1. No category

Position Papers
20 October 2014,
Rio de Janeiro, Brazil
CC
EU Brazil Cloud Connect
EU Brazil Cloud Computing for Science
Index
Welcome Speech......................................................................................................................................................... 1
A Strategy for the Implementation of the Brazilian Academic Cloud...................................................... 2
High Performance Computing as Service for Scientific Applications...................................................... 8
Start-Up Brasil: the national startup acceleration program of Brazil........................................................ 9
A galaxy server for a virtual biodiversity Lab, Conneccted to Cloudscape Brazil..............................11
A federated cloud infrastructure for scientific research on biodiversity and climate change......12
Product Recognition Platform for Mobile Commerce - VTX Brasil..........................................................13
Intercontinental Data Platforms for Global Challenges..............................................................................14
The evolution of a Cloud Technology to face both IT challenges and user needs............................15
An integrated environment for blood flow and heart simulation...........................................................17
Stingray@Galaxy cloud-based platform: applications for genomic epidemiology studies...........19
Virtual laboratory to fight Leishmaniasis..........................................................................................................20
A Pan-European e-infrastructure for the agricultural research community breaking
EU barriers....................................................................................................................................................................21
The EGI Federated Cloud infrastructure platform: Delivering e-Infrastructure
resources at an unprecedented scale for the Europea................................................................................23
Welcome Speech
Encouraged by the success of the Cloudscape
Europe series, now in its seventh year, the EU
Brazil Cloud Connect project is delighted to rollout the first edition of Cloudscape Brazil.. High
on our agenda as you can read is the ambition
to shape cloud developments in both Brazil and
Europe by bringing insights into current market
trends, challenges slowing down mainstream
adoption of cloud services and best practices to
address them. Better policy and more informed
consumer choices are essential to build trust, as
well as to ensure safe and fair contracts and a
level playing field for the supply side.
Brazil has a massive IT market. According to
IDC, it is the fifth largest market in the world,
accounting for USD 144 billion or 2% of global IT revenues. This is, in itself, an incentive for
companies to invest in the country. However,
the business model requires proper infrastructure and regulatory framework, which Brazil is
still building. We will share best practices from
Europe and look for ways in which we can address data protection, privacy and security
challenges.
address real-world problems in cities, homes
and everyday life. Market demand is therefore
a key driver underpinned by specific support
mechanisms and stakeholders from the public
and private sector. We will also compare efforts in Europe and consider practical steps to
increase business participation in international
co-operation partnerships whilst introducing
cross-cutting collaborations with EU & BR scientific achievements.
Beyond the business perspectives, Cloudscape
Brazil presents new developments to advance
scientific knowledge, which is key to tackling
global societal challenges. Examples span a
better understanding of biodiversity patterns
and more effective ecosystem research, improved eHealth services, large-scale analysis for
neglected diseases, and data-driven analysis for
climate change research.
Web entrepreneurs, start-ups and ICT-savvy
SMEs are the innovators taking new products
and services to market, creating new jobs and
boosting economic growth. Both Brazil and
Europe are making significant investments to
create a healthy environment where new businesses can flourish.
Scientific applications also have specific requirements that most commercial service providers are not currently able to meet. Cloudscape Brazil explores on-going developments
for new cloud platforms like EU Brazil Cloud
Connect, which are specifically designed for
better performance, enabling researchers to
focus on their core work and speed up the
time it takes to make new discoveries. We look
at where we stand today and set out priorities
for the next twelve months so we can present
results at Cloudscape Brazil 2015, and beyond.
A key feature of Cloudscape Brazil is the showcase of the Start-up Brazil programme, as a
virtuous cycle of innovation. Funded by the
Brazilian Ministry of Science, Technology and
Innovation (MCTI), the programme helps accelerators take new solutions to market that
We wish all participants, speakers, chairs and
panellists a very fruitful workshop and encourage them to make the most of the networking opportunities so we can all play a part in
strengthening EU-Brazil synergies, whether for
business, research or policy making.
1
A Strategy for the Implementation of the Brazilian
Academic Cloud
Author(s):
José L. Ribeiro Filho, Antonio C. F. Nunes,
Gorgônio Araújo, Graciela M. L. Martins, Leandro M. O. Guimarães
Rede Nacional de Ensino e Pesquisa
Abstract
This article presents a brief overview of the
strategies currently adopted by some National
Research and Education Networks (NREN) to
implement and offer scientific cloud computing services. It describes the constraints, opportunities and the strategy chosen by the Brazilian NREN – Rede Nacional de Ensino e Pesquisa
(RNP) to build and provide cloud services to
and with public universities and research institutes in Brazil.
Keywords:
2
cloud implementation strategies, scientific
cloud, cloud services middleware; National
Research and Education Networks, hybrid and
community cloud, federated cloud.
I. INTRODUCTION
The Brazilian National Research and Education
Network (NREN) – Rede Nacional de Ensino e
Pesquisa (RNP), is the organization that plan,
design, deploy and operates a nationwide
networking infrastructure under a contract
with the Ministry for Science, Technology and
Innovation (MCTI). A governmental program
that currently includes four ministries – MCTI,
Education (MEC), Culture (MinC) and Health
(MS) defines, on an annual basis, the contract
objectives and its funding. The four ministries
are represented in a program governance committee, which supervises the program’s execution. Among the program’s objectives are the
connection of university, research institutes,
hospitals, museums, and many other public Research and Education (R&E) institutions
through RNP’s network infrastructure – Rede
Ipê, shown in Figure 1.
Besides connecting more than 800 points, of
around 350 public institutions (universities
and research institutes) through an advanced
multi-gigabit national backbone, and more
than 35 optical metropolitan area networks
(through owned infrastructure1), RNP also offers advanced services on top of this network,
potentially benefiting more than 3.5 million
users, including VoIP, web conferencing, video
conferencing and telepresence rooms and services, VoD, live streaming, federated authentication for most of the services and eduroam.
RNP also hosts in its data center several partner institutions’ applications such as the CAPES
Portal de Periodicos – a federated web portal
which offers access to a large variety of international scientific journals to all public universities in the country.
One of the main goals of RNP’s mission is to
provide those and new advanced Information
and Communication Technology (ICT) services to the Brazilian academic community. To
achieve this goal, RNP is permanently seeking
new technologies, products, services and processes, through partnerships and collaboration
with the academy, industry and world’s leading
NRENs.
The ever increasing production of scientific
data (e.g. environmental monitoring, biodiversity data bases, a variety of simulation and visualization systems like climate forecast, astronomy and cosmology, high energy physics data
collection), cultural related data (e.g. historical
and rare collections, audiovisual content, also
as a means of data preservation) and management data (e.g. government ICT policies and
R&E programs execution, assessment and management indicators, data bases and big data
processing) require an scalable and sustainable data center infrastructure to support their
demands. These facilities must be located in a
distributed way and in places that offer telecommunication, energy and security services,
as well as appropriate physical space/infrastructure. For most of the mentioned demands,
the cloud computing technology and services
can provide a cost effective solution.
1 REDECOMEP (Metropolitan Community Education and Research Networks) – a fiber optics
infrastructure build by RNP in more than 35 cities to connect R&E institutions to RNP’s backbone -. http://www.redecomep.rnp.br/
Fig. 1. RNP’s national network backbone – Rede Ipê
The study considered two basic scenarios: a)
universities and higher education institutes
outsource services to public clouds or to their
NREN; b) NRENs and research organizations
outsource services or sub-services to public
clouds; and a question to a panel of experts.
“What kind of services, sub-services or functions can be outsourced by Universities and/or
NRENs to public cloud service providers, how,
and under what conditions and circumstances?”
The panel discussed issues such as privacy, application types (commodity and specialized),
data protection, risks, costs, thrust (on public
commercial providers x NRENs) and the conclusion was as follows:
This paper presents the strategy defined by
RNP to plan, deploy and operate cloud services to and in collaboration with Brazilian public
universities and research institutes. The strategy is explained in the next sections, starting
with a brief survey of current cloud strategies
and services of other NRENs. The planning, deployment, operation and the pilot project are
also discussed, taking into account the alternatives considered and the chosen options.
II. NRENS CLOUD STRATEGIES
Our work started with a survey that looked at
what other NRENs are planning and doing, regarding their strategies about cloud computing services and infrastructure. Many NRENs are
already offering cloud services in a variety of
degrees and through different business models. However, in Europe, the Trans-European
Research and Education Networking Association (TERENA) has been following closely the
European NRENs strategies to offer storage/
cloud computing services and infrastructure.
Its annual TERENA Compendium [1] presents
comprehensive information about all European
and other NRENs in the world, where one can
see how cloud computing deployment and
services are evolving over time. Besides the
annual compendium, TERENA also publishes
studies produced by their working groups. A
2011 green paper which discussed the European NRENs strategic perspective on storage
and cloud computing [2] was very influential in
RNP’s own cloud strategy definition, presented
here.
»» The outsourcing of commodity application
services (e.g. student e-mails and document
sharing) from universities to public clouds
can be done with low risk. Moreover, significant cost benefits can be achieved through a
NREN coordinated and centralized contracting process.
»» For infrastructure related services (e.g. computing and storage) outsourcing to public
clouds, it was considered that the risks concerning service operation, data protection,
authentication and access control were an issue for individual universities. However, outsourcing these services to NRENs were considered acceptable, due to the established
relationship and thrust between NRENs and
universities.
»» In case of the NREN itself, the outsourcing of
commodity application services (e.g. calendar system) to commercial clouds seemed
straightforward.
»» Finally, for infrastructure related services (e.g.
network operation, storage, videoconferencing, computing), the mixing of the NRENs
own infrastructure with public clouds was
considered a value-added IaaS scenario.
Figure 2 shows a simplified strategy decision
tree for NRENs that came out of the TERENA
discussions [2]. Regarding application services, NRENs can develop and provide their own
services or can exploit the joint buying force of
their users and brokering towards commercial
cloud service providers. Regarding infrastructure services, NRENs can build their own cloud
infrastructure or can aggregate user demands
and channel them in to commercial cloud infra-
3
structures.
Fig. 2. Cloud strategy decision tree
Based on user demands, networking capabilities, funding schemes and the above conclusions, NRENs have adopted three major national deployment strategies for e-infrastructure
services offerings:
»» building private storage/cloud infrastructure
on top of the national R&E network;
4
»» connecting public (commercial) storage/
cloud infrastructure via the national R&E network;
»» creating hybrid storage/cloud infrastructure
(a mix of public and private infrastructures)
connected via the national R&E network.
The next section presents RNP’s cloud strategy,
as planned and under deployment, based on
the strategy options discussed above.
III. RNP CLOUD STRATEGY
The cloud services/infrastructure strategy chosen by RNP came out of a process which was
guided and constrained by the demands of the
Brazilian R&E community, RNP operation and
funding models, as explained in the introduction of this article, and other NREN cloud strategies discussed in the previous section.
Additionally, four main stakeholders that play
major roles in the strategy definition and implementation were identified: public R&E institutions (universities and research institutes), research groups, RNP and R&E funding agencies.
The Brazilian academic cloud strategy was then
built around those stakeholders. The R&D institutions can be, at the same time or separately,
customers and providers of infrastructure and
services. RNP has the coordination role, being
responsible for the cloud architecture definition, contracting and operating its services,
to develop and deploy applications, and the
coordination of the partnerships with other
stakeholders. The research groups contribute
with their scientific application’s requirements
as well as with the development of new functionalities and the cloud funding, through and
proportionally to their use of the cloud. Finally,
the strategy includes the R&E funding agencies
to help them promote a change in the current
research funding model. The proposed funding model will take the portion of the money granted to research projects, destined to
ICT infrastructure (including servers, storage
and networking equipment, basic software
and even some specialized applications), and
transfer it directly to a National Scientific Cloud
Program. Instead of having to build a usually
expensive and fragile ICT infrastructure, which
also takes time to buy and setup, granted projects will receive an equivalent quota of the required platforms as services from the national
scientific cloud.
Another dimension considered in our work
pointed out to two main classes of user profiles: institutional users (represented by IT
managers of R&E institutions) and individuals
(e.g. researchers and their labs). These two user
classes have specific demands for cloud services and infrastructure, which can be grouped
according to the three layers of cloud services:
SaaS, PaaS and IaaS. Institutional users demand
mainly SaaS services such as staff e-mail, student registration and storage/backup services.
They may also want to mirror some parts of
their local infrastructure to a private cloud, like
virtual processors and raw storage, corresponding to the IaaS service. On the other hand, research groups show the desire to have more
control over the cloud infrastructure, therefore
requiring mainly an IaaS service, which allow
them to develop, test and run their own applications and services on top of a virtualized
infrastructure (e.g. processing, storage /backup
and networking). They might also need PaaS
services for collaboration projects using wiki,
portals, data bases, etc. Besides these two user
classes, RNP itself can migrate most of its current advanced services to the cloud infrastructure, including VoD/media streaming, web and
videoconferencing, and some of its partners
services like the CAPES Portal de Periodicos2
scientific journal web portal.
As a result of the above described “environment” and NREN’s major national deployment
strategies for e-infrastructure services, discussed in the previous section, the best strategy that emerged for RNP’s cloud service/
infrastructure was a hybrid, community and
federated cloud. The hybrid model allows RNP
to act as a public (commercial) contract broker
for “low risk” services, such as student e-mail,
document sharing, etc. Through the community model, universities and research institutes
can offer their own data center infrastructure
(in full or partially) to the national cloud. They
should be able to dynamically change the
amount of resources shared with the national
cloud and receive privileged access to other
partner’s infrastructure (virtual processors and
storage) in return. Finally, the federated model
ensures the required level of security and trustiness among all the partners as well as to the
users through RNP’s federated services. This
strategy is also an answer to the geographical
distribution requirement for a redundant and
reliable cloud, once the partner institutions are
distributed nationwide.
To make this model work seamlessly to the users and partners, a middleware is required to
provide an isolation layer between the cloud
service user interface, as well as the application
program interface (API), and the specific physical and virtualized resources offered by the
community/federated infrastructure providers, including contracted public (commercial)
cloud providers. This middleware is still under
development by various cloud computing research groups, such as the GT-PID: Distributed
IaaS Platform [3] from Universidade Federal do
Rio de Janeiro (UFRJ), based in open software
platforms. It should be able to integrate the
most common cloud platforms (e.g., Xen and
vSphere Hypervisors ) and orchestration software like OpenStack and CloudStack, in a transparent and easy way. The goal is to provide a
high level abstraction layer to allow the integration of resources, and let users access cloud
services and infrastructure unaware of its management and operation details. On the other
2 http://www-periodicos-capes-gov-br.ez106.
periodicos.capes.gov.br/
hand, when required, users should be able to
choose where they run their virtual machines/
applications or move them from one cloud to
another, regardless of where the cloud nodes
are geographically located. The challenge to
implement these features nowadays derives
from the high heterogeneity of cloud provider’s infrastructure. RNP is therefore modeling
a service that should be able to use resources
of as many cloud providers as possible, which
requires supporting different Hypervisors and
Orchestrators.
The strategy also includes other definitions like
an Acceptable Use Policy (AUP) for the national cloud, the basic operation model (required
to all partner institutions), the national cloud
sustainability model, user interfaces and APIs,
application migration support, to mention a
few. Another concept defined in RNP’s cloud
strategy is the shared data center component,
the CDC (Centro de Dados Compartilhados).
The CDC is a physical structure that hosts all the
required infrastructure for a Tier 2 data center,
including redundant energy (also with power
generators and UPS), fire control, independent
cooling systems, unified management platform
(that collects status of temperature, humidity,
smoke, etc.), and access control systems. It can
be a building or a container based platform,
which can support rapid “horizontal or vertical”
expansion.
IV. IMPLEMENTATION AND CURRENT STATUS
After the definition of the national cloud services and infrastructure strategy, RNP started
in 2013 a pilot project, comprising the deployment of two container-based CDCs. The platform is the Huawei IDS1000 - C cluster container data center. It provides a flexible, mixing and
modular design concept, committed to help
customers to build the green cloud computing
data center infrastructure, and realize the availability, safety, agility, scalability and an optimal
TCO. The IDS1000-C can grow horizontally or
vertically providing a path for rapid infrastructure expansion. The hardware with the unified
management software and the cloud platform
were donated to the Brazilian government by
the Chinese company. The smallest configuration comprises 2 container modules: one with
the cooling and power generators/UPS and
the other hosts the ICT platforms. It currently
5
6
supports 132 processor cores and 0.5Pb storage. It is installed at the Instituto Nacional de
Pesquisas da Amazônia (INPA) in Manaus. The
other CDC has 3 container modules with separated cooling, power generators/UPS and ICT
platforms. It supports 612 processor cores and
1.0Pb storage. They are installed at the Instituto
Federal de Educação, Ciência e Tecnologia de
Pernambuco (IFPE), in Recife, and is expected
to start its assisted operation stage in July 2014.
ence, Technology and Innovation for the support to the academic cloud program and the
partners of the CDC project, including INPA,
IFPE and Huawei.
Additionally, RNP’s CDC project team is currently analyzing the integration of Huawei’s
software components with other Orchestration
platforms, like CloudStack and OpenStack. The
project team expects the cloud environment
ready for the pilot phase by the end of October
2014. The CDCs will also be used to test the integration middleware that is being developed
to support the hybrid, community and federated strategy model.
[2] Szegedi, P., NRENs’ strategic perspective on
storage and cloud “buy or build” (April 2011):
http://www.terena.org/activities/tf-storage/
Storage-and-cloud-v5.pdf
RNP is also discussing with some public universities and institutions (e.g. Cinemateca Brasileira) the partnership details that will allow them
to enter and provide additional infrastructure
to the national academic cloud. Besides this,
RNP is comparing public/commercial cloud
services, business models, pricing and contract
clauses to start another pilot which will assess
the broker role, as planned for the hybrid model.
V. FINAL REMARKS
This paper presented a brief description of
NREN’s cloud strategies and the scenario chosen by the Brazilian National Research and Education Network, RNP, for the Brazilian academic
cloud. The hybrid, community and federated
strategy was chosen as the most flexible and
suitable for the current Brazilian NREN operation and funding models.
RNP strongly believes that the Brazilian academic cloud will augment the security and the
national sovereignty. It will also reduce current
fragilities that many public R&E institutions
demonstrate regarding the safety of an ever
increasing amount of strategic and vital information, as a consequence of a lack of adequate
e-infrastructure services and support.
REFERENCES
[1] van Pinxteren, B., Editor; TERENA Compendium 2013: http://www.terena.org/activities/
compendium/2013/
[3] GT-PID: Distributed IaaS platform: http://
www.gta.ufrj.br/gt-pid/index.php/proj
[4] GT-CNC – Computação em Nuvem para
Ciência (2012-2014) http://www.gt-cnc.gercom.ufpa.br/
[5] GT-MCC 2 – Minha cloud científica (realizado em 2012-2013) http://www.lncc.br/sinapad/projectmanager/public/projects/gt-mcc/
wiki
[6] European cloud computing strategy:
https://ec.europa.eu/digital-agenda/en/european-cloud-computing-strategy
[7] Boyle, Brian; Byrne, Ronan; Nisbet, Brian.
HEAnet cloud strategy. TERENA Networking
Conference 2014: https://tnc2014.terena.org/
core/presentation/34
[8] Costa, R. E. O.; Brasileiro, F.; Lemos Filho, G.;
Souza, D. M. T., Analyzing the impact of elasticity on the profit of cloud computing providers.
Future Generation Computer Systems, v. 29, p.
1777-1787, 2013
[9] The adoption of cloud services (September
2012):
http://www.terena.org/publications/
files/”ASPIRE The Adoption of Cloud Services.
pdf”
[10] SURFnet GigPort3 project, “Cloud Storage
and Peer-to-Peer (P2P) Storage”
http://www.surfnet.nl/nl/Innovatieprogramma’s/gigaport3/Documents/co nceptmap-v1.0.pdf
[11] SURFnet, “Connecting to cloud services - A
guideline for NRENs”, (November 2010)
ACKNOWLEDGMENT
http://www.terena.org/mail-archives/tf-msp/
pdfsIUEA3OSlJ.pdf
The authors thank RNP and the Ministry for Sci-
[12] Szegedi, P. at all, TERENA trusted cloud
drive (May 2013) http://www.terena.org/publications/files/TERENA%20Trusted%20Clou
d%20Drive%20Facility.pdf
[13] Jitcloudhttp://jitclouds.lsd.ufcg.edu.br/
site/index.php/pt/publicacoes
[14] AutoStratushttp://www.dimap.ufrn.br/
altostratus/publicacoes.php
[15] FileSender project http://www.filesender.
org
[16] Peter Mell, Timothy Grance, “The NIST Definition of Cloud Computing (Draft)”, (January
2011)
http://csrc.nist.gov/publications/
drafts/800-145/Draft-SP-800-145_cloud-definition.pdf
7
High Performance Computing as Service for
Scientific Applications
Author(s):
Who stands to benefit and how:
Bruno Schulze
Currently, the group of Distributed Scientific Computing at the National Laboratory for
Scientific Computing is developing a set of
research projects aiming to understand the
relationship among: scientific applications,
virtualization layers and infrastructure, based
on a private development cloud platform. The
platform enables to prospect new technologies
and solutions in optimizing the use of cloud environments for scientific applications.
Focus area:
8
Several studies have been carried out to check
possibilities and limitations of clouds in providing support to scientific applications. The major part of these studies is dedicated to the behavior of scientific applications, most of them
characterized by large amounts of information
processing and massive use of computational
resources. In this context clouds emerge in providing additional resources, or in minimizing
cost in the acquisition of new resources. The
use of clouds in support to scientific applications have inherited characteristics, different
from the commercial ones. The virtualization
technologies, are the basic elements of clouds’
infrastructure, and despite of their significant
advances they still present limitations when
confronted with the needs of high computational power and communication, demanded
by several scientific applications. However, for
better use these virtualized resources it is necessary a better and deeper understanding of
the characteristics of the cloud architecture(s)
being used.
Focus of your position paper:
The studies being carried out by this group is
corroborated by other research groups, and
suggest that different virtualization layers and
hardware architecture used in the cloud infrastructure, influence the performance of scientific applications. This influence leads to the
concept of affinity, i.e., which group of scientific applications has a better performance associated to the virtualization layer and hardware
architecture being used. These aspects involve:
reducing cloud environment limitations in support to scientific applications; b) to provide the
basis for the development of new cloud scheduling algorithms; and assisting the acquisition
of new resources and cloud providers, looking
for performance and resource usage optimization.
Start-Up Brasil: the national startup acceleration
program of Brazil
Author(s):
Felipe Matos
Focus area:
Start-Up Brasil is the national program for startups acceleration in the country. It provides seed
funding and access to acceleration programs
of the 12 best accelerators from all over Brazil.
After 3 batches of startups selection, counting
more than 150 supported companies; the program will be closing its first cycle at its very first
Demo Day that will take place in November 6
in São Paulo. In this speech, the Director of Operations of Start-Up Brasil will be presenting
the program and its benefits, the Demo Days
and other events, as well as some of the results
achieved so far.
Who stands to benefit and how:
Start-Up Brasil is an initiative from the Brazilian’s
Ministry of Science, Technology and Innovation
in partnership with accelerators and with Softex as operational manager. As we have many
partners and institutions to support, we have a
wide range of stakeholders that we can count
on and we must be held accountable. They are
entrepreneurs, investors, policy makers, supporter institutions, companies such as IBM,
which is our sponsor, government, society and
whoever is interested in the startups, entrepreneurship and innovation ecosystem. Society
in general will be benefited as startups create
solutions to real problems in the cities, houses, and lives. Also, as they grow more jobs are
opened, generating more families’ revenue and
purchasing power that leads to more work to
do. That is, a virtuous cycle for innovation.
Focus of your position paper:
Taking to the market real solutions that matter Taking ideas to market is about working
daily to create something new, different or innovative. It is a deep research on what is out
there and what we can do to make it better,
to change it, to recreate it, to facilitate it, or to
bring a desire in acquiring something we never thought we wanted. Start-Up Brasil is about
that. For being a National Startup Acceleration
Program, an initiative of the Brazilian Ministry
of Science, Technology and Innovation (MCTI),
in partnership with accelerators, Start-Up Brasil
is everyday looking new solutions for real problems. Startups that apply to participate in the
program are asked to show what they can do to
bring solutions to problems we face everyday
in our lives. It does not matter in which area this
solution; the main thing is to take this idea to
the market. How do we that? Start-Up Brasil is a
public-private partnership between the federal
government of Brazil partnering with qualified
accelerators by the program to support new
technology-based companies: startups. Startups have the role of constantly revitalizing the
market, but they need a healthy environment
to develop and be successful. The accelerators
play in this context as a market-oriented agent,
usually in the private sector and with capacity
for financial investment, and have the function
of directing and strengthening startups’ development. Each edition of Start-Up Brasil lasts
one year and has two public calls, one to select
and qualify accelerators and another one to select startups, every six months. During the year,
the selected startups are monitored, attend
events, and have the possibility to participate
in the national and/or international Demo Day,
promoted by the Program. Start-Up Brasil integrates the so called TI Maior Program, a strategic program for software and IT services, which
is one of the ENCTI (National Science, Technology and Innovation Strategy) initiatives to select
IT companies. So far, we have important startups coming out with solutions for everyday life.
Many of them are cloud solutions customized
to your specific requirements, such as the three
mentioned above:
»» Razoom: Web platform for tour operators to
tourism agencies that wants to manage their
operations and sell online. All books, changes and different tours can be manage online
and in an easy way.
»» Agenda Beleza – In www.agendabeleza.com.
br website, users will find several providers
of Beauty and Cosmetic services and they
will be able to schedule safely an appointment with their favorite professional from
anywhere at any time. Scheduling is free and
happens in a few clicks. For professionals,
9
Agenda Beleza is also a facilitator, already
providing tools that optimize time and provide a more responsive communication with
clients. This speed also benefits customers,
who may, for example, know about changes
in the appointment through an SMS.
»» Memed - Memed is online software where
doctors can search all drug information from
10
the pharmaceutical industry, available for
consultation and prescription in the Brazilian
market. In addition, Memed is prescription
tool where doctors can use all the updated
information about medications and dosages,
to make their prescriptions directly from the
computer screen into the hands of patients,
avoiding errors in reading by the patient or
the pharmacist.
A galaxy server for a virtual biodiversity Lab,
Conneccted to Cloudscape Brazil
Author(s):
Yec’han Laizet, Philipe Chaumeil, Jean-Marc
Frigerio and Alain franc
Focus area:
Community Ecology is a venerable discipline
which developed from both Natural History and
theoretical modelling ever since the first half of
20th century. Linked with population genetics
and macroecology, it aims at understanding
biodiversity pattern at all scales, from habitats
until full biomes. It has experienced several revolutions, both conceptual and technological.
The end of last century saw the emergence of
molecular systematics, where species could be
identified from markers in their genomes. This
has developed as barcdoding. This approach
has been revolutionized a second time when
NGS techniques permitted a mass production
of sequences from an environmental sample,
giving birth to metagenomics and metabarcoding.
Who stands to benefit and how:
We propose to connect our galaxy server to
cloudskape Brazil, to offer a service to a large
community having question on biodiversity
patterns, including pant, animal and human
health.
Focus of your position paper:
A team composed by Yech’an Laizet, Philipe
Chaumeil, Jean-Marc Frigerio and Alain Franc,
all from BioGeCo research unit at INRA and University Bordeaux 1 at Bordeaux, has developed
a galaxy platform for making available to many
ecologists a series of tools to decipher biodiversity patterns. These tools elaborate data analysis and some models from molecular based
inventories. Form sequences of two specimen
on the same marker it is possible to compute
a distance, based on score of local alignment
(Smith-Waterman algorithm). Several analyses
can be performed from pairwise distance of a
data set of sequences of a marker in a community. They can be currently organized into categories
»» A series of classical and public programs in a
first category, such as multiple alignments,
inferring molecular phylogenies by maximum likelihood
»» A key program for computing pairwise distances between specimen known by their sequences through a score of local alignment
computed by Smith-Waterman algorithm
»» A visualization of the pattern of given characters versus these distances, with graph based
methods, such as exhibiting cliques, communities or connected components from graph
build on distance thresholds
»» Dimensionality reduction method, which
build an Euclidean image of a pairwise distance knowledge, in a low dimensional
space, which facilitates interpretation
»» A way to build an inventory from a set of
reads (short sequences) of an environmental sample, knowing a reference data base of
taxonomically annotated sequences
»» A way to infer a statistically accurate taxonomic annotation of an unknown sequence,
with tools like mixture models or support
vector machines. This is particularly useful for
diagnosis of diseases as soon as a high quality reference data base does exist.
All these tools run on a laptop. However, those
involving data sets produced by NGS require
production clusters for running in a reasonable
time. Therefore, our galaxy server has been connected to a local server, to European Grid Infrastructure and, which is relevant for cloudscape
Brazil, to a cloud using Dirac as middleware.
This is transparent for the user.
11
A federated cloud infrastructure for scientific
research on biodiversity and climate change
Author(s):
I. Rufino, H. Seijmonsbergen, C. de O. Galvao, W.
Los, V. Canhos, D. Lezzi, S. Fiore, G. Aloisio
Focus area:
cross-border collaboration through e-infrastructure services, cloud federation and user
requirements, data infrastructure.
Who stands to benefit and how:
12
LiDAR and GIS technologies are increasingly
supporting biodiversity and climate change research of global ecosystem. The growing image
and measurement data availability is promoting
success stories. Governmental agencies (both
research & education) and commercial companies are starting to benefit from such innovative
information sources. They include users from
forestry, earth science, biology, environmental
conservation, agriculture, food industry, environmental engineering companies and others.
The services as provided in the scientific gateway will also be deployed by professionals in hydrology, agriculture, climatology, remote sensing, and by environmental managers.
Focus of your position paper:
Environmental systems (biosphere, atmosphere, soil) have strong interactions, but we
have limited knowledge of their interdependencies. Research on biodiversity and climate
change at the global scale assumes the availability of large-scale data sets with observations and measurements of the systems components, together with advanced analytical
and modelling software. It also requires the
computational capacity to run the demanding
workflows on huge data sets. The interaction
between climate and biodiversity change acts
at the global scale and requires the involvement of experts on both sides of the Atlantic. A
first case study is located in the semiarid region
of Brazil, a large drought and desertification
prone region, with 1 million km2, and one of
the main targets of Brazil to tackle poverty. The
existing early warning systems make little use
of remote sensing information. Therefore, satellite images derived from several sensors will
be processed to produce calculations of energy
balance and evapotranspiration of water to the
atmosphere. These estimates, combined with
the analysis of historical time-series, allow the
detection of changes in the terrestrial plant
systems and they will be used to discriminate
the influences from human occupation and
those from climate variability and/or change
on energy fluxes and land cover. Identification
of a basic set of climate change indicators will
be cross-related with biodiversity indicators
data and plant species occurrences data, to improve understanding climate change and biodiversity dynamics of terrestrial plant systems
through multi-level and multi-dimensional
analysis. The Adolfo Ducke Forest is a 10,000 ha
protected forested area near the city of Manaus
at the confluence of the Amazon and Rio Negro Rivers. The forest reserve hosts numerous
research plots that are representative for the
regional biodiversity and allow for studying
the impact of forest fragmentation in the Amazon region. Light Detection And Ranging (LiDAR) technology is used to efficiently extract
the 3D vegetation structure and sub-canopy
terrain geomorphology. Supplemented with
multi-spectral satellite imagery this combination of 3D vegetation structure and quality of
the vegetation can be used as transparent and
consistent proxies for the actual biodiversity
and habitat suitability. Although the processing of LiDAR data into 3D forest metrics, such
as gap density and sub-canopy biomass, is still
in its infancy, it will be explored how machine
learning can enhance the results, although it
generates the need for extensive computational power. In the EUBrazil Cloud Connect project, applications and services will be tuned to
support research on the relationships between
biodiversity and climate change. The cooperation of Brazilian and European organisations
is combining Brazilian expertise on biodiversity modelling (e.g. OpenModeller) and data
analysis deploying tools and webservices from
SpeciesLink (CRIA) with those from European
(CMCC) and Brazilian (UFCG)centres on climate
change. The EUBrazil Cloud Connect Use Case 3
will deploy the adapted tools and applications
in the common federated resources.
Product Recognition Platform for Mobile
Commerce - VTX Brasil
Author(s):
Fernando Ponciano
Focus area:
Success story of VTX Brasil from the development of a proprietary cloud based technology
to define the business model and go to the
market. How the company created the Product
Recognition Platform with researchers from top
universities in Brazil and US, how and who to offer the solution, business model definition and
success cases.
Who stands to benefit and how:
Direct Customer: Almost any kind of retailer
that would like to sell their products through
mobile apps, creating a new sales channel or
enhancing the currently shopper experience
through smartphones and tablets by offering a
easier and faster way to find and purchase the
desired product, anywhere and anytime. End
Customer: Shoppers that would like a better experience in merchants mobile apps.
Focus of your position paper:
VTX Brasil is a startup that spent two years researching and developing an image recognition solution partnering with PHDs from top
universities such as Unicamp, USP, Virginia Tech
and Unical. VTX started incubated in Virginia
Tech University where image recognition researchers and artificial intelligence specialists
supported the company to create and improve
the technology. Back to Brazil hired a very talented team of developers (iOs, Android, Im-
age Recognition, AI, UX designers and project
manager) that understood and improved even
more the technology. The patent technology
from VTX was named PRP (Product Recognition Platform) and the strategy defined by the
company was to focus on enhancing the mobile commerce. The problem to solve was that
mobile search is awful and It is very difficult to
purchase a product through the smartphone
using merchants mobile apps, so the idea is to
integrate our platform in merchants apps so the
user can find and purchase a desired product
just by opening the app and taking a picture of
It, anytime, anywhere. For the business model
the company defined two possibilities: 1st - Revenue Share: merchant shares the revenue from
our platform sales with VTX 2nd - SaaS: monthly
fee based on the number of requisitons to our
system (number of pictures uploaded to our
servers) VTX also partnered with Elavon - one of
the biggest US payment companies - to provide
a payment gateway for the users, simplifying
even more the experience of purchase through
mobile app. Following the strategy VTX developed big retail customers in Brazil from several
areas such as: bookstores, drugstores, shoes,
electronics, price grabbers and etc. All the technology runs in the VTX cloud, what makes the
solution reliable, fast and capable of work anywhere in the world at anytime. The challenge
now is keep growing in Brazil and expand to
other countries; VTX already started that movement by US.
13
Intercontinental Data Platforms for Global
Challenges
Author(s):
Andrea Manieri, Engineering Ingegneria Informatica spa Massimo Gentile, Engineering do
Brasil sa.
Focus area:
Cloud Federation, Innovation and Commercialisation
Who stands to benefit and how:
Digitalisation and implied digital economy will
benefit the whole set of stakeholders, from
researchers to industries, from citizens to Governement. The key issue is to concentrate the
efforts in baseline technologies and platform
to handle the various data sets produced and
those that will be produced in the future, enabling their exploitation using a win-win approach among all the stakeholders.
Focus of your position paper:
14
The world is going digital and we are experimenting this in every-day life. Digital are the
communications among people, digital are
now a significant number of our interactions
with public administration, digital are all the
most advanced services provided by Industries.
The invariant of all of these are the availability
of an high capacity network, able to easily interconnect the very last man in the earth with
the biggest facility in the world, and the possibility to access useful information and data in
a seamlessly way. If dat are then the new gold,
Networks are the rivers where this gold can be
mined. Of course there’s the need to have tools,
to avoid search-by-hand in the mountains: such
tools are the cloud services and software in general. Current research is addressing – separately
– some of the most urgent challenges: - Standardization and interoperability of cloud services and data repositories, - Opening of available
data, - Contractual and Privacy rules, including
SLAs aspects, - Security and Access Control over
services, data and networks, -Nurturing of new
businesses and start-ups The most relevant gap
in analyzing the current initiatives, successfully
run until now, is the reduced ability to access
and re-use existing data (any type of data) on
top of which, applications can be experiment-
ed. The current various platforms provide useful
access to interconnected physical facilities or isolated data-sets using dedicated technologies; it’s
then up to the single developer to use needed
data uploading or merging to run its research or
experimentation or business. This is sound only
when you can work with a subset of the potential
data, or when you have the capacities (technically and legally speaking) to duplicate such data to
be hosted by a third-party. However, when you
want to experiment real big-data algorithms, or
running in real-life conditions with, say, the Sentinel Data (order of a Terabyte/day) or by exploiting
the IoT/sensors data, you will fail. The availability
of data sources is the main enabler for develop
new cloud or mobile services, for instance, related to access control mechanisms, searching algorithms, but also experiment with real-people
in a controlled environment new mobile solutions. Technology and function commons exist
in all the new solutions and the way to merge
the effort among various experts, industries and
funding agencies should be pursuit. In particular
an intercontinental data platform should provide:
- discoverability; - accessibility; - availability; - use
and re-use. The International dimension is key for
EU to bring forward the consensus-based standards and to compete with de-facto standards.
Cooperation with other countries and Brazil in
particular can bring significant benefits. Sharing
of data sets as well as applications can allow the
implementation of various interesting – from a
commercial point of view – scenarios: - Useful
data sets available in one country can be used “inone-click” from other one; - Distribution of workload and data set duplication are essential for
optimize performance and reduce traffic over the
network, as well as ensuring business continuity
and disaster recovery; - Properly developed applications can be re-used in other countries and
context, with the same data sets or semantically
equivalent ones belonging to the other country.
All of these scenarios may have an interesting and
immediate commercial benefit, provide that the
governance of any such platform will embrace a
win-win business model where all the stakeholders generating value are involved and participate
in sharing the revenue stream.
The evolution of a Cloud Technology to face both
IT challenges and user needs
Author(s):
Alfonso Ríos Alonso
Focus area:
Our success story shows how innovation, leadership and cutting edge technology can create
an important technological asset that provides
an interesting alternative for companies in different sectors that are in need of high-tech,
problem solving, solutions to gain productivity and competitiveness. Creating technology
and new procedures implies that companies
have to assume the challenge of changing paradigms and the way traditional computing is
conceived. Highly experienced teams can recommend real Cloud computing native’s platforms which emerge as options to provide cost
efficiency, flexibility, security, integration and
quick deployment, among other benefits.
Who stands to benefit and how:
Indra has developed assets that can bring benefits to cross-sectorial enterprises. The Smart
& Cloud platform provides horizontal technological capabilities as an application server,
with mobile app support; a graph-oriented,
in-memory multitenant DBMS; big data capabilities, internet of things, Machine to Machine;
a form manager; human workflow, document
management; reporting and data integration
features. Indra’s platform provides an advanced
and rich set of application platform capabilities,
fully compatible, which enables user organizations to address a wide variety of use cases
on top of a share-everything, elastically scalable cloud infrastructure supporting a variety of
enterprise-class, high-availability disaster recovery, monitoring, security and SLA arrangements.
Focus of your position paper:
Indra Sistemas is the premier consulting and
Technology Company in Spain and a leading
multinational in Europe and LATAM and is the
second European company in its sector by investment in R+D, this commitment translates
into an investment of 8% of the sales figure. It
is currently orienting its strategy towards new
technologies and alternatives to create value in all business processes, as a result of its
experience, Indra has developed the Smart &
Cloud platform: a proprietary, seamless, new
generation open suite which provides high
IoT integration, Big data, cloud development
and execution capabilities. Two of the main
components in Indra’s cloud architecture have
been created based on European initiatives,
namely GPaaS and Sofia2. Indra incorporated
GPaaS to its strategy by the acquisition in 2013
of Gnúbila, strengthening its differential business model based on innovation. Gnúbila had
its beginning in 2002 and its first European R&D
projects were developed in close relationship
with CERN, aiming to apply and make available
the latest scientific technological advantages
to the commercial world; Gnúbila’s goal was to
achieve world class research in graph oriented databases, federated databases and highly
sophisticated systems that were evolving into
the creation of a new technological group –G
technology— which included an application
server, an unstructured database, integration
middleware, and several services to provide
native Cloud services, plus integrating this disruptive platform with other market technologies as well. GPaaS has evolved into a complete
suite with advanced capabilities to support not
only the most representative market standards
but cloud capabilities such as high availability, multitenancy, self-provisioning, and elastic
scalability, in order to offer a complete cloud
Platform as a Service ready to go. To reach that
level of maturity, the creation of research and
innovation centers in Spain, Colombia, France,
and Switzerland has been necessary as well
as the hiring and retaining of a highly specialized team. GPaaS has had a sizeable number
of recognitions; one of the most remarkable
is the Gartner’s reference where the platform
has been located in the Magic Quadrant for
the third time in a row. The last time, in 2013,
GPaaS was referenced in the category for Enterprise Application Platform as a Service, this
magic quadrant mentions only 19 companies
in the world and Indra is placed in the visionary
quadrant. Also among Indra’s assets: Sofia2 integrates and orchestrates information for smart
business (Smart cities, Smart Eficiency, Smart
15
Home, Smart Tourism, etc..) & Intelligence Infrastructures and it covers IoT, M2M and Big
Data integration in real time. Sofia2 was developed based on Sofia (Smart Objects for
Intelligent Applications), an European R&D+i
project in which Indra played a very active
role, developing and optimizing it to make it
useful for businesses. Sofia2 is a middleware
that allows the interoperability of multiple
systems and devices, offering a semantic platform to make real world information available
to smart applications (Internet of Things) by
using multi-language and multi-protocol, SDK,
APIs and extension mechanisms to enable the
16
interconnection of heterogeneous devices. It
provides publishing and subscription mechanisms, facilitating the orchestration of sensors
and actuators in order to monitor and act on
the environment Sofia2 In Cloud (http://sofia2.
com) is an instance of Sofia2 deployed in the
Cloud that allows every person, company, organization, developer or citizen to access to
the public data managed with Sofia2 and to
create experimental applications for free. Currently, following the references and guides that
important R&D projects are deploying we are
evaluating and integrating other components,
like OpenStack or IM.
An integrated environment for blood flow and
heart simulation
Author(s):
Pablo Blanco, Antonio Tadeu Gomes, Daniele
Lezzi, Roger Rafanell, Alfonso Santiago, Mariano Vazquez
Focus area:
cross-border collaboration through e-infrastructure; cloud federation
Who stands to benefit and how:
The potential users of the integrated environment are cardiologists and researchers who
are dedicated to better understanding cardiovascular diseases. Although this is a very large
community, the tools developed in the EUBrazil
Cloud Connect project will be used by a small
group of about 10 researchers working at BSC
and LNCC before they can be used for cardiovascular research. Future uptake of the simulation environment includes the integration
within the Hemodynamic Modelling Laboratory (HeMoLab), which is an online tool for the
simulation of the human cardiovascular system
developed by LNCC, and and within a BigData
visualization tool developed by the Computer
Applications in Science and Engineering (CASE)
department at BSC.
Focus of your position paper:
Cardiovascular diseases have a huge impact
on population, particularly people with a lowand middle-income. Since the early 1950s,
there have been increasing efforts to develop
computational models and simulation-based
techniques in order to assess physiological
and pathophysiological conditions accounting for the multiple time scales and levels of
spatial organization present in the cardiovascular system (CVS). Applications such as
diagnosis, treatment and surgical planning
have been enormously benefitted from these
complementary tools. Simulating a heartbeat
is a complex, multi-scale problem. This means
that many scales are coupled, covering different orders of magnitude from descriptions of
electrical propagation, cells arrangement into
a spatial description, generally known as myofibre orientation; and up to the geometry of
the cardiac chambers. EUBrazilCC leverages the
integration of heterogeneous supercomputing
and virtualized infrastructures with the orchestration through the components integrated in
the platform of two simulation codes from Brazil and Spain, addressing two complementary
problems in cardiovascular modelling, Cardiac
Electromechanical Modeling and Arterial Blood
Flow Modeling. For the first problem the project
adopts the Alya Red System, the BSC’s in-house
simulation tool. It is fully developed in-house,
from the numerical methods up to the parallel
implementation, including mesh-generation
and visualization. The Alya System is a Computational Mechanics code specially designed for
running with high efficiency standards in largescale supercomputing facilities, capable of solving different physics in a coupled way (fluids,
solids, electrical activity, species concentration,
free surface, combustion, embedded bodies,
etc.). The goal of the Alya System is to develop
a Cardiac Computational Model at organ level,
to simulate fluid-electro-mechanical coupling.
The Anatomically-Detailed Arterial Network
(ADAN) model, developed at LNCC, starts from
anatomical data and physiological concepts in
order to perform cutting-edge cardiovascular
research supported by modelling of physical
phenomena and simulation-based techniques.
The ADAN model incorporates, in the definition
of the vascular topology, most of the arteries
which are acknowledged in the medical and
anatomical literature for an average male. This
requires taking over 1585 arteries into account.
EUBrazil Cloud Connect will couple the Alya
Red heart model with the ADAN model in order to deliver an unprecedented model of the
blood flow circulation in the cardiovascular
system, making possible to widen the range of
cardiovascular scenarios that the model is able
to address. In this sense, it is possible to study
the effect of wave propagation back into the
heart to analyze, for instance, the impact of aortic regurgitation on hypertrophy in the cardiac
muscle, or the consequences of arterial stiffening into the heart efficiency. Likewise, changing
parameters in the heart functioning allows us
to understand how this affects the pressure
pulse conformation in detail. What makes a
breakthrough is EUBrazil Cloud Connect effort
17
to put together these simulation tools under a
cloud computing umbrella, including software
coupling and access to both input and output
data. For this purpose the project leverages
18
programming frameworks as COMPSs that allows the automatic parallelization of applications and their orchestration on distributed infrastructures, and execution services as CSGrid.
Stingray@Galaxy cloud-based platform:
applications for genomic epidemiology studies
Author(s):
Rodrigo Jardim & Alberto M. R. Dávila
Focus area:
Surveillance programs should be continuously
updated according to the changes in the epidemiological scenario, the adoption of new
analytical platforms such as NGS, allow a better
understanding of the evolutionary dynamics of
micro-organisms and their impact on human
health and environment. Using a metagenomic
approach, new pathogens could be identified
in clinical samples, mainly in cases of unknown
etiology with inconclusive results. The development of a cloud-based version of the Stingray@
Galaxy system aims to meet the necessary requirements for the treatment, analysis and information extraction of NGS data for genomic
epidemiology inferences of major pathogenic
micro-organisms affecting human health.
Who stands to benefit and how:
Initially, the main beneficiaries will be the researchers belonging to reference laboratories, most of them acting as national, regional
(PAHO) and international (WHO) reference laboratories, monitoring circulating strains as part
of a network. Later, microbiological collections
containing species/strains of relevance for surveillance will also benefit by analysing and storing the genome sequences of Brazilian strains
impacting human health. The general public
will benefit with: (i) the adoption of “state of
the art” technologies (NGS and cloud-based) by
public health researchers for genomic surveillance, and (ii) a better and efficient detection
of circulating pathogenic micro-organism in
the population, allowing a faster adoption of
improved control programs by health agencies.
Focus of your position paper:
The cloud-based solution Stingray@Galaxy
aims to meet a growing need to process large
volumes of data in an increasingly shorter time.
The response time for genomic surveillance
needs to be as small as possible so that people
in charge can access updated information and
take the right actions at the right time. This determines the effectiveness of the monitoring
service. The Stingray@Galaxy is a system built
on two web platforms: System for Integrated
Genomic Resources and Analysis (http://stingray.biowebdb.org) and Galaxy Project (http://
galaxyproject.org). Bioinformatics tools for
distributed processing were incorporated into
Stingray@Galaxy. Other computational tools
have been incorporated with the purpose of
providing distributed processing and data,
such as: Torque/PBS, OpenMPI, Hadoop and
HDFS. Available as an image, Stingray@Galaxy
can be launched on any virtualization environment (KVM, Xen, VirtualBox), either as master
node or client node, allowing elasticity according to processing and/or storage needs. This
new platform also meets other criteria: ease of
installation and use. One of the major barriers
in the ​​
bioinformatics area to non-specialists
or end-users is the installation complexity and
programs execution. Stingray@Galaxy allows
researchers to focus on the results interpretation, not in data processing, providing a complete platform for processing and visualization
of data, without requiring the installation or
configuration of bioinformatics programs. One
of the current and future challenges in bioinformatics is the fast processing of large volume
of data generated by NGS technologies. This
is only possible by distributing the processing
and data in a cloud-based solution with capacity for rapid and efficient growth environment.
Stingray@Galaxy stands as a flexible platform
for high performance analysis, able to supply
the needs of scientific projects on genomic surveillance and epidemiology. As a proof of concept, we expect to perform a pilot experiment
using a large genomic dataset with the help of
SGI and other companies.
19
Virtual laboratory to fight Leishmaniasis
Author(s):
Israel Cruz (ISCIII), Gabriel Melim (FIOCRUZ)
Focus area:
Cross-border collaboration through e-infrastructures on the research in the etiology of
Leishmania and to improve the knowledge of
the outburst of the disease.
Who stands to benefit and how:
The potential users of the LVL include researchers, international organizations, and public sector bodies, such as government departments
and public health authorities. This community
has a vast experience in the use of online databases and research tools, such as GenBank,
PubMed and the Eukaryotic Pathogen Database Resources Centre (EuPathDB). We expect
this community to bring laboratory researchers
and field workers from all disciplinary areas
together for sharing new discoveries and exchange of new ideas, provide opportunities of
international collaboration, and training of the
next generation.
20
Focus of your position paper:
Leishmaniasis is one of the world’s most neglected diseases, affecting largely the poorest
of the poor, mainly in developing countries;
350 million people are considered at risk of contracting leishmaniasis, and 1.5-2 million new
cases occur every year. Main endemic areas include the Indian subcontinent, Latin America,
North and East Africa, and the Euro-Mediterranean basin. It is caused by protozoan parasites
of the Leishmania genus, and transmitted by
an insect vector, the sand flies. The disease is
spreading because its control is hampered by
three escalating risk factors: human-made and
environmental changes; immune status (essentially because of Leishmania/HIV co-infection);
treatment failure and drug resistance. More
effective control of neglected tropical diseases
like Leishmaniasis is vital to achieving poverty
reduction and spurring social-economic development without waiting for countries to fully
develop and living conditions to improve over
a potentially long period of time. The intersection between ecology and epidemiology has
been explored by a few studies on host-par-
asites-diseases scenarios. Further, the recent
northward and southward spread of leishmaniasis may be related to environmental and/
or climate change with a recent emergence
in previously non-endemic areas. The correct
identification of the etiological agent is crucial
for the prognostic of the disease in that different species or strains can produce different
clinical outcomes. Also, treatments or even
diagnostic tools could be inefficient regarding different species or genetic populations.
Molecular methods like Multilocus Sequence
Analyses (MLSA) and Multilocus Microsatellite
Typing (MLMT) have been applied to the identification of Leishmania species and strains, and
to assess its population structure. The Leishmaniasis Virtual Laboratory will adapt GIS tools
and process pipelines for molecular data in
the platform through the programming framework integrated. LVL will enable public health
workers and researchers to access and supply
relevant and in-depth information or data on
the parasite and vector responsible for leishmaniasis. LVL will seamlessly integrate data
sources and computing systems to execute
experiments through a unique entry point.
The LVL will require the integration of distributed data (geographical, biomolecular and
clinical) and it will make use of the EUBRazilCC
infrastructure for the provision of computing
resources for executing the proper processing pipelines. The LVL will allow researchers to
share the produced knowledge in an effective
way. The Leishmaniasis Virtual Laboratory (LVL)
use case needs to integrate data from four different sources (CLIOC (http://clioc.fiocruz.br/) The Leishmania collection of the Oswaldo Cruz
Institute, registered in the World Federation
for Culture Collections, WFCC, WDCM 731; the
COLFLEB (http://colfleb.fiocruz.br/) collection
of phlebotomine sand flies, which has approximately 90,000 sand flies specimens distributed
across 320 species; the ISCIII-WHO-CCL collection; and speciesLink network (http://splink.
cria.org.br/). It will also link information from
PubMed (www.ncbi.nlm.nih.gov/pubmed) and
the NIH genetic sequence database GenBank®
(www.ncbi.nlm.nih.gov/genbank/).
A Pan-European e-infrastructure for the
agricultural research community breaking EU
barriers
Author(s):
Andreas Drakos, Vassilis Protonotarios
Focus area:
The pan-European research infrastructure for
agri-food called agINFRA (http://aginfra.eu)
was created to promote data sharing and development of trust in agricultural sciences. The
outcomes of the agINFRA project have helped
shape collaboration not only inside Europe, but
also international connecting and supporting
user cases from Asia, Africa and Latin America.
The agINFRA project is considered a pioneer
on providing data solutions specialized for the
agricultural community from the management
of data and metadata, to the openness and the
discovery of the data.
Who stands to benefit and how:
The agINFRA e-infrastructure has many different types and layers of stakeholders. The main
targeted user category is agricultural data repository owners who can use the agINFRA services to manage and register their data. End-users as agricultural or food researchers – data
scientists – are also to gain from the agINFRA
e-infrastructure since it provides a number of
services to discover and re-use data. Software
developers and SMEs can also take advantage
of the infrastructure to develop new services,
running on the grid or cloud.
Focus of your position paper:
agINFRA is European project funded under the
FP7 framework and is pioneering the connection of Agricultural Data through an Open and
Participatory Data Infrastructure. The aim of the
project is to set up a pan-European research
grid- and cloud- based infrastructure for agrifood, promoting data sharing and development of trust in agricultural sciences. agINFRA
understands that Open Data has the power to
make massive advances in agriculture. When researchers, educators or scientists set out to improve agriculture, one of the things of highest
importance to them is reliable access to high
quality information. In this direction, having to
ask many different institutions for permission
to use their data is not only time-consuming
but also an additional overhead. To get the
most out of research, data are needed in a timely and an easy-to-use format. Opening data not
only makes it easier for new research and ideas
to emerge; it makes life better for everyone by
improving the way agriculture is done. In fact,
opening data is such an important thing that
most of the world’s governments are now backing up an initiative called Global Open Data
for Agriculture and Nutrition (GODAN; www.
godan.info) to do just this. The agINFRA project
went beyond building a research infrastructure
but actually took the chance to create new services or evolve existing services to serve the
agricultural and food community. To this end
the CIARD-RING (http://ring.ciard.net), a global registry of information and services for the
agricultural community, was one of the main
services that the project improved and helped
evolve over the years. Moreover the agINFRA
services power-up important and well known
services as the FAO AGRIS service (http://agris.
fao.org) – a global information system collecting and making accessible bibliography (currently more than 8M bibliographic records)
on agricultural science and technology. With
the help of international partners and with
strategic collaborations across the globe, the
agINFRA project managed to export its know
how and support users coming from Asia (e.g.
the Chinese Academy of Agricultural Sciences),
Africa (e.g. OER Africa) and Latin America (e.g
Latin American Federation of Learning Object
Repositories - LAFLOR). With the support of the
European Commission, the agINFRA project
managed to get positioned in a global environment and help research and research institutes
in an international scale. From our participation
in the agINFRA project, we have witnessed the
importance of a cross-border collaboration
regarding data sharing and cloud-based data
infrastructure. Especially regarding the niche
sector of the agricultural and food area, global
collaboration is necessary if we are to succeed
surpassing main societal challenges as pro-
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viding a sustainable environment feeding the
world. The agricultural sector is historically one
of the main bases of the country’s economy
contributing more than 5,7% to GDP (World
Bank Data, 2013) and further collaboration with
22
the EU on the subject, exchanging knowledge,
data, infrastructure as well any other related aspect will be of help to scientist and researchers
from both regions.
The EGI Federated Cloud infrastructure platform:
Delivering e-Infrastructure resources at an
unprecedented scale for the Europea
Author(s):
Michel Drescher, EGI.eu and David Wallom, University of Oxford
Focus area:
This position paper focuses on the focus themes
“Virtualized resource federation using clouds”,
and “Cross-border cloud, data infrastructure &
security challenges” by describing how the EGI
Federated Clouds activity has designed and
implemented a service platform providing its
users with unprecedented flexibility in consuming connected resources from across Europe.
As an activity organised and implemented at a
European level incorporating services delivered
at national or local level, the described activity
is federated by design and sheer necessity, and
consequently addresses cross-border issues
around Cloud use, data infrastructures and security coordination.
Who stands to benefit and how:
Researchers and scientists in the EGI community over the entire spectrum of large communities (such as bioinformatics and Earth Observation) to small and micro research groups doing
research on a local scale benefit from flexibility in services integrated in the EGI Federated
Cloud service portfolio. Resource providers (at a
national, local, or individual level) benefit from
a lowered TCO through leveraging the difference between costs for federation membership
(software/services integration, membership
fees, etc.) and the total worth of services they
receive and get access to through the federation.
Focus of your position paper:
The EGI Federated Cloud solution is the result of
a 3-year process, beginning with its conception
in March 2011 at ISGC 2011 in Taipei, Taiwan,
and its first hallmark milestone in May 2014
at the EGI Community Forum in Helsinki, Finland, demarcating the release of the Federated
Cloud testbed into official production status.
Beginning with a first set of six federated Cloud
usage scenarios which drove required technical architecture and surrounding process-
es this underwent an iterative improvement
process to arrive at a solution that eventually
supports eleven principal usage scenarios. The
technical realisation of the federated Clouds
infrastructure and solution are based on a few
fundamental principles: (1) Utilise open standards wherever available and suitable to ensure
that there is inherently now vendor bias (2) Reuse existing software and services wherever
possible, protecting EGI’s investment in these
solutions (3) Appreciate resource provider’s expressed and explicit need to retain control over
any software that is installed in their respective
physical infrastructure, and (4) that resource
providers may come from any domain, the academic, public and private sector so that we
are able to support user communities from the
same. Consequently, the EGI technical architecture decomposes the production infrastructure
into well-defined and well-scoped platforms
building on top of each other, with defined
and implemented processes surrounding each
of these. The EGI Core Infrastructure Platform
comprises of a set of fundamental technical
services and support processes necessary for
any type of federated e-infrastructure exposing
resources for shared use. This includes technical subsystems such as Accounting, AAI, Monitoring as well as non-technical services such
as first point of contact Helpdesk and support
services, federated security policy management and advice, as well as operational security
activities such as Computer Security Incident
Response, Risk Assessment, and Vulnerability
Handling. This platform, unlike others EGI build
on top of it, does not include any technology
availing ICT resources to EGI’s user communities. The EGI Cloud Infrastructure Platform
incorporates at its heart IaaS Cloud deployments, which primarily deliver IaaS Compute
and IaaS Storage services. Integrating with the
Core Infrastructure Platform, it inherits all its
federation properties and supplementary services without having to reimplement these. It
is completed with a set of services supporting
the user in their day-to-day work with the fed-
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erated Cloud infrastructure. Since institutional
resource providers wish to retain control over
which Cloud Management Framework (CMF)
they wish to deploy, the federation technical
architecture models institutional Clouds as
abstract entities that must implement/integrate with mandatory interfaces. Southbound
interfaces are defined through the integration
with the underpinning EGI Core Infrastructure
Platform; northbound interfaces define how
Cloud-managed virtualised resources are made
available to the users within the framework of
the federation. Together, these form a set of
federation requirements that each member resource provider must meet, irrespective of the
individually chosen CMF. This decomposition
of the production infrastructure has federation
services, policies, procedures and governance
built-in from inside-out, meeting requirements
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from resource providers and resource consumers alike. As this is a pan-European federation of
resources, it incorporates by design cross-border infrastructure aspects including perpetual
CSIRT and security policy management procedures. The user engagement program operates
such that any user community can come forward and is automatically granted a 6-months
test-drive period to evaluate integrating with
the EGI Federated Cloud. This includes a set
of defined exit states, enabling both parties
to make a decision whether to continue as a
regular production-level user community, or
dismantling the collaboration and removal
from the activities. Through extensive support
provided by its User Community Support Team,
EGI automatically elicits user requirements for
further continuous evolution of the EGI Federated Cloud solution.
EUBrazil Cloud Connect (614048) is a Small or medium-scale focused research project (STREP)
funded by the European Commission under the Cooperation Programme, Framework 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
European Commission