this project is funded by the european union cloud computing to assist surveillance of neglected...
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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 in EUBrazilCC
Ignacio Blanquer (UPV)Israel Cruz (ISCIII)
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 13/2012 - 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.
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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.
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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
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ONE OStack HPC Clusters
Fogbow CSGRID
COMPSs eSC
mc2
IM / VMRC
PDAS
Leishmaniasis Virtual
Laboratory
Vascular system
simulation
Climate change & ecology
PMES-COMPSs
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).
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Cloud >1000 cores + <500 op cores
UPVLC
BSC
CMCC
UFCG
LNCC
HPC > 5500 cores
LNCC
BSC
UNEW
CMCC
The EUBrazilCC Software Architecture
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PDASCOMPS
s
eScienceCentra
lIM /
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.
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.
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The EUBrazilCC Use Cases
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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 bioinformatics 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)
Selected case: Leishmaniasis Virtual Laboratory
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98 countries 350 Million people at risk Spread
Prevalence: 12 Million Incidence: 2 Million Changes immune status
Mortality: 60 000 /yr 3rd parasitic disease Environmental variation
DALYs: 2 357 000 9th infectious disease Drug resistance
Davies et al 2003
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.
COLFLEB (http://colfleb.fiocruz.br/), ISCIII-WHO-CCL collection and speciesLink (http://splink.cria.org.br/) for the georeferenced information of vectors.
GenBank® (www.ncbi.nlm.nih.gov/genbank/) for the molecular data of Leishmania parasites and sand fly.
PubMed (www.ncbi.nlm.nih.gov/pubmed) to index related scientific articles.
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.
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LVL collection main dataThe 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.
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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.
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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.
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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.
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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.
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LVL
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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
Dissemination and Future
The EUBrazilCC web site has additional information.
There are other ways to get informed:
Twitter: @EUBrazilCC
www.facebook.com/EUBrazilcloudconnect
www.linkedin.com/in/eubrazilcloudconnect
Join our newsletter mailing list! http://www.eubrazilcloudconnect.eu/content/stay-touch
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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.
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