Kary Ocaña

D.Sc., LABINFO/LNCC
Pleno Technologist

LABINFO / Laboratory of Bioinformatics
LNCC / National Laboratory of Scientific Computing
Petrópolis, Rio de Janeiro - Brazil


Main

Short Bio

Research Interests

Collaborations

Publications

Projects

Software

Contact

Short Bio

    Kary Ocaña is a Pleno Technologist of the Bioinformatics Laboratory (LABINFO) at the National Laboratory of Scientific Computing (LNCC). She was Post-Doc (2010 - 2015) of the Department of Computer Science at the COPPE Institute of the Federal University of Rio de Janeiro (Brazil) and was supported by a FAPERJ's grant "Post-doc nota 10" (2013 - 2015). She received both her D.Sc. (2010) and M.Sc. (2006) in Cellular and Molecular Biology from the Oswaldo Cruz Institute (FIOCRUZ) (Rio de Janeiro, Brazil) and her B.Sc. (2002) in Pharmaceutical Biochemistry from the National University of San Marcos (Lima, Peru). She participates in research projects in those areas, with funding from Brazilian government agencies as CNPq, CAPES and FAPERJ and is a member of IEEE, ACM and of the Brazilian Computer Society.

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Research Interests

    My research interests covered areas in bioinformatics and computer science, working on the following topics: evolutionary and comparative genomics , phylogenomics , development of software applications for bioinformatics and computational biology , e-Science , scientific workflows for bioinformatics , cloud computing , parallelism , provenance and data mining

Collaborations

Publications

  1. Marinho, A; Oliveira, D. C. M.; Ogasawara, E; Silva, V; Ocaña, K.A.C.S.; Murta, L; Braganholo, V; Mattoso, M. Deriving scientific workflows from algebraic experiment lines: A practical approach. Future Generation Computer Systems, v. 68, p. 111-127, 2017.
  2. Coutinho, R; Frota, Y; Ocaña, K; de Oliveira, D; Drummond, L. M. A. A Dynamic Cloud Dimensioning Approach for Parallel Scientific Workflows: a Case Study in the Comparative Genomics Domain. Journal of Grid Computing, v. 14, p. 443-461, 2016.
  3. Mattoso, M. L. Q.; Dias, J.; ocaña, K.A.C.S.; Ogasawara, E.; Costa, F.; Horta, F.; Silva, V.; Oliveira, D. C. M. Dynamic steering of HPC scientific workflows: A survey. Future Generation Computer Systems, v. 46, p. 100-113, 2015.
  4. Ocaña, K.A.C.S.; Oliveira, D. C. M. Parallel computing in genomic research: advances and applications. Advances and Applications in Bioinformatics and Chemistry, p. 23-35, 2015.
  5. Wagner, G.; Jardim, R.; Tschoeke, D.; Loureiro, D. R.; Ocaña, KARY ACS; Ribeiro, A. C. B.; Emmel, V. E.; Probst, C. M.; Pitaluga, A. N.; Grisard, E. C.; Cavalcanti, Maria C; Campos, M. L. M.; Mattoso, M. L. Q.; Davila, A. M. R. STINGRAY: system for integrated genomic resources and analysis. BMC Research Notes, v. 7, p. 132, 2014.
  6. Gonçalves, J.; Oliveira, D. C. M.; Oliveira, D. C. M.; Ocaña, K.A.C.S.; Ogasawara, E.; Dias, J.; Mattoso, M. L. Q. Performance Analysis of Data Filtering in Scientific Workflows. Journal of Information and Data Management - JIDM, v. 4, p. 17-26, 2013.
  7. Ocaña, K.A.C.S.; Oliveira, D. C. M.; Dias, J.; Ogasawara, E.; Mattoso, M. L. Q. Designing a parallel cloud based comparative genomics workflow to improve phylogenetic analyses. Future Generation Computer Systems, v. 29, p. 2205-2219, 2013.
  8. Oliveira, D. C. M.; Oliveira, D. C. M.; Ocaña, K.A.C.S.; Ogasawara, E.; Dias, J.; Gonçalves, J.; Baião, F. A.; Mattoso, M. L. Q. Performance evaluation of parallel strategies in public clouds: A study with phylogenomic workflows. Future Generation Computer Systems, v. 29, p. 1816-1825, 2013.
  9. Oliveira, D. C. M.; Ocaña, K.A.C.S.; Baião, F. A.; Mattoso, M. L. Q. A Provenance-based Adaptive Scheduling Heuristic for Parallel Scientific Workflows in Clouds. Journal of Grid Computing, v. 10, p. 521-552, 2012.
  10. Oliveira, D. C. M.; Ocaña, K.A.C.S.; Ogasawara, E.; Baião, F. A.; Mattoso, M. L. Q. An Adaptive Parallel Execution Strategy for Cloud-based Scientific Workflows. Concurrency and Computation, v. 24, p. 1531-1550, 2012.
  11. Kary A. C. S. Ocaña; Davila, A. M. R. Phylogenomics-Based Reconstruction of Protozoan Species Tree. Evolutionary Bioinformatics Online, p. 107-121, 2011.
  12. Davila, A. M. R.; Mendes, P. N.; Wagner, G.; Tschoeke, D.; Cuadrat, R. R. C.; Liberman, F.; Matos, L.; Satake, T.; Ocaña, K.A.C.S.; Triana, O.; Cruz, S. M. S.; Jucá, H.; Mattoso, M. L. Q. ProtozoaDB: dynamic visualization and exploration of protozoan genomes ( the Annual Database Issue). Nucleic Acids Research, v. 36, p. D547-D552, 2008.

  1. Ramos, L. S; Ocaña, K.A.C.S.; Oliveira, D. C. M. Um Sistema de Informação para Gerência de Projetos Científicos baseados em Simulações Computacionais. In: Simpósio Brasileiro de Sistemas de Informação - SBSI, 2016, Florianópolis. Anais do Simpósio de Sistemas de Informação - SBSI. Porto Alegre: Sociedade Brasileira de Computação, 2016.
  2. Oliveira, W.; Missier, P.; Ocaña, K.A.C.S.; Oliveira, D. C. M.; Braganholo, V. Analyzing Provenance across Heterogeneous Provenance Graphs. In: International Provenance and Annotation Workshop (IPAW), 2016, Washington, D.C. Provenance and Annotation of Data and Processes, 2016. v. 9672. p. 57-70.
  3. Mondelli, M. L.; Tonelli, M.; Ocaña, K.A.C.S.; Vasconcelos , A. T. R.; Gadelha, L. HPSW-Prof: A Provenance-Based Framework for Profiling High Performance Scientific Workflows. In: XXXI Simpósio Brasileiro de Banco de Dados, 2016, Bahia. Sessão de Demos do XXXI Simpósio Brasileiro de Banco de Dados, 2016.
  4. Tallarida, G.; Ocaña, K.A.C.S.; Aline Paes; Braganholo, V.; Oliveira, D. C. M. Gerência de Incerteza em Bancos de Dados de Proveniência em Bioinformática. In: XXXI Simpósio Brasileiro de Banco de Dados, 2016, Salvador, Bahia. Anais do XXXI Simpósio Brasileiro de Banco de Dados, 2016.
  5. Ocaña, K.A.C.S.; Oliveira, D. C. M.; Silva, V.; Mattoso, M. L. Q. Data Analytics in Bioinformatics: Data Science in Practice for Genomics Analysis Workflows. In: 11th IEEE International Conference on eScience, 2015, Munique, Alemanha. Proceedings of the 11th IEEE International Conference on eScience, 2015.
  6. Castro, R.; Souza, R.; Silva, V.; Kary A. C. S. Ocaña; Oliveira, D. C. M.; Mattoso, M. L. Q. Uma Abordagem para Publicação de Dados de Proveniência de Workflows Científicos na Web Semântica. In: XXX Simpósio Brasileiro de Banco de Dados, 2015, Petrópolis, RJ. Anais do XXX Simpósio Brasileiro de Banco de Dados, 2015.
  7. Ocaña, K.A.C.S.; Benza, S.; Oliveira, D. C. M.; Dias, J.; Mattoso, M. L. Q. Exploring Large Scale Receptor-Ligand Pairs in Molecular Docking Workflows in HPC Clouds. In: 13th IEEE International Workshop on High Performance Computational Biology (HiComb 2014), 2014, Phoenix, Arizona, USA. Proc. of the 13th IEEE International Workshop on High Performance Computational Biology (HiComb 2014), 2014.
  8. Coutinho, R.; Drummond, L.; Frota, Y.; Oliveira, D. C. M.; Ocaña, K.A.C.S. Evaluating Grasp-based Cloud Dimensioning for Comparative Genomics: a Practical Approach. In: Second International Workshop on Parallelism in Bioinformatics, 2014, Madrid. Proc. of the Second International Workshop on Parallelism in Bioinformatics, 2014.
  9. Oliveira, W.; Neves, V.; Ocaña, K.A.C.S.; Murta, L.; Oliveira, D. C. M.; Braganholo, V. Captura e Consulta a Dados de Proveniência Retrospectiva Implícita Intra-Atividade. In: XXIX Simpósio Brasileiro de Banco de Dados, 2014, Curitiba - Parana. Anais do XXIX Simpósio Brasileiro de Banco de Dados. Porto Alegre: Sociedade Brasileira de Computação, 2014.
  10. Oliveira, D. C. M.; Costa, F.; Silva, V.; Ocaña, K.A.C.S.; Mattoso, M. L. Q. Debugging Scientific Workflows with Provenance: Achievements and Lessons Learned. In: XXIX Simpósio Brasileiro de Banco de Dados, 2014, Curitiba - Paraná. Anais do XXIX Simpósio Brasileiro de Banco de Dados. Porto Alegre: Sociedade Brasileira de Computação, 2014.
  11. Ocaña, K.A.C.S.; Oliveira, D. C. M.; Silva, V.; Benza, S.; Mattoso, M. L. Q. Exploiting the Parallel Execution of Homology Workflow Variants in HPC Compute Clouds. In: 4th International Workshop on Cloud Computing and Scientific Applications (CCSA 2014), 2014, Paris. Proc. of the 4th International Workshop on Cloud Computing and Scientific Applications (CCSA 2014), 2014.
  12. Costa, F.; Silva, V.; Oliveira, D. C. M.; Ocaña, K; Ogasawara, E.; Dias, J.; Mattoso, M. L. Q. Capturing and Querying Workflow Runtime Provenance with PROV: a Practical Approach. In: International Workshop on Managing and Querying Provenance Data at Scale (Held in conjunction with EDBT/ICDT 2013), 2013, Genova, Italy. Proceedings of the International Workshop on Managing and Querying Provenance Data at Scale, 2013.
  13. Oliveira, D. C. M.; Viana, V .G.; Ogasawara, E.; Ocaña, K.; Mattoso, M. L. Q. Dimensioning the Virtual Cluster for Parallel Scientific Workflows in Clouds. In: Workshop on Scientific Cloud Computing (ScienceCloud), 2013, New York, NY. Proc. of the 4th Workshop on Scientific Cloud Computing (ScienceCloud), 2013.
  14. Mattoso, M. L. Q.; Dias, J.; Oliveira, D. C. M.; Ocaña, K; Ogasawara, E.; Costa, F.; Horta, F.; Silva, V.; Araujo, I . User-Steering on HPC Workflows: State of the Art and Future Directions. In: The 2nd international workshop on Scalable Workflow Enactment Engines and Technologies (SWEET'13), 2013, New York. Proc. of the The 2nd international workshop on Scalable Workflow Enactment Engines and Technologies (SWEET'13), 2013.
  15. Araujo, I; Dias, J.; Oliveira, D. C. M.; Ogasawara, E.; Ocaña, K; Mattoso, M. L. Q. Runtime Dynamic Structural Changes of Scientific Workflows in Clouds. In: International Workshop on Clouds and (eScience) Applications Management - CloudAM 2013. In: International Workshop on Clouds and (eScience) Applications Management - CloudAM 2013, 2013, Dresden. Proceedings of the International Workshop on Clouds and (eScience) Applications Management - CloudAM 2013. New York: IEEE Computer Society, 2013., 2013.
  16. Pintas, J.; Oliveira, D. C. M.; Ocaña, K.; Ogasawara, E.; Mattoso, M. L. Q. SciLightning: a Cloud Provenance-based Event Notification for Parallel Workflows. In: 3rd International Workshop on Cloud Computing and Scientific Applications (CCSA), 2013, Berlim. Proceedings of the 3rd International Workshop on Cloud Computing and Scientific Applications (CCSA), 2013.
  17. Oliveira, D. C. M.; Ocaña, K; Ogasawara, E.; Dias, J.; Gonçalves, J.; Mattoso, M. L. Q. Cloud-based Phylogenomic Inference of Evolutionary Relationships: A Performance Study. In: 2nd International Workshop on Cloud Computing and Scientific Applications (CCSA), held in conjunction with the 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2012), 2012, Ottawa, Canadá. Proceedings of the 2nd International Workshop on Cloud Computing and Scientific Applications (CCSA), held in conjunction with the 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2012), 2012., 2012.
  18. Gonçalves, J.; Oliveira, D. C. M.; Ogasawara, E.; Ocaña, K; Mattoso, M. L. Q. Using Domain-Specific Data to Enhance Scientific Workflow Steering Queries. In: 4th International Provenance and Annotation Workshop, 2012, Santa Barbara, CA. Proceedings of the 4th International Provenance and Annotation Workshop. Heildelberg: Springer Verlag, 2012.
  19. Ocaña, K; Oliveira, D. C. M.; Horta, F.; Dias, J.; Ogasawara, E.; Mattoso, M. L. Q. Exploring Molecular Evolution Reconstruction Using a Parallel Cloud-based Scientific Workflow. In: Brazilian Symposium on Bioinformatics, 2012, Campo Grande. MT. Proceedings of the Brazilian Symposium on Bioinformatics 2012. Heildelberg: Springer Verlag, 2012.
  20. Costa, F.; Oliveira, D. C. M.; Ocaña, K; Ogasawara, E.; Mattoso, M. L. Q. Enabling Re-Executions of Parallel Scientific Workflows Using Runtime Provenance Data. In: 4th International Provenance and Annotation Workshop, 2012, Santa Barbara, CA. Proceedings of the 4th International Provenance and Annotation Workshop. Heildelberg: Springer Verlag, 2012.
  21. Pintas, J.; Oliveira, D. C. M.; Ocaña, K.A.C.S.; Dias, J.; Mattoso, M. L. Q. Monitoramento em Tempo Real de Workflows Científicos Executados em Paralelo em Ambientes Distribuídos. In: VI e-Science Workshop (em conjunto com CSBC 2012), 2012, Porto Alegre, Curitiba. Anais do VI e-Science Workshop (em conjunto com CSBC 2012), 2012.
  22. Gonçalves, J.; Oliveira, D. C. M.; Ocaña, K.A.C.S.; Ogasawara, E.; Dias, J.; Mattoso, M. L. Q. Using Provenance Analyzers to Improve the Performance of Scientific Workflows in Cloud Environments. In: 27º Simpósio Brasileiro de Bancos de Dados (SBBD 2012), 2012, São Paulo. Anais do 27º Simpósio Brasileiro de Bancos de Dados (SBBD 2012). Porto Alegre: Sociedade Brasileira de Computação, 2012.
  23. Ocaña, K.A.C.S.; Oliveira, D. C. M.; Dias, J.; Ogasawara, E.; Mattoso, M. L. Q. Discovering Drug Targets for Neglected Diseases Using a Pharmacophylogenomic Cloud Workflow. In: 8th IEEE International Conference on eScience 2012, 2012, Chicago, IL. Proceedings of the 8th IEEE International Conference on eScience 2012. New York: IEEE Computer Society, 2012.
  24. Kary A. C. S. Ocaña; Oliveira, D. C. M.; Ogasawara, E.; Davila, A. M. R.; Lima, A. A. B.; Mattoso, M. L. Q. SciPhy: A Cloud-based Workflow for Phylogenetic Analysis of Drug Targets in Protozoan Genomes. In: Brazilian Symposium on Bioinformatics, 2011, Brasilia, DF. Proceedings of the Brazilian Symposium on Bioinformatics. Advances in Bioinformatics and Computational Biology. Springer Berlin Heidelberg: Berlin, Heidelberg, 2011. v. 6832. p. 66-71.
  25. Ocaña, Kary A.C.S.; Oliveira, D. C. M.; Dias, J.; Ogasawara, E.; Mattoso, M. L. Q. Optimizing Phylogenetic Analysis Using SciHmm Cloud-based Scientific Workflow. In: 2011 IEEE 7th International Conference on EScience (eScience), 2011, Stockholm. 2011 IEEE Seventh International Conference on eScience. p. 190-197.
  26. Oliveira, D. C. M.; Kary A. C. S. Ocaña; Ogasawara, E.; Dias, J.; Baião, F. A.; Mattoso, M. L. Q. A Performance Evaluation of X-ray Crystallography Scientific Workflow Using SciCumulus. In: Fourth IEEE 2011 International Conference on Cloud Computing (CLOUD 2011), 2011, Washington D.C. Proceedings of the Fourth IEEE 2011 International Conference on Cloud Computing (CLOUD 2011).
Active Projects

  • 2017 - Atual: Mineração de Dados de Experimentos de Bioinformática Executados em Larga Escala no Apoio ao Estudo de Doenças Negligenciadas e Doenças Genômicas em Humanos, Universal MCTI/CNPq 01/2016 R$ 30,000.00
  • 2016 - Atual: Gerenciamento e Análise de Dados Biológicos em Plataformas de Computação de Alto Desempenho (HPC) e de Processamento de Grandes Massas de Dados (Big Data), PRONEM Nº 04/2016 R$ 250.000,00
  • 2016 - Atual: Estudo Molecular das Doenças Genéticas Crônicas: Defeitos Congênitos, Doença do Desenvolvimento e Câncer Infantil, a partir da Via das RASopatias - Apoio as Instituições de Ensino Sediadas no RJ
  • 2016 - Atual: Metodologias, Ferramentas e Abstrações para Produtividade em Computação Científica de Alto Desempenho, DCTR E_15/2016 R$ 400,000.00
  • 2016 - Atual: Apoio à manutenção da infraestrutura do centro multiusuário Unidade de Genômica Computacional Darcy Fontoura de Almeida (UGCDFA) - Edital FAPERJ No 13/2016
  • 2016 - Atual: BioMiningHPC: Arquitetura baseada em Workflows, Mineração e Proveniência de Dados de Experimentos de Bioinformática para Ambientes HPC no Apoio ao Estudo de Doenças Negligenciadas e Doenças Genômicas Raras em Humanos, APQ1_2015/2, R$ 11,000.00
  • 2016 - Atual: Genômica Computacional do Vírus da Zika (ZIKV)
  • 2016 - Atual: Plataforma Computacional Multiusuária para Análises de Bioinformática em Larga Escala, no Apoio à Rede Nacional Estruturante de Bioinformática
  • 2015 - Atual: Estruturação da Rede Nacional de Bioinformática
  • 2014 - Atual: RABICÓ: Advanced Network on Computational Biology (LNCC/UFRJ/UFRGS)
  • 2014 - Atual: Advanced Research Network on Marine Biotechnology (IB-UFRJ/COPPE-UFRJ/LNCC)
  • 2014 - Atual: Music – Scientific Data Management in a Multi-site Cloud, FAPERJ-INRIA, 2014-2016, International Collaboration.
  • 2014 - 2016: SciCumulus/C2 – Parallel Scientific Workflow Management System
  • 2014 - 2016: Windows Azure for Research Proposal: User-Steering Phylogenetic Workflows in the Cloud
  • 2013 - 2015: TargFlow: Descoberta de Alvos Potenciais para Desenho de Novas Drogas por meio de Sistemas de Gerência de Workflows Científicos
  • 2012 - 2015: Apoio computacional ao desenvolvimento científico em larga escala, Universal 14/2011 - R$ 144.000,00
  • 2010 - 2013: Análises de Filogenia e Evolução Explorando Sistemas de Gerência de Workflows Científicos na Descoberta de Alvos Potenciais para Desenho de Novas Drogas para Protozoários
  • 2009 - 2010: CNPQ - MAPA - 578730/2008-1 - Desenvolvimento e Validação de um Sistema Integrado para Diagnóstico e Genotipagem de Protozoários Patogênicos de Interesse Veterinário

Software

Contact

Kary Ocaña at LABINFO - LNCC