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Andréa Matsunaga
I'm currently an Assistant Research Professor at the Advanced Computing and Information Systems (ACIS) Laboratory. I'm working on the NSF-funded iDigBio project, contributing with my experience on cloud computing, machine learning, application virtualization, web services, relational databases, design of middleware architectures and development of web-based infrastructures for digital government and a variety of science disciplines, including bioinformatics, materials sciences, nanoelectronics, neuroscience and digital government. In iDigBio, I'm responsible for conducting IT research, with focus on my areas of interest: distributed computing, autonomic computing, and data management.

I got my Ph.D degree from the University of Florida under Dr. Fortes's guidance. As research assistant at ACIS, I worked on different projects, namely: ACIS/AIMS information system, In-VIGO Grid middleware, Transnational Digital Government, In-VIGO/nanoHUB collaboration, In-VIGO/ICBR/UF-HPC collaboration, ACIS/Whitney Laboratories collaboration, Atomic-scale Friction Research and Education Synergy Hub and CloudBLAST.

I'm also on the ACIS team working on the DARPA Restoring Plasticity and Acceleration of Injury Recovery (REPAIR) program, in particular, to investigate middleware solutions for remote execution of brain models on high-performance computers to improve our ability to model and interface with the brain. For more information go to:.

Current Projects

 * iDigBio Project (EF-1115210) - The Home Uniting Biocollections (HUB) established and funded by the NSF Advancing Digitization of Biological Collections (ADBC). ADBC is a national effort to support digitization of all vouchered biological and paleontological collections housed in US institutions. iDigBio coordinates this challenging undertaking by fostering partnerships, training, and innovations, and serving as a central site for integrating data and techniques, and establishing cohesion and interconnectivity among all the digitization projects, especially with Thematic Collections Networks (TCNs). The resource will provide access to information critical to scientific research and education, including that designed to understand biodiversity and societal consequences of climate change and other environmental issues.
 * RAPID Thailand Project (CNS-1240171) - investigates the effectiveness of virtualized Internet data centers on improving IT service continuity during and after a disaster through virtual machines (VM) live migration and backup/checkpointing, conducting research on the use of virtualization technologies. These technologies enable mitigating and recovering from the impact of catastrophic events on IT infrastructures and the services they deliver. Working with Thammasat University in Thailand, Internet Data Centers (IDCs) will be leveraged as disaster recovering sites, where government and corporate data can be backed up and operational servers can be temporarily located in order to provide high-availability and resiliency for the organizations' operations and services.
 * DARPA REPAIR Project - investigates middleware to support parallel MATLAB-based models in online real-time BMI experiments.
 * Prediction Project - investigates the use of machine learning algorithms to predict the time and resources consumed by applications
 * Atomic-scale Friction Research and Education Synergy Hub (AFRESH) Project - development of a wiki-based cyberinfrastructure for the atomic-scale friction research community
 * CloudBLAST Project - combining machine and network virtualization with MapReduce across Science Clouds to attain a scalable virtual cluster for running NCBI BLAST
 * In-VIGO ICBR Project - a collaboration with Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida, developing a web portal for bioinformatics applications such as Basic Local Alignment Search Tool (BLAST) that facilitates the use of resources in the University of Florida High Performance Computing Center.

Publications
2015 2014 2013 2012 2011
 * Deck, John; Guralnick, Robert; Walls, Ramona; Blum, Stanley; Haendel, Melissa; Matsunaga, Andréa; and Wieczorek, John, “Meeting report: Identifying practical applications of ontologies for biodiversity informatics,” Standards in Genomic Sciences C7 - 25, vol. 10, no. 1, pp. 1-6, 2015. DOI:10.1186/s40793-015-0014-0 [ PDF]
 * Soomro, Sarfaraz; Matsunaga, Andréa; and Fortes, José A.B., "Simplifying Extract-Transform-Load for Ranked Hierarchical Trees via Mapping Specifications," Formalisms for Reuse and Systems Integration, Advances in Intelligent Systems and Computing T. Bouabana-Tebibel and S. H. Rubin, eds., pp. 203-225: Springer International Publishing, 2015. DOI:10.1007/978-3-319-16577-6_9. [ Abstract]
 * Tsugawa, Maurício; Matsunaga, Andréa; and Fortes, José A.B., "Cloud Networking to Support Data Intensive Applications," Cloud Computing for Data-Intensive Applications, X. Li and J. Qiu, eds., pp. 61-81: Springer New York, 2014. DOI:10.1007/978-1-4939-1905-5_3. [ Abstract][ PDF]
 * Kang, Tae Seung; Tsugawa, Mauricio; Matsunaga, Andrea; Hirofuchi, Takahiro; and Fortes, Jose A. B., “Design and Implementation of Middleware for Cloud Disaster Recovery via Virtual Machine Migration Management,” in 2014 IEEE/ACM 7th International Conference on Utility and Cloud Computing (UCC), London, United Kingdom, 2014, pp. 166-175. DOI:10.1109/ucc.2014.25 [ Abstract][ PDF]
 * Lee, Giljae; Matsunaga, Andréa; Dura-Bernal, Salvador; Zhang, Wenjie; Lytton, William; Francis, Joseph; and Fortes, Jose, “Towards real-time communication between in vivo neurophysiological data sources and simulator-based brain biomimetic models,” Journal of Computational Surgery, vol. 3, no. 1, pp. 12, 2014. DOI:10.1186/s40244-014-0012-3[ Abstract][ PDF]
 * Matsunaga, Andréa; Mast, Austin; and Fortes, José A.B., "Reaching Consensus in Crowdsourced Transcription of Biocollections Information," in Proceedings of the 2014 IEEE 10th International Conference on e-Science, Guarujá, Brazil: IEEE, 2014, pp. 57-64. DOI:10.1109/eScience.2014.30 [ Abstract][ PDF][ Presentation]
 * Walls, Ramona; Guralnick, Robert; Deck, John; and Matsunaga, Andréa, “A Specimen-based View of the World: Using the Biological Collections Ontology to Model Biodiversity Collections,” in 2014 ICBO Workshop: Starting an OBI-based Biobank Ontology, Houston, TX, USA, 2014, pp. 64-66. [ PDF]
 * Soomro, Sarfaraz; Matsunaga, Andréa; and Fortes, José A.B., “Mapping Specifications for Ranked Hierarchical Trees in Data Integration Systems,” in 2014 IEEE International Conference on Information Reuse and Integration (IRI 2014), San Francisco, California, USA, 2014, pp. 269-276. DOI:10.1109/IRI.2014.7051899[ Abstract][ PDF]
 * Walls, Ramona L.; Deck, John; Guralnick, Robert; Baskauf, Steve; Beaman, Reed; Blum, Stanley; Bowers, Shawn; Buttigieg, Pier Luigi; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Morrison, Norman; Tuama, Éamonn Ó.; Schildhauer, Mark; Smith, Barry; Stucky, Brian J.; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; and Wooley, John, "Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies," PLoS ONE, vol. 9, no. 3, pp. e89606, 2014. DOI:10.1371/journal.pone.0089606
 * Tsugawa, Maurício; Matsunaga, Andréa; and Fortes, José A. B., "Cloud Computing Security: What Changes with Software-Defined Networking?," Secure Cloud Computing, S. Jajodia, K. Kant, P. Samarati et al., eds., pp. 77-93: Springer New York, 2014. DOI:10.1007/978-1-4614-9278-8_4.
 * Matsunaga, Andréa, Thompson, Alex, Figueiredo, Renato J., Germain-Aubrey, Charlotte C., Collins, Matthew, Beaman, Reed S., MacFadden, Bruce J., Riccardi, Greg, Soltis, Pamela S., Page, Lawrence M., and Fortes, José A.B., "A Computational- and Storage-Cloud for Integration of Biodiversity Collections," in Proceedings of the 2013 IEEE 9th International Conference on e-Science, Beijing, China: IEEE, 2013, pp. 78-87. DOI:10.1109/eScience.2013.48 (acceptance rate: 41%)[ PDF]
 * TDWG 2013 abstracts and presentations:
 * Andréa Matsunaga, Renato Figueiredo, Alex Thompson, Gregory Traub, Reed Beaman, José A. B. Fortes. "Integrated Digitized Biocollections (iDigBio) Cyberinfrastructure Status and Futures," Symposium Big Data Coming From Earth Observation Networks, TDWG 2013 conference, Florence, Italy, Oct 2013. [Abstract][Presentation]
 * Sarfaraz Soomro, Andréa Matsunaga, José Fortes. "iDigBio Data Integration with Self-Referential Schemas," general track, TDWG 2013 conference, Florence, Italy, Oct 2013. [Abstract][Presentation]
 * Alex Thompson, Andréa Matsunaga, José Fortes. "An iDigBio Perspective on Darwin Core Archives," Workshop Darwin Core Archives: beyond star schema, TDWG 2013 conference, Florence, Italy, Oct 2013. [Abstract][Presentation]
 * Fortes, José; Figueiredo, Renato; Matsunaga, Andréa; Thompson, Alex; Collins, Matthew; and Xu, Jiangyan, "Integrated Digitized Biocollections (iDigBio) Cloud-Based Cyberinfrastructure," 27th Annual Meeting of the Society for the Preservation of Natural History Collections, 2012. [ [[Media:IDigBioSpnhc2012Abstract_final.pdf|Abstract]]][ [[Media:MatsunagaCyberArchitecture-Spnhc2012.pdf|Presentation]]]
 * Matsunaga, Andréa; Riteau, Pierre; Tsugawa, Maurício; Fortes, José. 'Crosscloud Computing'. Advances in Parallel Computing, High Performance Computing: From Grids and Clouds to Exascale, volume 20, 2011, pp. 109-123. ISBN 978-1-60750-802-1. DOI:10.3233/978-1-60750-803-8-94. [Abstract], FutureGrid Project
 * Rattanatamrong, Prapaporn; Matsunaga, Andréa; Brockmeier, Austin; Sanchez, Justin C.; Principe, Jose; Fortes, José. 'Towards Closed-Loop Brain-Machine Experiments across Wide-Area Networks'. In Proc. of the 5th International IEEE EMBS Conference on Neural Engineering, Cancun, Mexico, April 27-May 1, 2011. [Abstract]

2010
 * Tsugawa, Maurício; Riteau, Pierre; Matsunaga, Andréa; and Fortes, José. 'User-level Virtual Networking Mechanisms to Support Virtual Machine Migration Over Multiple Clouds'. In IEEE International Workshop on Management of Emerging Networks and Services, Miami, Florida, 2010, pp. 568-572. DOI:10.1109/GLOCOMW.2010.5700384. [Abstract][PDF]
 * Rattanatamrong, Prapaporn; Matsunaga, Andréa; and Fortes, José A.B. BMI CyberWorkstation: a Cyberinfrastructure for Collaborative Experimental Research on Brain-Machine Interfaces. In Proc. of the 6th International ICST Conference on Collaborative Computing: Networking, Applications and Worksharing, Chicago, Illinois, October 9-12, 2010. ISBN: 978-963-9995-24-6. (acceptance rate: 37%)[Abstract][PDF]
 * Rattanatamrong, Prapaporn; Matsunaga, Andréa; Raiturkar, Pooja; Mesa, Diego; Zhao, Ming; Mahmoudi, Babak; DiGiovanna, Jack; Principe, Jose; Figueiredo, Renato; Sanchez, Justin C.; Fortes, and Fortes, José A.B. 'Model Development, Testing and Experimentation in a CyberWorkstation for Brain-Machine Interface Research'. In Proc. of the 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Buenos Aires, Argentina, p.4339-4342, August 31-September 4, 2010. DOI:10.1109/IEMBS.2010.5626234. [Abstract][PDF]
 * Riteau, Pierre; Tsugawa, Maurício; Matsunaga, Andréa; Fortes, José; Freeman, Tim; LaBissoniere, David; and Keahey, Kate. 'Sky Computing on FutureGrid and Grid’5000' (poster). TeraGrid’10, Pittsburgh, PA. August 2010.
 * Matsunaga, Andréa; and Fortes, José A.B. On the use of machine learning to predict the time and resources consumed by applications. In Proceedings of the 10th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, Melbourne, Australia, pp.495-504, May 17-20, 2010. DOI:10.1109/CCGRID.2010.98. (acceptance rate: 23%)[Abstract][PDF]
 * Matsunaga, Andréa. 'Automatic enablement, coordination and resource usage prediction of unmodified applications on clouds'. Ph.D. dissertation. [Gainesville, Fla.]: University of Florida, 2010, 138 pages. 3416699 [Abstract][PDF]

2009
 * Keahey, Katarzyna; Tsugawa, Maurício; Matsunaga, Andréa; Fortes, José A.B. Sky Computing. Internet Computing, IEEE, vol.13, no.5, p.43-51, Sept.-Oct. 2009. DOI:10.1109/MIC.2009.94. [Abstract][PDF]
 * Tsugawa, Maurício; Matsunaga, Andréa; and Fortes, José A.B. 'User-level Virtual Network Support for Sky Computing'. In Proceedings of the 5th IEEE International Conference on e-Science, p.72-79, December, 2009. DOI:10.1109/e-Science.2009.19. (acceptance rate: 29%)[Abstract][PDF]
 * Sinnott, Susan B.; Matsunaga, Andréa; Bucholz, Eric. W.; Fortes, José A.B. 'Atomic-Scale Friction Research Education and Synergy Hub'. In Proceedings of the 2009 NSF Engineering Research and Innovation Conference, Honolulu, Hawaii, 2009. [PDF]

2008
 * Matsunaga, Andréa; Tsugawa, Maurício; and Fortes, José A.B. 'CloudBLAST: Combining MapReduce and Virtualization on Distributed Resources for Bioinformatics Applications'. In Proceedings of the 4th IEEE International Conference on e-Science, 10-12 December, 2008. DOI:10.1109/eScience.2008.62. [Abstract][PDF]
 * Kadirvel, S.; Matsunaga, A.; Tong, Y.; Chen, K.; Yu, F.; Liu, L.; Farmerie, W.G.; Fortes, J.A.B. 'Enabling high performance computing for the UF genetics research community through a web-based BLAST portal' (poster). In Proceedings of the Florida Genetics 2008, 29-30 October, 2008. [PDF]
 * Matsunaga, Andréa; Tsugawa, Maurício; and Fortes, José A.B. 'Getting on the Virtual Bus: By way of some common virtualization tools, agencies can make SOA their next stop for legacy apps'. FEDTECH, v.5, number 2, p.31-32, May 2008. [HTML]
 * Maurício Tsugawa, Andréa Matsunaga and José A. B. Fortes. "Collaborative Cyberinfrastructure for Transnational Digital Government". Digital Government, chapter 17, p.283-305, Springer US, 2008. DOI:10.1007/978-0-387-71611-4_15. [Chapter]

2007
 * Matsunaga, Andréa; Tsugawa, Maurício; and Fortes, José A.B. 'Integration of text-based applications into service-oriented architectures for transnational digital government'. In Proceedings of the 8th Annual international Conference on Digital Government Research: Bridging Disciplines & Domains (dg.o '07), Philadelphia, Pennsylvania, v.228, p.112-121, 20-23 May, 2007. (acceptance rate: 55%) [PDF][presentation] TDG project

2006
 * Matsunaga, Andréa M.; Tsugawa, Maurício O.; Adabala, Sumalatha; Figueiredo, Renato J.; Lam, Herman; and Fortes, José A.B. 'Science gateways made easy: the In-VIGO approach'. Concurrency and Computation: Practice and Experience, Wiley Press, v. 19(6), p.905-919, October, 2006. DOI:10.1002/cpe.1083. [Abstract][PDF]
 * Tsugawa, Maurício; Matsunaga, Andréa; and Fortes, José A.B. 'Virtualization technologies in transnational DG'. In Proceedings of the 2006 international Conference on Digital Government Research (dg.o '06) (poster), San Diego, California, v. 151, p.456-457, 21-24 May, 2006. DOI:10.1145/1146598.1146747. [PDF]

2005
 * Zhu, Liping; Matsunaga, Andréa; Sanjeepan, Vivekananthan; Lam, Herman; Fortes, José A.B. 'Application Modeling and Representation for Automatic Grid-enabling of Legacy Applications'. In Proceedings of First International Conference on e-Science and Grid Computing, p.24-31, 5-8 December, 2005. DOI:10.1109/E-SCIENCE.2005.20. [PDF]
 * Matsunaga, Andréa; Tsugawa, Maurício; Zhao, Ming; Zhu, Liping; Sanjeepan, Vivekananthan; Adabala, Sumalatha; Figueiredo, Renato; Lam, Herman and Fortes, José A.B. 'On the Use of Virtualization and Service Technologies to Enable Grid-Computing'. In Proceedings of Euro-Par 2005 Parallel Processing: 11th International Euro-Par Conference (Lecture Notes in Computer Science, v.3648, p.1-12), August, 2005. DOI:10.1007/11549468_1. [PDF][presentation]
 * Tsugawa, Maurício; Matsunaga, Andréa; Zhu, Liping; Sanjeepan, Vivekananthan; Lam, Herman; Figueiredo, Renato J.; Fortes, José A.B. 'In-VIGO Virtual Networks and Virtual Application Services: Automated Grid-enabling and Deployment of Applications'. In Proceedings of 14th International Symposium on High Performance Distributed Computing (HPDC) 2005 (poster), p.312-313, July, 2005. DOI:10.1109/HPDC.2005.1520990. [PDF]
 * Sanjeepan, Vivekananthan; Matsunaga, Andréa; Zhu, Liping; Lam, Herman; Fortes, José A.B. 'A Service-Oriented, Scalable Approach to Grid-Enabling of Legacy Scientific Applications'. In Proceedings of 2005 International Conference on Web Services (ICWS-2005), Orlando, Florida, p.553-560, 11-15 July, 2005. DOI:10.1109/ICWS.2005.17. (acceptance rate: 19%) [PDF]
 * Matsunaga, Andréa; Tsugawa, Maurício; Adabala, Sumalatha; Figueiredo, Renato; Lam, Herman; and Fortes, José A.B. 'Science gateways made easy: the In-VIGO approach'. In Workshop on Science Gateways, Global Grid Forum, June, 2005. [PDF][presentation]
 * Su, S.; Fortes, J.; Kasad, T. R.; Patil, M.; Matsunaga, A.; Tsugawa, M.; Cavalli-Sforza, V.; Carbonell, J.; Jansen, P.; Ward, W.; Cole, R.; Towsley, D.; Chen, W.; Antón, A. I.; He, Q., McSweeney, C.; De Brens, L.; Ventura, J.; Taveras, P.; Connolly, R.; Ortega, C.; Pineres, B.; Brooks, O.; Murillo, G. A.; and Herrera, M. 'Transnational Information Sharing, Event Notification, Rule Enforcement and Process Coordination' In International Journal of Electronic Government Research (IJEGR), v.1, n.2, p.1-26, April-June, 2005.
 * Matsunaga, Andréa; Tsugawa, Maurício; Fortes, José A.B. 'Virtual Machines in Transnational Digital Government: a Case Study'. In Proceedings of the 2005 national conference on Digital government research (dg.o 2005) (poster), p.255-256, May, 2005. [PDF]
 * Adabala, Sumalatha; Chadha, Vineet; Chawla, Puneet; Figueiredo, Renato; Fortes, José; Krsul, Ivan; Matsunaga, Andrea; Tsugawa, Mauricio; Zhang, Jian; Zhao, Ming; Zhu, Liping; Zhu, Xiaomin. 'From Virtualized Resources to Virtual Computing Grids: The In-VIGO System'. In Future Generation Computer Systems, v.21, n.6, April, 2005. DOI:10.1016/j.future.2003.12.021. [PDF]

2004
 * Su, S., Fortes, J., Kasad, T. R., Patil, M., Matsunaga, A., Tsugawa, M., Cavalli-Sforza, V., Carbonell, J., Jansen, P., Ward, W., Cole, R., Towsley, D., Chen, W., Antón, A. I., He, Q., McSweeney, C., de Brens, L., Ventura, J., Taveras, P., Connolly, R., Ortega, C., Piñeres, B., Brooks, O., and Herrera, M. 'A prototype system for transnational information sharing and process coordination'. In Proceedings of the 2004 Annual National Conference on Digital Government Research, Seattle, WA, p.199-208, 24-26 May, 2004. [PDF]
 * Adabala, Sumalatha; Matsunaga, Andréa; Tsugawa, Maurício; Figueiredo, Renato; Fortes, José A.B. 'Single Sign-On in In-VIGO: Role-based Access via Delegation Mechanisms Using Short-lived User Identities'. In Proceedings of 18th International Parallel and Distributed Processing Symposium (IPDPS-2004), Santa Fe, New Mexico, p.22, 26-30 April, 2004. DOI:10.1109/IPDPS.2004.1302930. (acceptance rate: 31.8%)[PDF][presentation]

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Demos
2010 2004
 * Matsunaga, Andréa; Tsugawa, Maurício; and Fortes, José A.B. 'Scaling-out CloudBLAST: Combining Technologies to BLAST on the Sky'. In the third IEEE International Scalable Computing Challenge (SCALE 2010).
 * Su, S., Fortes, J., Kasad, T. R., Patil, M., Matsunaga, A., Tsugawa, M., Cavalli-Sforza, V., Carbonell, J., Jansen, P., Ward, W., Cole, R., Towsley, D., Chen, W., Antón, A. I., He, Q., McSweeney, C., de Brens, L., Ventura, J., Taveras, P., Connolly, R., Ortega, C., Piñeres, B., Brooks, O., and Herrera, M. 'A prototype system for transnational information sharing and process coordination: system demo'. In Proceedings of the 2004 annual national conference on Digital government research, Seattle, WA, p. 287-288, 2004. PDF

Grants

 * NSF grant CNS-1240171: Enabling continued operation of IT services and infrastructures during floods and other disasters. (06/15/2012 - 05/31/2013)
 * Microsoft Azure Offer for Research Institutions from Microsoft Research: Drug discovery on Azure using DOCK; (09/16/2014 - 09/15/2015)
 * NSF grant 1458640: Collaborative Research: ABI Innovation: Connecting resources to enable large-scale biodiversity analyses; Recommended.

On the news

 * Reaching for sky computing, iSGTW
 * Large-Scale Cloud Computing Research: Sky Computing on FutureGrid and Grid’5000

Past Projects

 * Transnational Digital Government (TDG) Project
 * In-VIGO Grid Middleware Project IvWiki:Main Page
 * Querying over P2P Project
 * ACIS Web Site Project
 * Bioinformatics@ACIS (BACIS) Project - a collaboration with Whitney Labs

Course Projects

 * AIMS Information Management Project - supports ACIS web site (Fall 2001)
 * Speech Controlled Keyboard (Spring 2002)
 * Hardware-Software Interactions also known as Distributed Database (Spring 2002)