Atos as a global IT partner in Life Science projects...The Atos brand for cloud, Canopy is a...

1st December 2015 Grid Computing Workshop 2015 | Natalia Jiménez 1st December 2015 Grid Computing Workshop 2015 | Natalia Jiménez

Natalia Jiménez

Life Sciences Business Development Manager

[email protected]

+34638743475

@njlozano

Atos as a global IT partner in Life Science

projects


10,000 UK & Ireland United Kingdom, Ireland

7,500 Benelux & The Nordics

Belgium, Denmark, Estonia, Finland,

Luxembourg, Sweden, The Netherlands

8,300

North American Operations

16,400 France

10,800 Central &

Eastern Europe Austria, Bulgaria, Croatia, Cyprus,

Czech Republic, Greece, Hungary, Italy, Lithuania, Poland, Romania, Russia,

Serbia, Slovakia, Switzerland, Turkey

6,200 Iberia Andorra, Portugal,

Spain

3,300 South America Argentina, Brasil, Chile,

Colombia, Uruguay

5,600 Asia Pacific

Australia, China, Hong Kong,

Indonesia, Japan, Malaysia, New-Zealand, Philippines,

Singapore, Taiwan, Thailand

Headcount as of September 2015

15,100 India, Middle East &

Africa

9,800 Germany

Circa 93,000 Business Technologists

working in over 72 countries.

Total 2014 revenue: €11B

A global workforce to cover out client’s needs


Systems Integration

Managed Services

Consulting

Big Data & Security

Transactional & Payment Services

Cloud & Enterprise Software

Creating business advantages for clients with our global IT services

Atos is leading player in global IT services and payments solutions.

With its deep technology expertise, Atos drives business progress for its clients to achieve measurable results.


Transforming solutions for every sector

Financial Services

Public & Health

Doing more with less remains a dominant theme in public organizations. But more and more citizens expect public services to delivered online. These factors drive the need for new digital models of IT service.

Manufacturing, Retail & Transportation

Banking and insurance companies need to excel in building reputation and loyalty and reach maximum efficiency of back office processes.

New technologies, data-driven business models, consumer experience and operational efficiency are the defining forces of these markets.

Telcos, Media & Utilities

Success in manufacturing, retail and transportation today hinges on the ability to join everything up across the value chain.

We apply our expertise and in-depth knowledge of global market sectors to help our customers respond to business and organizational challenges with transformational IT solutions.


As Worldwide IT Partner of the Olympic & Paralympic Games, Atos leads the technology effort for the staging of the Games.

This same effort and skill-base can help your company, as you pursue a record-breaking competitive advantage.

Digital empowerment for the Olympic Games


Expert brands to pave your way to digital transformation

We are a leader in digital services serving a global client base. Atos is the masterbrand of the Group, providing the fundamental values and identity that the sub-brands are based on.

Atos Consulting is the global consulting practice of Atos. With 1,600 management consultants worldwide, it is a leading provider of business, process and technology consulting services.

Bull is the Atos brand for its technology products and value-added software which assist clients in their digital transformation, specifically in the areas of Big Data and Cyber-security. Bull is the European leader in HPC.

Atos Worldgrid is a subsidiary of Atos and a unique player in smart energy. It delivers integration projects and real time Smart Energy solutions to Energy & Utilities companies across the power, water, oil & gas value chains.

The Atos brand for cloud, Canopy is a cloud services integrator, enabling customers to drive business transformation through open, orchestrated cloud services.

Worldline is an Atos company and the European leader in the payments and transactional services industry. Worldline employs 7,300 people and generated € 1.15 billion revenues in 2014.


Bioinformatics is the field of science in which biology, computer science and information technology merge to form a single discipline

“ “


The life sciences comprise the fields of science that involve the scientific study of living organisms, such as microorganisms, plants, animals, and human beings

“ “


Microorganisms Animals

BIOINFORMATICS APPLICATION AREAS

• Waste cleanup • Climate change studies • Alternative energy sources • Biotechnology • Antibiotic resistance • Forensic analysis • Bio-weapon creation • Evolutionary studies

• Breed success • Advanced

aquaculture • Domesticated bliss

• Increase crop yield • Insect resistance • Improve nutritional

quality • Grow in power soils

and drought resistance

Plants

Humans • Drug development • Forensic genomics • Population

Genomics • Molecular Medicine


Bioinformatics

The alive Big Data avalanche

© Bull, 2014


Information Technologies

1st December 2015 Grid Computing Workshop 2015 | Natalia Jiménez 1st December 2015 Grid Computing Workshop 2015 | Natalia Jiménez © Bull, 2014

… and the Big Solution


Boost the translation of OMICS to the clinical environment

| 17-02-2015 | Natalia Jiménez | InforSalud 1st December 2015 Grid Computing Workshop 2015 | Natalia Jiménez

PATIENT STRATIFICATION


COST CONTROL


ALERTS TO PREVENT SADR


Boost the translation of OMICS to the Pharma & Biotech environment


VIRTUAL SCREENING

LIGAND-BASED DRUG DESIGN

STRUCTURE-BASED DRUG DESIGN

The computation of pair-wise interactions between atoms, which is a prerequisite for the operation of many virtual screening programs, is of computational complexity


CLINICAL TRIALS


POST-MARKET SURVEILLANCE


WE PARTICIPATE IN KEY INITIATIVES

The Computational Genomics Chair is a public-private collaboration model founded by Atos in 2012 in the Centro de Investigación Príncipe Felipe de Valencia (CIPF) with the aim of allowing the construction of the first link of the value chain towards the implementation of personalised medicine. The mission of the Computational Genomics Chair was the creation of tools that will allow handling and extracting the knowledge from big volumes of heterogeneous data produced in the genomics sequencing experiments.

COMPUTATIONAL GENOMICS CHAIR

Public-Private collaboration model CHAIR

The Chair took two different flavours. During the two first years, a person belonging to the CIPF was sitting in the Chair. Then, we decided to have an Atos person in situ full time during the last year.

Two of the most relevant developments produced as a result of this Chair are the optimization of the algorithms for genomics data processing as well as the development of viewers. These advancements suppose a set forward in the translation of genomics to the clinical practice and its adoption by the healthcare systems.


ELIXIR

"ELIXIR unites Europe’s leading life science organisations in managing and safeguarding the

massive amounts of data being generated every day by publicly funded research. It is a pan-

European research infrastructure for biological information.

"ELIXIR will provide the facilities necessary for life science researchers - from bench biologists to

cheminformaticians - to make the most of our rapidly growing store of information about living

systems, which is the foundation on which our understanding of life is built.“ Dr. Niklas Blomberg,

ELIXIR Director.

European Life Sciences Infrastructure for Biological Information

Industry Advisory Committee ELIXIR

• Martin Ebeling, Hoffmann-La Roche, Switzerland • Anita Eliasson, Biocomputing Platforms Ltd, Finland • Wendy Filsell, Unilever R&D, UK (Vice Chair) • Mark Forster, Syngenta, UK (Chair) • Iain Hrynaszkiewicz, Nature Publishing Group - Macmillan,

UK • Natalia Jiménez Lozano, Atos, Spain • Claus Stie Kallesøe, Gritsystems A/S, Denmark • Angel Pizarro, Amazon Web Services, USA • Philippe Sanseau, GlaxoSmithKline, UK • Montserrat Vendrell, Biocat, Spain • Jakob de Vlieg, Bayer CropSciences Innovation Center,

Belgium


HELIX NEBULA

Customer value

▶ Compliant with EC data protection legislation, it avoids the Patriot Act

▶ Delivered through a hosted high performance computing environment

▶ More flexibility and cost effectiveness for IT as well as research

▶ ESA project boosts European research innovation and competitiveness.

Why Atos?

▶ Expertise and track record in developing and delivering cloud services

▶ End-to-end delivery of IT services, to deliver a complete package of offerings.

Management summary

▶ Helix Nebula, the ‘Science Cloud’, is a catalyst for major changes in how European scientists use IT services. It aims to ensure an accessible, sustainable, competitive and secure cloud infrastructure for research. Designed specifically for organizations in Europe, data will not be subject to the US Patriot Act.

“Helix Nebula - the Science Cloud – is a partnership with the potential to support an optimal exploitation of ESA satellite data, as well as to bring other communities on board to better

understand the geophysical phenomena of our planet.” Volker Liebig, ESA Director for Earth Observation Programmes


The Research Centre of Vine-and- Wine-related Science (ICVV) is an institution which deals with Viticulture and Oenology, created by the Government of La Rioja (by means of the Regional Agricultural Ministry), the Advisory Board for Scientific Research and the University of La Rioja.

The ICVV was born with the aim of generating new knowledge and technologies, as regards Viticulture and Oenology, which can be useful for a technological development within the viticultural sector, inherent in our culture and our farming economy. ICVV

Project: The grapevine genetics and genomics department is interested in understanding the genetic and molecular mechanisms responsible for the reproductive development of grapevine. Especially its activity is focused on traits such as precociousness and fertility, as well as bunch compactness and size and shape of the cluster and the berries, which have an important impact in the production and quality of grape and wine.

Challenges: Their approximation is based in characterizing and exploiting the natural genetic variation that exists in grapevine for these traits using genetic and genomic tools with the consequent computation challenges.

Solution provided: Computation node devoted to the research in the selection and combination of different grapevine strains genomes.

LIFE SCIENCE REFERENCES

RESEARCH CENTRE OF VINE-AND- WINE-RELATED SCIENCE


The National Centre for Biotechnolgy (CNB) is a research centre that forms part of the Spanish National Research Council (Consejo Superior de Investigaciones Científicas, CSIC), Spain’s most important public scientific institution. The CNB opened in 1992 to lead in developing modern biotechnology in Spain. The CNB is distinguished by its versatile interdisciplinary research that combines molecular biology methods with the latest technology in the fields of functional and structural biology. We are a team of more than 600 professionals committed to research excellence. The CNB has been recognised by an international jury as one of the eight Severo Ochoa Centres of Excellence in medicine and the life sciences.

CNB

Project: The Biocomputing Unit (BCU) of the National Center for Biotechnology /Instruct Image Processing Center (I2PC) works in the area of Three-dimensional electron and X-ray microscopy to develop the well known XMIPP software suite, together with other advanced tools as part of the European Strategic Infrastructure on Structural Biology (Instruct).

Challenges: The service activities of the Biocomputing Unit are structured around the recently established Instruct Image Processing Center(I2PC), developing new software infrastructures for advanced image and data processing in Electron and X-ray Microscopy.

Solution provided: Computing node to speed up the image processing processes.

LIFE SCIENCE REFERENCES CENTRO NACIONAL DE BIOTECNOLOGÍA

http://www.structuralbiology.eu/

http://i2pc.cnb.csic.es/

http://i2pc.cnb.csic.es/


NGSgoesHPC is a German science project dealing with the improvement of genome assembly algorithms, which are currently the bottleneck in the workflow of genome analysis. Headed by the University Cologne, various other prestigious universities and science labs take part – the TU Dresden, FZ Jülich, Atlas Biolabs, Cologne Center for Genomics, Max-Planck-Institute Age and BIOTEC. On the industrial side, the German Bull subsidiary takes an active part, together with Intel and Data Direct Networks.

GERMAN MINISTRY OF EDUCATION AND SCIENCE

Analyse the different existing algorithms and select the best candidates.

Improve the key parts of the algorithms speed wise.

Consolidate the results and publish them as a library for open use

▶ To improve the speed in genomic analysis.

▶ Both oncology and pharmagogenetics will also become boosted by this development.

Put together the puzzle of the massive amount of many million DNA pieces by using their overlap information, using computer science techniques as hashing and graph simplification & traversal.

Improve the runtime while keeping a reasonable memory footprint.

Project funded by the German Science & Education Ministry NGSgoesHPC

Solution Challenges Benefits



AGENCIA VALENCIANA DE SALUD (AVS) Future Clinic project was founded by the local Valencian Government (Generalitat Valenciana) and by the EU through Fondo Europeo de Desarrollo Regional (FEDER) in the framework of the Program “Ayudas para la Financiación de Acciones Estratégicas de Diversificación Industrial de la Comunidad Valenciana 2011. It aim was the integration of the genomics data into the Valencian Regional Healthcare System (Agencia Valenciana de Salud) to promote the implementation of the Precision Medicine. This was a collaborative project with several partners being Centro de Investigación Príncipe Felipe (CIPF), Indra, Imegen and Atos the most relevant ones.

Solution Genomic pipeline optimization is

the first step towards the implementation of a healthcare system based on Precision Medicine.

Powerful genomic pipelines are provided in HPC environment to isolate the doctor from genomic processing complexities.

Challenges Benefits Implementation of a mapping software

in Bull HPC environment. This SW is a trade-off between speed and quality, and takes part of a genomic pipeline named High Performance Genomics (HPG) that address the issue of raw data processing from FASTQ filtering & quality control to variant annotation.

This developments have been carried out by the close collaboration of CIPF researchers together with Bull’s HPC experts.

The HPC infrastructure is based on 15 bullx servers and 6 GPUs for computation and 260 TB for storage.

Floods of meaningless data outputs from NGS sequencing. Download some software and press the button” is definitely not sufficient.

Billions of short reads to be matched every day against...

• ...very long references (3/6 Gb), with... • ...several mismatches (typically one each 25 nt).

Leaded the first personalised medicine prototype in Spain AVS



Centro Nacional de Investigaciones Oncológicas (Spanish National Cancer Research Centre, or CNIO) was founded in 1998 by the Carlos III Institute of Health, part of the Spanish Ministry of Health. The mission of CNIO is to conduct research of excellence and to bring the very latest technology in the field of cancer to the Spanish National Health System.

NATIONAL CENTRE FOR ONCOLOGICAL INVESTIGATIONS (CNIO)

To speed up the simulation processes to optimize their research.

Management of data coming from an important project to find the best chemotherapeutic treatment for oncological patients based heavily on genomic profiles. The partners in the project are public and private hospitals, important pharmaceutical companies and different departments from CNIO.

CNIO has implemented a Bull HPC cluster with 720 cores, more than 1 TB of RAM, an Infiniband QDR low latency network, and 12 TB of storage.

Among the 3 best Oncological Centers in the world!

Solution Challenges Benefits

CNIO


CNIO has enhanced their capabilities in molecular dynamic simulation. Now the computational biophysics and the experimental therapeutics groups, get the results of their research in less than a month, versus the six months that where necessary before. Thus greatly improves both, the study of the effect of oncogenic mutations in the activation of key proteins for cancer progression, as obtaining more potent treatments for cancer.


The Institute of Biomedicine of Seville (Instituto de Biomedicina de Sevilla - IBiS), was created on the 24th March 2006 by virtue of an agreement signed by the Department of Health of the Junta of Andalusia, the Department of Innovation, Science and Business of the Junta of Andalusia, the Andalusian Health Service, the University of Seville, and the Spanish Scientific Research Council (Consejo Superior de Investigaciones Cientificas - CSIC).

A centralised framework for life science data IBiS

The European Project ITRIBIS "Improving

Translational Research Potential at the Institute of

Biomedicine of Seville", is envisaged to enhance the

IBiS' excellence to become a reference of biomedical

translational research applied to prevalent diseases

in South Europe; to improve the transfer of results

and, thereby, increase the production of benefits for

the region.

Project: itribis “improving translational research potential at the institute of biomedicine of seville” Challenge: Need of centralizing the data produced by the different departments at IBiS (Genomics, Histology, Microscopy …). Solution provided:

Isilon technology with a unique file system, 194,8TBs protected N+2:1, 3 active controllers, 36GB distributed global memory and 24 processing cores.

Autobalanced data system. Autobalanced connection system. Failover system. Unlimited Snapshots system.

INSTITUTO DE BIOMEDICINA DE SEVILLA (IBiS)



FRANCE GENOMIQUE rassemble et mutualise les ressources des principales plateformes françaises de génomique et de bio-informatique. Créée grâce à un financement « Investissements d’Avenir », elle a pour ambition de maintenir la recherche française au plus haut niveau de compétitivité et de performance dans la production et l’analyse des données de génomique, à la pointe de l’état de l’art à l’échelle internationale. Elle offre à la communauté scientifique publique et privée l’accès aux plateformes françaises les plus performantes, un accompagnement des projets, le plus haut niveau d’expertise et de compétences mutualisées ainsi que la possibilité de participer à des projets ambitieux au niveau national et international.

OMICS-EL solution France Génomique

Project: Ce projet vise à intégrer à l’échelon national les capacités d’analyse du génome et de traitement bioinformatique des données à haut débit ainsi générées. Cette infrastructure intégrée fournira, dans le domaine de la génomique, tout l’éventail des services nécessaires pour renforcer la compétitivité des communautés nationales d’utilisateurs, chercheurs publics et industriels, et pour attirer des projets internationaux.

Challenge: Il s’agit d’une infrastructure distribuée s’appuyant sur

plusieurs centres aux compétences complémentaires, avec une gouvernance intégrée, une coordination des services, et un accès unique à l’échelon national qui permetra de couvrir tous les domaines des sciences du vivant (biodiversité, génomique médicale, génomique animale, génomique végétale etc).


FRANCE GÉNOMIQUE


FPGMX mission is to promote the development of a competitive genomics medicine in Galicia and its integration in the national and international networks in the clinic and molecular research fileds. To this aim, FPGMX has the necessary human and technological resources for the efficient development of the genomics research in Galicia, establishing programmes and quality standards.

GALLEGAN PUBLIC FOUNDATION FOR GENOMICS MEDICINE (FPGMX)

HPC-PLUS FPGMX

Project: To build a singular infrastructure to support the research through a powerful equipment.

Challenge:

To cope with the computing requests from Pharma companies (drug screening), Biotech companies and Research Centres working in different areas of life sciences

Solution provided: Singular infrastructure called HPC-PLUS Platform that provides with an elastic and versatile computing environment in the following fields: biomedicine, medical informatics and health informatics.



Anaxomics is a company committed to the discovery and development of new and better drugs to improve human health. Anaxomics is committed to the discovery and development of new and better drugs to improve human health. Its goal is to help the biopharma industry to maximize the value of their discovery and clinical development by leveraging the potential indications of all the compounds in their pipeline, and by identifying and minimizing their potential safety risks.

ANAXOMICS

FPGMX

Project: Anaxomics is helping the biopharma industry to maximize the value of their discovery and clinical development by leveraging the potential indications of all the compounds in their pipeline, and by identifying and minimizing their potential safety risks.

Challenge: To find innovative approaches to solve current bottlenecks in drug discovery and clinical development.

Solution provided: Anaxomic’s systems biology-based drug repositioning combines the best from the heuristic and rational drug repositioning approaches, while overcoming their limitations. This system is implemented in an Atos HPC environment.



The Research Institute 12 de Octubre hospital (i+12) was created the 15th December 2009 by means of an agreement signed by the following entities: Servicio Madrileño de Salud, Universidad Complutense de Madrid, Universidad Autónoma de Madrid, la Fundación para la Investigación Biomédica del Hospital Doce de Octubre and the Agency "Pedro Laín Entralgo" de Formación, Investigación y Estudios Sanitarios de la Comunidad de Madrid. i+12 aims to become in a reference centre in multidisciplinar Biomedical Research in the fields of clinic and traslational research at the national and international level.

RESEARCH INSTITUTE 12 DE OCTUBRE HOSPITAL (I+12)

Genomics Data Processing Platform I+12

Project: To build a Genomics Data Processing Platform that will centralize the analyses from 3 different departments at i+12: oncology, hematology and genetics. Challenge:

Bottlenecks in genomics analysis. Lack of a centralized storage. Lengthy data transfer.

Solution provided:

High Performance Compute system. Network infrastructure. OMICS repository.

HEALTHCARE REFERENCES


INGEMM is the clinical reference center in Spain for Genetics. INGEMM was opened by the

former Healthcare Minister in 2011 as a Department belonging to the Research Institute La

Paz Hospital (IdiPaz). INGEMM is focused in the study, diagnosis and treatment of rare

diseases. In the last 5 years, INGEMM has participated in more than 25 research projects

and has published more than 350 scientific papers in the world best journals. INGEMM

researchers have been involved in cloning five genes, in the description of the

microdelection syndrome and in the discovery of a new overgrowth syndrome called Clapo.

MEDICAL AND MOLECULAR GENETICS INSTITUTE (INGEMM)

Genomics Data Processing Platform INGEMM

INGEMM is the only Genetics Centre ISO

certified in the molecular genetics and

molecular cytogenetics labs and has

developed more than 15 lab protocols

acredited by the European Molecular Quality

Network. INGEMM has the service portfolio

more revelant in Spain.

Project: To offer a service porfolio to diagnose more than 350 genetic disorders. INGEMM currently carries out more than 40,000 genetic testing per year.

Challenge:

Genetic diseases are the second cause of children’s death in Europe. Diagnose should be done at the right time to save children’s lives. To do that, INGEMM had to overcome the challenges in genomic processing.

Solution provided:

High Performance Compute system. Network infrastructure. OMICS repository.




EMC Isilon

The LUMC is a modern knowledge center employing more than 7000 people with the objective of improving patient care through scientific research. The LUMC proposes courses and continuing education for doctors, focusing on top clinical and highly specialized care. It gathers patient care and research labs in one place, to have patients, doctors and researchers collaborating to develop new treatment methods.

LUMC

Challenges

Compute and data intensive capabilities required for the research department, with activities such as unravelling of the human DNA.

Computing speed and fast I/O to attain results in an adequate timeframe.

Solution

EMC Isilon storage systems, Configuration of four 72NL-series

nodes. Capacity to address almost 200

TB of net storage. SnapshotIQ and SmartConnect

software for load balancing and failover.

Management by OneFS, Isilon’s integrated management suite.

Benefits

Capacity and performance, as crucial components.

Flexibility and management, as vital capabilities.

Full data redundancy and data recovery functionality.

In short, a storage environment that fully adheres to the needs and requirements of DNA research.

LEIDS UNIVERSITAIR MEDISH CENTRUM (LUMC)

Centralised Storage


The Centre for Genomics and Oncological Research (GENYO) is a mixed centre with stakes held by Junta de Andalucía the University of Granada and Pfizer. This centre has been devised as a space for excellence research in genomic medicine, focusing on the comprehensive study and understanding of the genetic basis of human diseases in general, placing special emphasis on cancer and its genetic disorders related to inheritance.

GENYO


http://www.elmundo.es/ciencia/2014/06/27/53ac79a8e2704ec1178b456b.html


The 100,000 Genomes Project


LIFE SCIENCES REFERENCES

IT4I is a National Supercomputer Center located at Ostrava (Czech Republic) whose mission is to deliver scientifically excellent and industry relevant research in the fields of high performance computing and embedded systems. IT4I is providing state-of-the-art technology and expertise in high performance computing and embedded systems and make it available for Czech and international research teams from academia and industry. IT4I aims to became top European Centre of Excellence in IT with the emphasis on high performance computing and embedded systems. With its research, know-how and infrastructure IT4I aspire to improve the quality of life, to increase the competitiveness of industrial sector and to promote the cross-fertilization of high-performance computing, embedded systems and other scientific and technical disciplines.

OMICS MASTER solution IT4I

Project: IT4I was appointed as a Reference Center of Personalized Medicine. Challenge:

Not much expertise on Bioinformatics. Need for a pipeline for genomic analyses. Disseminate new IT4I capabilities on Genomics among potential users.

Solution provided: Project of implementation of a pipeline for genomics analysis conceived in the framework of the Atos’ Computational Genomics Chair in the Centro de Investigación Príncipe Felipe (Valencia, Spain). The pipeline inputs NGS raw data to get the variant calling files that are then annotated by means of CellBase compendium database. Through the implemented solution, the annotated variant can be displayed in a diagnostic or a priorization tool. All the components of the pipeline are open source, have been published in scientific journals and tested in the framework of a research or healthcare project on rare diseases (CIBERER). The speed, sensitivity and availability to cope with longer reads of the mapper component included in this pipeline have been demonstrated in a scientific publication in comparison with the most extensively used DNA-seq mappers (BWA 0.7.5a MEM and Bowtie 2 2.1.0).

IT FOR INNOVATION


Natalia Jiménez

Life Sciences Business Development Manager

[email protected]

+34638743475

@njlozano

Technological Excellence at your service

1st December 2015 Grid Computing Workshop 2015 | Natalia Jiménez

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Atos as a global IT partner in Life Science projects...The Atos brand for cloud, Canopy is a...

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