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Supporting biodiversity studies with the EUBrazilOpenBio Hybrid Data Infrastructure

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Supporting biodiversity studies with the EUBrazilOpenBio Hybrid Data Infrastructure

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Amaral, R.; Badia, RM.; Blanquer Espert, I.; Braga-Neto, R.; Candela, L.; Castelli, D.; Flann, C.... (2015). Supporting biodiversity studies with the EUBrazilOpenBio Hybrid Data Infrastructure. Concurrency and Computation: Practice and Experience. 27(2):376-394. https://doi.org/10.1002/cpe.3238

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Title: Supporting biodiversity studies with the EUBrazilOpenBio Hybrid Data Infrastructure
Author: Amaral, Rafael Badia, Rosa M. Blanquer Espert, Ignacio Braga-Neto, Ricardo Candela, Leonardo Castelli, Donatella Flann, Christina De Giovanni, Renato Gray, William A. Jones, Andrew Lezzi, Daniele Pagano, Pasquale Perez-Canhos, Vanderlei Quevedo, Francisco Rafanell, Roger Rebello, Vinod Sousa-Baena, Mariane S. Torres Serrano, Erik
UPV Unit: Universitat Politècnica de València. Departamento de Sistemas Informáticos y Computación - Departament de Sistemes Informàtics i Computació
Universitat Politècnica de València. Instituto de Instrumentación para Imagen Molecular - Institut d'Instrumentació per a Imatge Molecular
Issued date:
[EN] EUBrazilOpenBio is a collaborative initiative addressing strategic barriers in biodiversity research by integrating open access data and user-friendly tools widely available in Brazil and Europe. The project deploys ...[+]
Subjects: Biodiversity , Data infrastructure , Virtual research environments , Cloud , Taxonomy , Ecological niche modelling
Copyrigths: Reserva de todos los derechos
Concurrency and Computation: Practice and Experience. (issn: 1532-0626 )
DOI: 10.1002/cpe.3238
Publisher version: http://dx.doi.org/10.1002/cpe.3238
Project ID:
info:eu-repo/grantAgreement/CNPq//MCT%2FCNPq 066%2F2010/
info:eu-repo/grantAgreement/EC/FP7/287805/EU/Latin America-Europe ICT Cooperation Advanced Strategies/
info:eu-repo/grantAgreement/MICINN//TIN2012-34557/ES/COMPUTACION DE ALTAS PRESTACIONES VI/
info:eu-repo/grantAgreement/Generalitat de Catalunya//2009 SGR 980/
EUBrazilOpenBio - Open Data and Cloud Computing e-Infrastructure for Biodiversity (2011-2013) is a Small or medium-scale focused research project (STREP) funded by the European Commission under the Cooperation Programme, ...[+]
Type: Artículo


EUBrazilOpenBio Consortium EU-Brazil Open Data and Cloud Computing e-Infrastructure for Biodiversity http://www.eubrazilopenbio.eu/

Triebel, D., Hagedorn, G., & Rambold, G. (2012). An appraisal of megascience platforms for biodiversity information. MycoKeys, 5, 45-63. doi:10.3897/mycokeys.5.4302

Edwards, J. L. (2000). Interoperability of Biodiversity Databases: Biodiversity Information on Every Desktop. Science, 289(5488), 2312-2314. doi:10.1126/science.289.5488.2312 [+]
EUBrazilOpenBio Consortium EU-Brazil Open Data and Cloud Computing e-Infrastructure for Biodiversity http://www.eubrazilopenbio.eu/

Triebel, D., Hagedorn, G., & Rambold, G. (2012). An appraisal of megascience platforms for biodiversity information. MycoKeys, 5, 45-63. doi:10.3897/mycokeys.5.4302

Edwards, J. L. (2000). Interoperability of Biodiversity Databases: Biodiversity Information on Every Desktop. Science, 289(5488), 2312-2314. doi:10.1126/science.289.5488.2312

Grassle, F. (2000). The Ocean Biogeographic Information System (OBIS): An On-line, Worldwide Atlas for Accessing, Modeling and Mapping Marine Biological Data in a Multidimensional Geographic Context. Oceanography, 13(3), 5-7. doi:10.5670/oceanog.2000.01

Constable, H., Guralnick, R., Wieczorek, J., Spencer, C., & Peterson, A. T. (2010). VertNet: A New Model for Biodiversity Data Sharing. PLoS Biology, 8(2), e1000309. doi:10.1371/journal.pbio.1000309

Roskov Y Kunze T Paglinawan L Orrell T Nicolson D Culham A Bailly N Kirk P Bourgoin T Baillargeon G Hernandez F De Wever A Species 2000 & ITIS Catalogue of Life 2013 www.catalogueoflife.org/col/

speciesLink Consortium speciesLink http://splink.cria.org.br 2013 http://splink.cria.org.br

List of Species of the Brazilian Flora Consortium List of Species of the Brazilian Flora http://floradobrasil.jbrj.gov.br/ 2013 http://floradobrasil.jbrj.gov.br/

Wieczorek, J., Bloom, D., Guralnick, R., Blum, S., Döring, M., Giovanni, R., … Vieglais, D. (2012). Darwin Core: An Evolving Community-Developed Biodiversity Data Standard. PLoS ONE, 7(1), e29715. doi:10.1371/journal.pone.0029715

De Giovanni R Copp C Döring M Güntscg A Vieglais D Hobern D Torre J Wieczorek J Gales R Hyam R Blum S Perry S TAPIR - TDWG Access Protocol for Information Retrieval http://www.tdwg.org/activities/abcd/

Jetz, W., McPherson, J. M., & Guralnick, R. P. (2012). Integrating biodiversity distribution knowledge: toward a global map of life. Trends in Ecology & Evolution, 27(3), 151-159. doi:10.1016/j.tree.2011.09.007

NICE Srl Enginframe 2013 http://www.nice-software.com/products/enginframe

Hiden, H., Woodman, S., Watson, P., & Cala, J. (2013). Developing cloud applications using the e-Science Central platform. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 371(1983), 20120085. doi:10.1098/rsta.2012.0085

Glatard, T., Montagnat, J., Lingrand, D., & Pennec, X. (2008). Flexible and Efficient Workflow Deployment of Data-Intensive Applications On Grids With MOTEUR. The International Journal of High Performance Computing Applications, 22(3), 347-360. doi:10.1177/1094342008096067

Kacsuk, P., & Sipos, G. (2005). Multi-Grid, Multi-User Workflows in the P-GRADE Grid Portal. Journal of Grid Computing, 3(3-4), 221-238. doi:10.1007/s10723-005-9012-6

Manuali, C., Laganà, A., & Rampino, S. (2010). GriF: A Grid framework for a Web Service approach to reactive scattering. Computer Physics Communications, 181(7), 1179-1185. doi:10.1016/j.cpc.2010.03.001

Goecks, J., Nekrutenko, A., Taylor, J., & Galaxy Team, T. (2010). Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology, 11(8), R86. doi:10.1186/gb-2010-11-8-r86

XSEDE consortium Extreme science and engineering discovery environment 2013 https://www.xsede.org/

NanoHUB.org Online simulation and more for nanotechnology http://nanohub.org/

SCI-BUS consortium Scientific gateway based user support 2011 https://www.sci-bus.eu/

Kacsuk, P., Farkas, Z., Kozlovszky, M., Hermann, G., Balasko, A., Karoczkai, K., & Marton, I. (2012). WS-PGRADE/gUSE Generic DCI Gateway Framework for a Large Variety of User Communities. Journal of Grid Computing, 10(4), 601-630. doi:10.1007/s10723-012-9240-5

Candela L Castelli D Pagano P D4science: an e-infrastructure for supporting virtual research environments Post-Proceedings of the 5th Italian Res. Conf. on Digital Libraries - IRCDL 2009 2009 166 169

Lobo, J. M., Jiménez-Valverde, A., & Hortal, J. (2010). The uncertain nature of absences and their importance in species distribution modelling. Ecography, 33(1), 103-114. doi:10.1111/j.1600-0587.2009.06039.x

Grinnell, J. (1917). Field Tests of Theories Concerning Distributional Control. The American Naturalist, 51(602), 115-128. doi:10.1086/279591

Peterson, A. T., Soberón, J., Pearson, R. G., Anderson, R. P., Martínez-Meyer, E., Nakamura, M., & Araújo, M. B. (2011). Ecological Niches and Geographic Distributions (MPB-49). doi:10.23943/princeton/9780691136868.001.0001

Brazilian Virtual Herbarium Consortium Brazilian Virtual Herbarium 2013 http://biogeo.inct.florabrasil.net/

De Souza Muñoz, M. E., De Giovanni, R., de Siqueira, M. F., Sutton, T., Brewer, P., Pereira, R. S., … Canhos, V. P. (2009). openModeller: a generic approach to species’ potential distribution modelling. GeoInformatica, 15(1), 111-135. doi:10.1007/s10707-009-0090-7

Hirzel, A. H., Hausser, J., Chessel, D., & Perrin, N. (2002). ECOLOGICAL-NICHE FACTOR ANALYSIS: HOW TO COMPUTE HABITAT-SUITABILITY MAPS WITHOUT ABSENCE DATA? Ecology, 83(7), 2027-2036. doi:10.1890/0012-9658(2002)083[2027:enfaht]2.0.co;2

Anderson, R. P., Lew, D., & Peterson, A. T. (2003). Evaluating predictive models of species’ distributions: criteria for selecting optimal models. Ecological Modelling, 162(3), 211-232. doi:10.1016/s0304-3800(02)00349-6

Farber, O., & Kadmon, R. (2003). Assessment of alternative approaches for bioclimatic modeling with special emphasis on the Mahalanobis distance. Ecological Modelling, 160(1-2), 115-130. doi:10.1016/s0304-3800(02)00327-7

Phillips, S. J., Anderson, R. P., & Schapire, R. E. (2006). Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190(3-4), 231-259. doi:10.1016/j.ecolmodel.2005.03.026

Schölkopf, B., Platt, J. C., Shawe-Taylor, J., Smola, A. J., & Williamson, R. C. (2001). Estimating the Support of a High-Dimensional Distribution. Neural Computation, 13(7), 1443-1471. doi:10.1162/089976601750264965

Armbrust, M., Stoica, I., Zaharia, M., Fox, A., Griffith, R., Joseph, A. D., … Rabkin, A. (2010). A view of cloud computing. Communications of the ACM, 53(4), 50. doi:10.1145/1721654.1721672

Foster I Zhao Y Raicu I Lu S Cloud computing and grid computing 360-degree compared Grid Computing Environments Workshop, 2008. GCE '08 2008 1 10

Candela, L., Castelli, D., & Pagano, P. (2013). Virtual Research Environments: An Overview and a Research Agenda. Data Science Journal, 12(0), GRDI75-GRDI81. doi:10.2481/dsj.grdi-013

Tsai W Service-oriented system engineering: a new paradigm Service-oriented system engineering, 2005. sose 2005. IEEE International Workshop 3 6 10.1109/SOSE.2005.34

Cattell, R. (2011). Scalable SQL and NoSQL data stores. ACM SIGMOD Record, 39(4), 12. doi:10.1145/1978915.1978919

Durão FA Assad RE Silva AF Carvalho JF Garcia VC Trinta FAM USTO.RE: A Private Cloud Storage System 13th International Conference on Web Engineering (ICWE 2013) - Industry Track 2013 452 466

Lezzi, D., Rafanell, R., Carrión, A., Espert, I. B., Hernández, V., & Badia, R. M. (2012). Enabling e-Science Applications on the Cloud with COMPSs. Lecture Notes in Computer Science, 25-34. doi:10.1007/978-3-642-29737-3_4

Boeres, C., & Rebello, V. E. F. (2004). EasyGrid: towards a framework for the automatic Grid enabling of legacy MPI applications. Concurrency and Computation: Practice and Experience, 16(5), 425-432. doi:10.1002/cpe.821

VENUS-C consortium Deliverable 6.1 - report on architecture 2012 http://www.venus-c.eu/Content/Publications.aspx?id=bfac02a9-9bc0-4c8f-80e0-7ceddc5c893b

Thain, D., Tannenbaum, T., & Livny, M. (2005). Distributed computing in practice: the Condor experience. Concurrency and Computation: Practice and Experience, 17(2-4), 323-356. doi:10.1002/cpe.938

Couvares, P., Kosar, T., Roy, A., Weber, J., & Wenger, K. (s. f.). Workflow Management in Condor. Workflows for e-Science, 357-375. doi:10.1007/978-1-84628-757-2_22

Sena, A., Nascimento, A., Boeres, C., & Rebello, V. (2008). EasyGrid Enabling of Iterative Tightly-Coupled Parallel MPI Applications. 2008 IEEE International Symposium on Parallel and Distributed Processing with Applications. doi:10.1109/ispa.2008.122

Edmonds, A., Metsch, T., & Papaspyrou, A. (2011). Open Cloud Computing Interface in Data Management-Related Setups. Grid and Cloud Database Management, 23-48. doi:10.1007/978-3-642-20045-8_2

Livenson, I., & Laure, E. (2011). Towards transparent integration of heterogeneous cloud storage platforms. Proceedings of the fourth international workshop on Data-intensive distributed computing - DIDC ’11. doi:10.1145/1996014.1996020

The rOCCI framework http://occi-wg.org/2012/04/02/rocci-a-ruby-occi-framework/

Mendelsohn N Gudgin M Ruellan H Nottingham M SOAP message transmission optimization mechanism W3C Recommendation 2005 http://www.w3.org/TR/2005/REC-soap12-mtom-20050125/

Sencha Sencha GXT application framework for Google web toolkit 2013 http://www.sencha.com/products/gxt/

Vicario, S., Hardisty, A., & Haitas, N. (2011). BioVeL: Biodiversity Virtual e-Laboratory. EMBnet.journal, 17(2), 5. doi:10.14806/ej.17.2.238

Lezzi D Rafanell R Torres E De Giovanni R Blanquer I Badia RM Programming ecological niche modeling workflows in the cloud Proceed. of the 27th IEEE Int. Conf. on Advanced Information Networking and Applications 2013 1223 1228

Lohmann, L. G. (2006). Untangling the phylogeny of neotropical lianas (Bignonieae, Bignoniaceae). American Journal of Botany, 93(2), 304-318. doi:10.3732/ajb.93.2.304

Flann C Use Case Study EUBrazilOpenBio Cross-mapping tool Assessment of usability for regional-GSD comparisons 2013 http://www.eubrazilopenbio.eu/Content/Factfile.aspx?id=0750dcd8-23f2-4bf1-bad4-52aa3277d002

Brazilian Ministry of Environment Instrução normativa no. 6, 23 de setembro de 2008 2008 http://www.mma.gov.br/estruturas/179/_arquivos/179_05122008033615.pdf




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