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This project is funded by the European Union Cloud computing to assist Surveillance of Neglected Tropical Diseases: The Leishmaniasis Virtual Laboratory.

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Presentation on theme: "This project is funded by the European Union Cloud computing to assist Surveillance of Neglected Tropical Diseases: The Leishmaniasis Virtual Laboratory."— Presentation transcript:

1 This project is funded by the European Union Cloud computing to assist Surveillance of Neglected Tropical Diseases: The Leishmaniasis Virtual Laboratory in EUBrazilCC Ignacio Blanquer (UPV) Israel Cruz (ISCIII)

2 What EUBrazilCC is? A project funded in the 2nd EU-Brazil coordinated call EUBrazil Cloud Connect (614048) is a Small or medium- scale focused research project (STREP) funded by the European Commission under the Cooperation Programme, Fra-mework Programme Seven (FP7) Esse projeto é resultante do Edital MCT/CNPq Nº 13/ Programa de Cooperação Brasil – União Europeia na Área de Tecnologias da Informação e Comunicação - TIC A team of 12 institutions co-led by UPV and UFCG. 20/10/14 2

3 What EUBrazilCC aims at? Foster EU-Brazil international cooperation in cloud infrastructures at three levels: Heterogeneous (especially cloud) infrastructure federation. Integration of Programming Services to efficiently Access infrastructure resources. User’s applications, creating shared spaces for the benefit of international collaborations Common (EU+Brazil) involvement in cloud standards definition. 20/10/14 3

4 Main pillars of EUBrazilCC The use – cases Three applications coming from the EU-Brazil cooperation The Platform Programming environments Workflows Scientific Gateways The infrastructure Heterogeneous Federated 20/10/14EUBrazilCC – FP ONEOStackHPCClusters Fogbow CSGRID COMPSs eSC mc2 IM / VMRC PDAS Leishmaniasis Virtual Laboratory Vascular system simulation Climate change & ecology PMES-COMPSs

5 The EUBrazilCC Infrastructure EUBrazilCC gathers resources from 6 centres Clusters, ONE & Ostack on-premise clouds. Federated at the level of resource provision (fogbow) and at the level of the services (PMES-COMPS and CSGRID). 20/10/14EUBrazilCC – FP Cloud >1000 cores + <500 op cores UPVLC BSC CMCC UFCG LNCC HPC > 5500 cores LNCC BSC UNEW CMCC

6 The EUBrazilCC Software Architecture 20/10/14EUBrazilCC – FP PDAS COMPSs eScience Central IM / VMRC CSGRID fogbow A framework for the execution of parallel applications. Offers a BES interface and talks directly OCCI Deployment and configuration of VAs. A rich-metadata repository of VMIs. A federation middleware for on-premise clouds and opportunistic resources. OCCI-compliant A Parallel Data Analysis service for processing Big Data cubes. Especially for multidimensional data. A workflow-based platform for data analysis. Supporting blocks in “R”, java, octave or javascript. An homogeneous interface for clusters and HPC infrastructures. Manages distributed & heterogeneous environments.

7 Interoperability EUBrazilCC services are compatible with other infrastructure providers Fogbow implemented a OCCI-compliant interface (fOCCI), tested on the CloudWATCH Cloud Plugfest and Standards Profile Workshop. PMES-COMPSs can talk through rOCCI with EGI Federated clouds infrastructures. Authentication through VOMS perun + keystone for managing credentials at the level of the private clouds. All the services to accept VOMS certificates for authentication. 20/10/14EUBrazilCC – FP

8 The EUBrazilCC Use Cases 20/10/14EUBrazilCC – FP A Virtual Lab to improving the monitoring of Leishmaniasis Every year 1-2 million new cases of leishmaniasis occur. The LVL aims to improve surveillance and research activities in the field of this neglected tropical disease by integrating data of parasites and vectors distribution from different databases (CLIOC, COLFLEB, ISCIII, speciesLink, Genebank, pubmed), together with molecular data and bioinformatic s processing pipelines. A scientific app to understand how biodiversity affects climate change Understanding the mutual interaction at a global scale between climate change & biodiversity dynamics is needed. EUBrazilCC will integrate two workflows combining models of plant species distribution and multi-level imaging data and processing in a scientific gateway. An integrated environment for blood flow and heart simulation Simulating a heartbeat is a complex, multi-scale problem. EUBrazilCC will deploy a complete blood simulation system with an accuracy beyond the state of the art by integrating the heart simulation system (ALYA) with a complete arterial simulation system (ADAN)

9 Selected case: Leishmaniasis Virtual Laboratory 20/10/14EUBrazilCC – FP

10 Selected case: Leishmaniasis Virtual Laboratory 20/10/14EUBrazilCC – FP countries350 Million people at riskSpread Prevalence: 12 MillionIncidence: 2 MillionChanges immune status Mortality: /yr3rd parasitic diseaseEnvironmental variation DALYs: th infectious diseaseDrug resistance Davies et al 2003

11 Selected case: Leishmaniasis Virtual Laboratory This will require three main components Integrating high-quality Databases CLIOC (http://clioc.fiocruz.br/) and the ISCIII-WHO-CCL collection for enriching molecular samples with associated clinical information.http://clioc.fiocruz.br/ COLFLEB (http://colfleb.fiocruz.br/), ISCIII-WHO-CCL collection and speciesLink (http://splink.cria.org.br/) for the georeferenced information of vectors.http://colfleb.fiocruz.br/http://splink.cria.org.br/ GenBank® (www.ncbi.nlm.nih.gov/genbank/) for the molecular data of Leishmania parasites and sand fly.www.ncbi.nlm.nih.gov/genbank/ PubMed (www.ncbi.nlm.nih.gov/pubmed) to index related scientific articles.www.ncbi.nlm.nih.gov/pubmed Integrating computing resources to efficiently deal with the workload of Multilocus Sequence Analyses (MLSA). Providing a community-like scientific Gateway to support researchers in sharing data, executing processing and accessing multiple data sources. 20/10/14EUBrazilCC – FP

12 Selected case: Leishmaniasis Virtual Laboratory 20/10/14EUBrazilCC – FP Client MVC framework Backbone.js JS map library OpenLayers 3 Web browser OAuth 2.0 AuthZ Server Apache Oltu IdP OAuth Token Load Balancer Nginx Server backend RESTful web service framework Jersey HTTP server Apache Tomcat Common libraries Google Guava Caching System Linux + JVM CLIOCCOLFLEBGenBank PubMedspeciesLink External datasources Cloud Provider Workflow Engine Database MongoDB Leishmania Collection Phlebotomine Habitat Models JSON OAuth Token

13 LVL collection main data The Leishmaniasis Virtual Laboratory will comprise information about Leishmania parasites (GeneBank+CLIOC/ISCIII) and sand fly vectors (SpeciesLink + COLFLEB/ISCIII). Filtering will allow to identify the set of samples that are of interest for a given study. 20/10/14 13

14 LVL experiment A typical experiment may consist on checking if whether the DNA sequence from a Leishmania isolate obtained from an outbreak was already described in other locations. The available DNA sequences from different collections plus the user’s sample (outbreak isolate) are stored in a FASTA file and send to the processing pipeline. 20/10/14 14

15 LVL experiment eScienceCentral processes the set of stages of a phylogeny study Multiple pipelines will be offered, including multiple algorithms, such as maximum parsimony, maximum likehood and neighbor-joining. Execution time may take hours, depending on the arguments. The result will be a phylogenetic tree showing how this new sequence isolate is related to others. 20/10/14 15

16 LVL collection view - heatmap Different branches of the tree define similarity subsets, which can be explored separately. Geographic maps will give a view of the “hot spots” where more entries are found for a given sequence. 20/10/14EUBrazilCC – FP

17 LVL collection view – sand flies Heat maps could be compared with maps from geo- referenced occurrences of the vectors from COLFLEB and other collections. Analysing the interactions of specific strains and specific vector species will increase the knowledge on disease control management. Potential use of Ecologic Niche Modelling will enable identifying potential risk areas under future climate conditions. 20/10/14EUBrazilCC – FP

18 LVL 20/10/14EUBrazilCC – FP Gathered information Parasite Host Location Host Immune Status Clinical Form Genotype Vector Location Species Host Preferences Genotype Surveillance System Mapping Distribution /Ecological Niche Modelling Assess Spread of Parasites and Vectors Parasite-Vector-Host Profiles Outbreak-associated Traits Emergence Preparedness

19 Dissemination and Future The EUBrazilCC web site has additional information. There are other ways to get informed: udconnect oudconnect Join our newsletter mailing list! ct.eu/content/stay-touch ct.eu/content/stay-touch 20/10/14EUBrazilCC – FP

20 Conclusions EUBrazilCC aims at demonstrating the use of cloud infrastructures for research as a basis for international cooperation All the activities are based on joint EU-Brazil work. The LVL is a use case with important social impact and which requires cloud computing infrastructures for production usage. 20/10/14EUBrazilCC – FP


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