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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www.who.int/tdr

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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