Research experience and scientific publications
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1. The document discusses the author's research experience including developing a storage architecture called uStorage that couples block and object storage models, creating a FAIR research data management system for next generation sequencing data, and developing a scientific cloud platform called mc2 that supports distributed and scalable bioinformatics applications using volunteer, cluster, and MapReduce processing models. 2. The author has published several papers on uStorage, a FAIR sequencing data repository based on iRODS, supporting bioinformatics applications through volunteer and scalable computing frameworks, and providing volunteer computing infrastructure to support e-science applications. 3. The document provides the author's contact information and date.
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Research experience and scientific publications
- 1. Research experience & Scientific publications Felipe Oliveira Gutierrez [email protected] February 1th, 2018
- 2. Summary 1. uStorage architecture Coupling of two storage models (blocks and objects) 2. FAIR RDM system Findable, Accessible, Interoperable, and Reusable Research Data Management system 3. Workflow to support Volunteer and Scalable computing Boinc and Hadoop 4. Personal projects 2 Feb 1th, 2018
- 3. 3 Feb 1th, 2018 1 - uStorage architecture. 2014/2016
- 4. Block Storage ● raw block ● same size ● no metadata ● scalability limited ● ID to local system ● good performance OS mount point ● needs HA for prepare to fail ● high performance hardware ● reduced availability ● random RW loads ● structured data sets 4 Object Storage ● buckets ● different size ● expandable metadata ● very scalable ● global unique ID on DS ● bad performance OS mount point ● already prepared to fail ● hardware flexibility ● high availability ● generally read ● unstructured data sets Feb 1th, 2018 uStorage architecture
- 5. uStorage architecture 5 Feb 1th, 2018
- 6. uStorage architecture 6 Feb 1th, 2018
- 7. 7 Block Storage Object Storage Feb 1th, 2018 uStorage architecture
- 8. 8 Cache LRU algorithm Feb 1th, 2018 uStorage architecture
- 9. uStorage architecture 9 uStorage cache cache free space Eviction Clean or remove buckets from the cache to open space for new buckets. Cache miss or Cache hit fails Restore or retrieve buckets from the cloud that are not present on the cache. Cache hit successful Bucket found on the cache Feb 1th, 2018
- 10. Equal size => Cache: 20 GiB = Files: 20 GiB 10 Feb 1th, 2018 uStorage architecture
- 11. 4x size => Cache: 5 GiB < Files: 20 GiB 11 Feb 1th, 2018 uStorage architecture
- 13. 2 - FAIR RDM system. 2016/2017 ● Problem ○ Inadequate RDM solution for NGS data ○ Individual storage and backup ○ Files and metadata decoupled ○ No exchange (meta)data ○ Not FAIR (Findable, Accessible, Interoperable, Reusable) 13 Feb 1th, 2018
- 14. 14 FAIR RDM system Feb 1th, 2018
- 15. 15 FAIR RDM system Feb 1th, 2018
- 16. FAIR RDM system ● FAIR - Findable, Accessible, Interoperable, and Reusable ● Distributed and Scalable ● Easy to use ● Manageable by the research organization ○ Security ○ Privacy of (meta)data (different access to different users and groups) ○ Variety of user roles (PI, Data steward, researcher, administrator) ○ Variety of data type (e.g.Next Generation Sequence, Metabolomics) 16 Feb 1th, 2018
- 17. 17 FAIR RDM system Feb 1th, 2018
- 18. 18 FAIR RDM system Feb 1th, 2018
- 19. 19 FAIR RDM system Feb 1th, 2018
- 20. 20 FAIR RDM system Feb 1th, 2018
- 21. 21 STANDARD steps STANDARD steps SPECIFIC steps FAIR RDM system
- 23. 3 - mc2 - My sCientific Cloud. 2012/2013 ● Distributed and scalable environment for bioinformatic applications ○ CSGrid ● Availability through different eScience workflow environments ● Different processing models to deploy applications ○ Cluster MPI ○ Volunteer processing ○ MapReduce 23 Feb 1th, 2018
- 24. 24 Feb 1th, 2018 mc2 - My sCientific Cloud
- 25. 25 Feb 1th, 2018 mc2 - My sCientific Cloud
- 26. 26 Feb 1th, 2018 mc2 - My sCientific Cloud
- 27. 27 Feb 1th, 2018 4 - Personal projects https://felipeogutierrez.blogspot.com & https://github.com/felipegutierrez #FileSystems#Storage
- 28. Scientific publications ● Gutierrez F.O. et al. uStorage - A Storage Architecture to Provide Block-Level Storage Through Object-Based Storage. Service-Oriented and Cloud Computing Conference. ESOCC 2017. Computer Science, Springer - https://doi.org/10.1007/978-3-319-67262-5_16 ● Felipe Gutierrez, et al. - FAIR Sequencing Data Repository based on iRODS - 9th iRODS UGM 2017 - Netherlands - https://goo.gl/wtBwGS ● Olabarriaga, S; Gutierrez, F.O. et al. FAIR Next Generation Sequencing Data Repository based on iRODS. BioSB 2017: Dutch Bioinformatics & Systems Biology - Netherlands. ● GUTIERREZ, F. O. et al. Support for bioinformatics applications through volunteer and scalable computing frameworks. Second International Workshop on Parallelism in Bioinformatics, 2014, Madri. https://doi.org/10.1109/CLUSTER.2014.6968780 ● GUTIERREZ, F. O. et al. . Providing volunteer computing at the infrastructure level to support e-science applications. VII Brazilian e-Science Workshop 2013, https://goo.gl/Wam9Ui ● GUTIERREZ, F. O. et al. Provisão de computação intensiva de dados para suporte a aplicações científicas. II Escola Regional de Alto Desempenho, 2013, Salvador. 28 Feb 1th, 2018
- 29. Felipe Oliveira Gutierrez [email protected] February 1th, 2018