Kary Ocaña

D.Sc., LABINFO/LNCC
Researcher Pleno Technologist I-II

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

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Short Bio

Research Interests

Student Supervision

Collaborations

Courses

Publications

Projects

Distinctions

Software

Contact

Short Bio

    Kary Ocaña is a Researcher Pleno Technologist of the Bioinformatics Laboratory (LABINFO) at the National Laboratory of Scientific Computing (LNCC). She was Post-Doc (2010 - 2015) and was supported by a FAPERJ's grant "Post-doc note 10" (2013 - 2015) of the Department of Computer Science at the COPPE Institute of the Federal University of Rio de Janeiro (UFRJ, RJ-Brazil). She was awarded as Young Scientist of Our State by FAPERJ since 2017. In 2018 realized a scientific visit at the Center of Bioinformatics, Biostatistics, and Integrative Biology at Institut Pasteur (Paris-France), reinforcing collaborative research. She received both her D.Sc. (2010) and M.Sc. (2006) in Cellular and Molecular Biology from the Oswaldo Cruz Institute (FIOCRUZ, RJ-Brazil) and her B.Sc. (2002) in Pharmaceutical Biochemistry from the National University of San Marcos (UNMSM, Lima-Peru) and UFRJ. She participates in research projects in those areas, with funding from Brazilian government agencies as CNPq, CAPES and FAPERJ and is a member of SBC, IEEE and ACM.

    • DBLP • CV Lattes • Google Scholar • ResearchGate • Orcid • Twitter • Linkedin

Research Interests

    My research interests covered areas in bioinformatics and computer science, working on the following topics: phylogenomics , genomics , development of bioinformatics software , e-Science , scientific workflows for bioinformatics , high performance computing , data analytics in bioinformatics , provenance and machine learning

Student Supervision

    I am available to supervise students undertaking research projects in the field of Bioinformatics and Computer Science in our Masters or PhD programs and supervision of undergraduate independent research projects that integrate Bioinformatics, Computational Biology, or a related field, with a strong genomic, phylogenetic and e-science components. Please find my contact details here.

Collaborations

Courses

  • 2018 - Apoio computacional a análises filogenômicas em larga escala. Ocaña, K. A. C. S.; Soares, A. E. R.; Saboia, G. D. D.
  • 2016 - Bioinfo-Portal: A Scientific Gateway for Integrating Bioinformatics Tools in the Brazilian National High-Performance Computing Network. Ocaña, K. A. C. S.; Vasconcelos, A. T. R.; Teixeira, S. M. R.; Oliveira, P. S. L.; Gadelha, L.; Galheigo, M.; Bastos, B. F.

Publications

    For a complete list of publications, please refer to my CV at Lattes platform.

    Papers in Journal

    1. De Azevedo-Martins, Allan C.; Ocaña, K. A. C. S.; de Souza, W.; Vasconcelos, A. T. R.; Teixeira, M. M. G.; Camargo, E. P.; Alves, J. M. P.; Motta, M. C. M. The Importance of Glycerophospholipid Production to the Mutualist Symbiosis of Trypanosomatids. Pathogens, v. 11, p. 41, 2022.
    2. Machado, V.; Bom, C.; Ocaña, K. A. C. S.; Terra, R.; Chaves, M. Using Deep Learning Transformer Networks to Identify Symptoms Associated with COVID-19 on Twitter. Notas Técnicas do CBPF, v. 12, p. 1-10, 2022.
    3. Guedes, T.; Jesus, L. A.; Ocaña, K. A. C. S.; Drummond, L. M. A.; Oliveira, D. C. M. Provenance-based fault tolerance technique recommendation for cloud-based scientific workflows: a practical approach. Cluster Computing-The Journal of Networks Software Tools and Applications, v. 23, p. 123-148, 2020.
    4. Guedes, T.; Martins, L. B.; Falci, M. L. F.; Silva, V.; Ocaña, K. A. C. S.; Mattoso, M.; Bedo, M.; Oliveira, D. Capturing and Analyzing Provenance from Spark-based Scientific Workflows with SAMbA-RaP. Future Generation Computer Systems, v. 112, p. 658-669, 2020.
    5. Ocaña, K. A. C. S.; Galheigo, M.; Osthoff, C.; Gadelha, L. M. R.; Porto, F.; Gomes, A. T. A.; Oliveira, D.; Vasconcelos, A. T. BioinfoPortal: A scientific gateway for integrating bioinformatics applications on the Brazilian national high-performance computing network. Future Generation Computer Systems, v. 107, p. 192-214, 2020.
    6. Guerine, Marcos; Stockinger, Murilo B.; Rosseti, Isabel; Simonetti, Luidi G.; Ocaña, K. A. C. S.; Plastino, Alexandre; de Oliveira, Daniel. A Provenance-based heuristic for preserving results confidentiality in cloud-based scientific workflows. Future Generation Computer Systems-The International Journal of eScience, v. 1, p. 1, 2019.
    7. Maria Luiza Mondelli, Thiago Magalhães, Guilherme Loss, Michael Wilde, Ian Foster, Marta Mattoso, Daniel S. Katz, Helio J. C. Barbosa, Ana Tereza R. Vasconcelos, Kary Ocaña, Luiz M. R. Gadelha Jr. BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments. PeerJ, v.1, p.1, 2018.
    8. Oliveira, W.; Ocaña, K. A. C. S.; Oliveira, D. C. M.; Braganholo, Vanessa. Querying Provenance along with Domain Data Using Prolog. Journal of information and Data Management, v. 8, p. 1-16, 2017.
    9. Neves, V.; Ocaña, K. A. C. S.; Oliveira, D. C. M.; Murta, L.; Braganholo, V. Managing Provenance of Implicit Data Flows in Scientific Experiments. ACM Transactions on Internet Technology, v. 1, p. 1, 2017.
    10. 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.
    11. 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.
    12. 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.
    13. 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.
    14. 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.
    15. 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.
    16. 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.
    17. 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.
    18. 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.
    19. 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.
    20. Kary A. C. S. Ocaña; Davila, A. M. R. Phylogenomics-Based Reconstruction of Protozoan Species Tree. Evolutionary Bioinformatics Online, p. 107-121, 2011.
    21. 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.

    Papers in Conference

    1. Silva, L. C.; Coelho, M.; Terra, R. S.; Carvalho, D.; Gadelha, L. M. R.; Osthoff, C.; Ocaña, K. A. C. S. Workflows Científicos de RNA-Seq em Ambientes Distribuídos de Alto Desempenho: Otimização de Desempenho e Análises de Dados de Expressão Diferencial de Genes. In: Brazilian e-Science Workshop (BreSci 2021), 2021, Florianópolis, Santa Catarina. Anais do XV Brazilian e-Science Workshop, 2021.
    2. Terra, R. S.; Osthoff, C.; Carvalho, D.; Ocaña, K. A. C. S.; Coelho, M.; Gadelha, L.; Garcia-Zapata, M. T. A.; Silva, L. C. Gerência e Análises de Workflows aplicados a Redes Filogenéticas de genomas de Dengue no Brasil. In: Brazilian e-Science Workshop (BreSci 2021), 2021, Florianópolis, Santa Catarina. Anais do XV Brazilian e-Science Workshop, 2021.
    3. Ocaña, K. A. C. S.; Silva, V. S.; Costa, M. O. C.; Castro, M. C. S.; Silva, H. S. ; Walter, M. E. M. T. ; Melo, A. C. M. A.; Santos, M. T.; Nicolas, M. F.; Carvalho, A. C. C.; Henriques-Pons, A.; Silva, F. A. B. CellHeap: a Workflow for Optimizing COVID-19 Single-Cell RNA-seq Data Processing in the Santos Dumont Supercomputer. In: Brazilian Symposium on Bioinformatics, 2021, Online. Brazilian Symposium on Bioinformatics, 2021.
    4. Ocaña, K. A. C. S.; Coelho, M.; Freire, G.; Osthoff, C. High-Performance Computing of BEAST/BEAGLE in Bayesian Phylogenetics using SDumont Hybrid Resources. In: Brazilian e-Science Workshop (BreSci 2020), 2020, Cuiabá, Mato Grosso. Anais do XIV Brazilian e-Science Workshop, 2020.
    5. Silva, L. C. ; Coelho, M. ; GADELHA, LUIZ M.R. ; Ocaña, K. A. C. S.; Osthoff, C. Avaliação de Desempenho de um Workflow Científico para Experimentos de RNA-Seq no Supercomputador Santos Dumont. In: Workshop de Iniciação Científica em Arquitetura de Computadores e Computação de Alto Desempenho (WSCAD 2020 - WIC), 2020. Anais do Workshop de Iniciação Científica em Arquitetura de Computadores e Computação de Alto Desempenho, 2020.
    6. Ocaña, K. A. C. S.; Guedes, T.; Oliveira, D. C. M. ArrOW: Experiencing a Parallel Cloud-based De Novo Assembler Workflow. In: 18th IEEE International Workshop on High Performance Computational Biology (HiCOMB, in conjunction with IPDPS 2019), 2019, Rio de Janeiro. Proceedings of the 18th IEEE International Workshop on High Performance Computational Biology, 2019.
    7. Ocaña, K. A. C. S.; Galheigo, M.; Osthoff, C.; Gadelha, L.; Gomes, A. T. A.; Oliveira, D. C. M.; Porto, F. A. M.; Vasconcelos, A. T. R. Towards a Science Gateway for Bioinformatics: Experiences in the Brazilian System of High Performance Computing. In: Workshop on Clusters, Clouds and Grids for Life Sciences (In conjunction with CCGrid 2019 - 19th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing), 2019, Cyprus. Proceedings of the Workshop on Clusters, Clouds and Grids for Life Sciences (In conjunction with CCGrid 2019 - 19th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing), 2019.
    8. Valduriez, P.; Mattoso, M. L. Q.; Akbarinia, R.; Borges, H ; Camata, J.; Coutinho, A.; Gaspar, D.; Lemus, N ; Liu, J.; Lustosa, H ; Masseglia, F ; Silva, F. N.; Silva, Vitor ; Souza, R.; Ocaña, K. A. C. S.; Ogasawara, E.; Oliveira, D. C. M.; Pacitti, E.; Porto, F. A. M.; Shasha, D. Scientific Data Analysis Using Data-Intensive Scalable Computing: the SciDISC Project. In: 1st LADaS - Latin American Data Science Workshop, 2018, Rio de Janeiro. Proceedings of the 1st LADaS - Latin American Data Science Workshop (in conjunction with VLDB'18), 2018.
    9. Saboia, G. D. D.; Souza, J.; Vasconcelos, A. T. R.; Soares, A. E. R.; Ocaña, K. A. C. S. Tratamento e Integração de Metadados Genômicos Mitocondriais em Filogenômica. In: Brazilian Symposium on Bioinformatics, 2018, Niterói, Rio de Janeiro. BSB - Short Papers Proceedings, 2018.
    10. Coelho, M.; Osthoff, C.; Ocaña, K. A. C. S. Avaliação do RAxML no Supercomputador Santos Dumont. In: Brazilian Symposium on Bioinformatics, 2018, Niterói, Rio de Janeiro. BSB - Short Papers Proceedings, 2018.
    11. Consulmagnos, A.; Kalinowski, M.; Ocaña, K. A. C. S.; Oliveira, D. C. M. SciAgile: Applying Agile Methodologies in Scientific Simulation-based Experiments. In: Ibero-American Software Engineering Conference - Experimental Software Engineering Track (ESELAW), 2017, Buenos Aires, Argentina. Proceedings of the Ibero-American Software Engineering Conference - Experimental Software Engineering Track (ESELAW), 2017.
    12. Guedes, T.; Ocaña, K. A. C. S.; Oliveira, D. C. M. SciPhyloMiner: a Workflow for Mining of Protozoan Phylogenomic Data. In: Brazilian e-Science Workshop (E-Science), 2017, São Paulo. Anais do XI Brazilian e-Science Workshop (BreSci). Porto Alegre: Brazilian Computer Society, 2017.
    13. Pina, D.; Campos, V.; Silva, V.; Ocaña, K. A. C. S.; Oliveira, D. C. M.; Mattoso, M. BioSciCumulus: a portal for analysis of provenance data in computational biology workflows. In: Brazilian e-Science Workshop (e-Science), 2017, São Paulo. XI Brazilian e-Science Workshop (BreSci). Porto Alegre: Brazilian Computer Society, 2017, 2017.
    14. Silva, F. N.; Ocaña, K. A. C. S.; Silva, V.; Braganholo, V.; Oliveira, D. C. M. A Strategy for Versioning of Scientific Workflows in Cloud Execution. In: Brazilian e-Science Workshop (e-Science), 2017, São Paulo. XI Brazilian e-Science Workshop (BreSci). Porto Alegre: Brazilian Computer Society, 2017.
    15. 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.
    16. 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.
    17. 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.
    18. 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.
    19. 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.
    20. 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.
    21. 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.
    22. 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.
    23. 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.
    24. 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.
    25. 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.
    26. 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.
    27. 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.
    28. 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.
    29. 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.
    30. 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.
    31. 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.
    32. 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.
    33. 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.
    34. 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.
    35. 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.
    36. 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.
    37. 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.
    38. 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.
    39. 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.
    40. 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).

Projects

    For a complete list of my main ongoing research activities, please refer to my CV at Lattes platform.

    1. 2018: “Computational Support for Genomic Analysis of Neglected Tropical Diseases through Data Mining and Machine Learning”, FAPERJ R$ 75,600.00.
    2. 2017: “Data mining for Bioinformatic Experiments Executed in Large-scale Supporting Neglected Diseases and Rare Genomic Diseases in Humans”, Universal MCTI/CNPq 01/2016 R$ 30,000.00.
    3. 2016: “Management and Analyze of Biological Data in High Performance Computing (HPC) Platforms and Processing of Big Data”, PRONEM Nº 04/2016 R$ 250.000,00.
    4. 2016: “Molecular Study of Chronic Genetic Diseases: Congenital Defects, Disease of the Development and Infant Cancer, from the RASopathies”, Support for Teaching Institutions at RJ, Edital FAPERJ Nº 15/2015.
    5. 2016: “Methodologies, Tools, and Abstractions for the Productivity of Scientific High Performance Computing”, DCTR E_15/2016 R$ 400,000.00.
    6. 2016: “Support for the maintenance of the infrastructure of the Multiuser Unit of the Computational Genomics Darcy Fontoura de Almeida (UGCDFA)”, Edital FAPERJ No 13/2016.
    7. 2016: “BioMiningHPC: Architecture Based on Workflow, Mining, and Provenance Data from Bioinformatics Experiments for HPC Environments in Support of the Study of Neglected Diseases and Rare Genomic Diseases in Humans”, APQ1_2015/2, R$ 11,000.00.
    8. 2016: “Computational Genomics of the Virus Zika (ZIKV). Public Selection of Proposal to support ZIKA Virus Research Projects”, MCTI/FINEP/FNDCT 01/2016.
    9. 2016: “Multiuser Computational Platform for Bioinformatics Analysis in Large Scale, Supporting the National Structuring Network of Bioinformatics”, Proposal for use of the Supercomputer Santos Dumont (SDumont).
    10. 2014: “RABICÓ: Advanced Network on Computational Biology”, (LNCC/UFRJ/UFRGS). Edital Computational Biology, CAPES n.º 051/201.
    11. 2014: “Advanced Research Network on Marine Biotechnology”, (IB-UFRJ/COPPE-UFRJ/LNCC). Call MCTI / CNPq / FNDCT - Transversal Action Nº 63/2013 - Structuring of a Marine Biotechnology Research Network.
    12. 2015 - 2017: “Structuring of the Brazilian Bioinformatics Network”, MCTI, CNPq 456644/2013-0.
    13. 2014 - 2017: “Music – Scientific Data Management in a Multi-site Cloud”, FAPERJ-INRIA, International Collaboration Edital 36/2013.
    14. 2014 - 2016: “SciCumulus/C2 – Parallel Scientific Workflow Management System”, Edital Universal 14/2013 - Range A.
    15. 2014 - 2016: “Windows Azure for Research Proposal: User-Steering Phylogenetic Workflows in the Cloud”, Sponsor: Microsoft Corporation.
    16. 2013 - 2015: “TargFlow: Discovery of Potential Targets for Designing New Drugs through Scientific Workflow Management Systems”, Grand Post-doctoral Note 10 – 2013. Edital FAPERJ n.º 04/2013.
    17. 2012 - 2015: “Computational Support for Large-Scale Scientific Development”, Universal 14/2011 - R$ 144.000,00.
    18. 2010 - 2013: “Analysis of Phylogeny and Evolution Exploring Management Systems for Scientific Workflows in the Discovery of Potential Targets for Designing New Drugs for Protozoa”, Edital FAPERJ nº10/2010.

Distinctions

    1. 2022: Master's Grade 10 - Student Orientation Rafael de Souza Terra, LNCC, FAPERJ.
    2. 2020: Honorable Mention for the Second Place in the Scientific Initiation Workshop on Computer Architecture and High-Performance Computing (WSCAD-WIC 2020), XXI Symposium on High-Performance Computing Systems.
    3. 2019-2020: Scientific Visit at the Gottingen University. Institute of Clinical Informatics in the University of Gottingen – Germany.
    4. 2018: Invitation for a scientific visit to develop the project entitled “Adaptive processes in HIV‐1 for detecting the population evolution and estimating the rate of persistence during infection”; hosted in the Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, from April 02th to June 26th, 2018..
    5. 2018: Young Scientist of Our State (JCNE) by the FAPERJ (Research Support Foundation of the State of Rio de Janeiro) Brazilian sponsor with the project title “Computational Support for Genomic Analysis of Neglected Tropical Diseases through Data Mining and Machine Learning”.
    6. 2016: The first IPAW best paper award for the paper “Analyzing Provenance across Heterogeneous Provenance Graphs”, International Provenance and Annotation Workshop (IPAW), sponsored by Springer.
    7. 2016: Best Demonstration Award “HPSW-Prof: A Provenance-Based Framework for Profiling High Performance Scientific Workflows”, XXXI Brazilian Symposium on Databases, Brazilian Computer Society.
    8. 2016: Third best work in the XI Conference of Scientific and Technological Initiation, LNCC, CNPq.
    9. 2015: Honorable mention “An Approach to Data Delivery of Scientific Workflows in the Semantic Web”, XXX Brazilian Symposium on Databases, Brazilian Computer Society.
    10. 2013: Grand Note 10. COPPE-UFRJ, FAPERJ.
    11. 2012: Best Paper Award - 2nd International Workshop on Cloud Computing and Scientific Applications (CCSA). In conjunction with The 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, Dell Inc.
    12. 2012: Fellowship award for EMBO 2012 conference "Computational Molecular Evolution Course" in Heraklion, Greece, European Molecular Biology Organization, EMBO.
    13. 2010: Grand Note 10. COPPE-UFRJ, FAPERJ.
    14. 2008: Fellowship award of the European Molecular Biology Organization (EMBO) 2008 conference “Advanced Methods for Reconstructing Molecular Phylogenetic Analyses” in Rio de Janeiro, Brazil.

Software

    1. Bioinfo-Portal: A Scientific Gateway for Integrating Bioinformatics Tools in the Brazilian National High-Performance Computing Network (https://bioinfo.lncc.br/).
    2. Stingray: System for Integrated Genomic Resources and Analysis.
    3. ProtozoaDB: dynamic visualization and exploration of protozoan genomes.
    4. HPSW-Prof: A Provenance-Based Framework for Profiling High Performance Scientific Workflows.
    5. SwiftPhylo: Phylogenetic workflow modeled with Swift (https://github.com/mmondelli/swift-phylo).
    6. SwiftGecko: Genomic workflow modeled with Swift (https://github.com/mmondelli/swift-gecko).
    7. Benchmark RASflow: Workflow for RASopathies analyses modeled with Swift (https://hub.docker.com/r/malumondelli/rasflow/).
    8. Bioinformatics Workflows in Clouds (Amazon AWS) executed with SciCumulus: Images available in publications.

Contact
Kary Ocaña at LABINFO - LNCC