = {Crete, Greece},\n\ttitle = {Challenges in managing implicit and abstract provenance data: experiences with {ProvManager}},\n\tlanguage = {en},\n\tbooktitle = {{TaPP}},\n\tpublisher = {USENIX Association},\n\tauthor = {Marinho, Anderson and Mattoso, Marta and Werner, Claudia and Braganholo, Vanessa and Murta, Leonardo},\n\tyear = {2011},\n\tpages = {1--6},\n}\n\n
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\n\n \n \n \n \n \n Distributed Database Research at COPPE/UFRJ.\n \n \n \n\n\n \n Mattoso, M.; Braganholo, V.; Lima, A.; and Murta, L.\n\n\n \n\n\n\n
Journal of Information and Data Management (JIDM), 2(2): 123–138. 2011.\n
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@article{mattoso_distributed_2011,\n\ttitle = {Distributed {Database} {Research} at {COPPE}/{UFRJ}},\n\tvolume = {2},\n\tnumber = {2},\n\tjournal = {Journal of Information and Data Management (JIDM)},\n\tauthor = {Mattoso, Marta and Braganholo, Vanessa and Lima, Alexandre and Murta, Leonardo},\n\tyear = {2011},\n\tpages = {123--138},\n}\n\n
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\n\n \n \n \n \n \n An Algebraic Approach for Data-Centric Scientific Workflows.\n \n \n \n\n\n \n Ogasawara, E.; Dias, J.; Oliveira, D.; Porto, F.; Valduriez, P.; and Mattoso, M.\n\n\n \n\n\n\n
PVLDB, 4(12): 1328–1339. 2011.\n
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@article{ogasawara_algebraic_2011,\n\ttitle = {An {Algebraic} {Approach} for {Data}-{Centric} {Scientific} {Workflows}},\n\tvolume = {4},\n\tissn = {2150-8097},\n\tnumber = {12},\n\turldate = {2011-05-20},\n\tjournal = {PVLDB},\n\tauthor = {Ogasawara, Eduardo and Dias, Jonas and Oliveira, Daniel and Porto, Fabio and Valduriez, Patrick and Mattoso, Marta},\n\tyear = {2011},\n\tkeywords = {Measurement, Workflow management, design, experimentation, performance, scientific databases},\n\tpages = {1328--1339},\n}\n\n
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\n\n \n \n \n \n \n Adding Ontologies to Scientific Workflow Composition.\n \n \n \n\n\n \n Oliveira, D.; Ogasawara, E.; Baiao, F.; and Mattoso, M.\n\n\n \n\n\n\n In
XXVI SBBD, pages 1–8, Florianópolis, SC, Brazil, 2011. \n
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@inproceedings{oliveira_adding_2011,\n\taddress = {Florianópolis, SC, Brazil},\n\ttitle = {Adding {Ontologies} to {Scientific} {Workflow} {Composition}},\n\tbooktitle = {{XXVI} {SBBD}},\n\tauthor = {Oliveira, Daniel and Ogasawara, Eduardo and Baiao, Fernanda and Mattoso, Marta},\n\tyear = {2011},\n\tpages = {1--8},\n}\n\n
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