Alberto Di Meglio

Making sense of big data in health research: Towards an EU action plan

Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation combined with automation and miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How are we going to deal with this exponential increase in data production? The potential of “big data” for improving health is enormous but, at the same time, we face a wide range of challenges to overcome urgently. Europe is very proud of its cultural diversity; however, exploitation of the data made available through advances in genomic medicine, imaging, and a wide range of mobile health applications or connected devices is hampered by numerous historical, technical, legal, and political barriers. European health systems and databases are diverse and fragmented. There is a lack of harmonization of data formats, processing, analysis, and data transfer, which leads to incompatibilities and lost opportunities. Legal frameworks for data sharing are evolving. Clinicians, researchers, and citizens need improved methods, tools, and training to generate, analyze, and query data effectively. Addressing these barriers will contribute to creating the European Single Market for health, which will improve health and healthcare for all Europeans.

Towards next generations of software for distributed infrastructures: The European Middleware Initiative

The last two decades have seen an exceptional increase of the available networking, computing and storage resources. Scientific research communities have exploited these enhanced capabilities developing large scale collaborations, supported by distributed infrastructures. In order to enable usage of such infrastructures, several middleware solutions have been created. However such solutions, having been developed separately, have been resulting often in incompatible middleware and infrastructures. The European Middleware Initiative (EMI) is a collaboration, started in 2010, among the major European middleware providers (ARC, dCache, gLite, UNICORE), aiming to consolidate and evolve the existing middleware stacks, facilitating their interoperability and their deployment on large distributed infrastructures, establishing at the same time a sustainable model for the future maintenance and evolution of the middleware components. This paper presents the strategy followed for the achievements of these goals : after an analysis of the situation before EMI, it is given an overview of the development strategy, followed by the most notable technical results, grouped according to the four development areas (Compute, Data, Infrastructure, Security). The rigorous process ensuring the quality of provided software is then illustrated, followed by a description the release process, and of the relations with the user communities. The last section provides an outlook to the future, focusing on the undergoing actions looking toward the sustainability of activities.

ETICS: the International Software Engineering Service for the Grid

The ETICS system is a distributed software configuration, build and test system designed to fulfil the needs of improving the quality, reliability and interoperability of distributed software in general and grid software in particular. The ETICS project is a consortium of five partners (CERN, INFN, Engineering Ingegneria Informatica, 4D Soft and the University of Wisconsin-Madison). The ETICS service consists of a build and test job execution system based on the Metronome software and an integrated set of web services and software engineering tools to design, maintain and control build and test scenarios. The ETICS system allows taking into account complex dependencies among applications and middleware components and provides a rich environment to perform static and dynamic analysis of the software and execute deployment, system and interoperability tests. This paper gives an overview of the system architecture and functionality set and then describes how the EC- funded EGEE, DILIGENT and OMII-Europe projects are using the software engineering services to build, validate and distribute their software. Finally a number of significant use and test cases will be described to show how ETICS can be used in particular to perform interoperability tests of grid middleware using the grid itself.

Build, configuration, integration and testing tools for large software projects: ETICS

Software development within geographically dispersed and multi-institutional projects faces challenges in the domain of validation and quality assurance of software products. Experience in such projects, especially in the area of Grid computing, has shown that the lack of appropriate tools and procedures may cause high overall development costs and delays in the deployment, development and maintenance of the software. In this paper, we introduce ETICS, an integrated infrastructure for the automated configuration, build and testing of Grid and distributed software. The goal of the infrastructure is to provide a service for software projects by integrating well-established procedures, tools and resources in a coherent framework and adapting them to the special needs of distributed projects. A set of versatile tools and best-practice guidelines for quality assurance implementation are also provided to maximize the projects chances of delivering reliable and interoperable software.

submitter : From Big Data to Big Insights: The Role of Platforms in Healthcare IT

The transformations that have taken place in Information and Communication Technology in the past 20 years have given rise to a new form of scientific research paradigm where data-intensive, large-scale projects combine experiment, theory and computing to address fundamental questions about ourselves and our universe. The complexity of the data analysis infrastructures can be tackled by a clear separation of roles and responsibilities and by the implementation of public and commercial computing and data platforms governed by clear agreements. Biomedical and healthcare research and practice could benefit from a broader use of such platforms, hiding the technical complexity behind agreed service definitions and allowing researchers and medical doctors to focus on the data collection, interpretation and usage in the respect of the social and human value of the data and within reasonable, unbiased frameworks where medical research, clinical practice and modern information technologies can constructively interact with each other. This chapter describes the state of the art of data analytics platforms and suggests possible applications and benefits in healthcare while cautioning against excessively utopian scenarios.

Erratum to: Making sense of big data in health research: towards an EU action plan

Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation combined with automation and miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How are we going to deal with this exponential increase in data production? The potential of “big data” for improving health is enormous but, at the same time, we face a wide range of challenges to overcome urgently. Europe is very proud of its cultural diversity; however, exploitation of the data made available through advances in genomic medicine, imaging, and a wide range of mobile health applications or connected devices is hampered by numerous historical, technical, legal, and political barriers. European health systems and databases are diverse and fragmented. There is a lack of harmonization of data formats, processing, analysis, and data transfer, which leads to incompatibilities and lost opportunities. Legal frameworks for data sharing are evolving. Clinicians, researchers, and citizens need improved methods, tools, and training to generate, analyze, and query data effectively. Addressing these barriers will contribute to creating the European Single Market for health, which will improve health and healthcare for all Europeans. European healthcare systems and the potential for big data Medicine has traditionally been a science of observation and experience. For thousands of years, clinicians have integrated the knowledge of preceding generations with their own life-long experiences to treat patients according to the oath of Hippocrates; mostly based on trial and * Correspondence: cauffray@eisbm.org; rudi.balling@uni.lu European Institute for Systems Biology and Medicine, 1 avenue Claude Vellefaux, 75010 Paris, France Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362 Esch-sur-Alzette, Luxembourg Full list of author information is available at the end of the article

Erratum to: Making sense of big data in health research: Towards an EU action plan [Genome Med., 8 (2016) (71)]

Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation combined with automation and miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How are we going to deal with this exponential increase in data production? The potential of “big data” for improving health is enormous but, at the same time, we face a wide range of challenges to overcome urgently. Europe is very proud of its cultural diversity; however, exploitation of the data made available through advances in genomic medicine, imaging, and a wide range of mobile health applications or connected devices is hampered by numerous historical, technical, legal, and political barriers. European health systems and databases are diverse and fragmented. There is a lack of harmonization of data formats, processing, analysis, and data transfer, which leads to incompatibilities and lost opportunities. Legal frameworks for data sharing are evolving. Clinicians, researchers, and citizens need improved methods, tools, and training to generate, analyze, and query data effectively. Addressing these barriers will contribute to creating the European Single Market for health, which will improve health and healthcare for all Europeans. European healthcare systems and the potential for big data Medicine has traditionally been a science of observation and experience. For thousands of years, clinicians have integrated the knowledge of preceding generations with their own life-long experiences to treat patients according to the oath of Hippocrates; mostly based on trial and * Correspondence: cauffray@eisbm.org; rudi.balling@uni.lu European Institute for Systems Biology and Medicine, 1 avenue Claude Vellefaux, 75010 Paris, France Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362 Esch-sur-Alzette, Luxembourg Full list of author information is available at the end of the article

Correction: Making sense of big data in health research: towards an EU action plan (vol 8, pg 71, 2016)

Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation combined with automation and miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How are we going to deal with this exponential increase in data production? The potential of “big data” for improving health is enormous but, at the same time, we face a wide range of challenges to overcome urgently. Europe is very proud of its cultural diversity; however, exploitation of the data made available through advances in genomic medicine, imaging, and a wide range of mobile health applications or connected devices is hampered by numerous historical, technical, legal, and political barriers. European health systems and databases are diverse and fragmented. There is a lack of harmonization of data formats, processing, analysis, and data transfer, which leads to incompatibilities and lost opportunities. Legal frameworks for data sharing are evolving. Clinicians, researchers, and citizens need improved methods, tools, and training to generate, analyze, and query data effectively. Addressing these barriers will contribute to creating the European Single Market for health, which will improve health and healthcare for all Europeans. European healthcare systems and the potential for big data Medicine has traditionally been a science of observation and experience. For thousands of years, clinicians have integrated the knowledge of preceding generations with their own life-long experiences to treat patients according to the oath of Hippocrates; mostly based on trial and * Correspondence: cauffray@eisbm.org; rudi.balling@uni.lu European Institute for Systems Biology and Medicine, 1 avenue Claude Vellefaux, 75010 Paris, France Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts Fourneaux, 4362 Esch-sur-Alzette, Luxembourg Full list of author information is available at the end of the article

On realizing the concept study ScienceSoft of the European Middleware Initiative: Open Software for Open Science

In September 2011 the European Middleware Initiative (EMI) started discussing the feasibility of creating an open source community for science with other projects like EGI, StratusLab, OpenAIRE, iMarine, and IGE, SMEs like DCore, Maat, SixSq, SharedObjects, communities like WLCG and LSGC. The general idea of establishing an open source community dedicated to software for scientific applications was understood and appreciated by most people. However, the lack of a precise definition of goals and scope is a limiting factor that has also made many people sceptical of the initiative. In order to understand more precisely what such an open source initiative should do and how, EMI has started a more formal feasibility study around a concept called ScienceSoft - Open Software for Open Science. A group of people from interested parties was created in December 2011 to be the ScienceSoft Steering Committee with the short-term mandate to formalize the discussions about the initiative and produce a document with an initial high-level description of the motivations, issues and possible solutions and a general plan to make it happen. The conclusions of the initial investigation were presented at CERN in February 2012 at a ScienceSoft Workshop organized by EMI. Since then, presentations of ScienceSoft have been made in various occasions, in Amsterdam in January 2012 at the EGI Workshop on Sustainability, in Taipei in February at the ISGC 2012 conference, in Munich in March at the EGI/EMI Conference and at OGF 34 in March. This paper provides information this concept study ScienceSoft as an overview distributed to the broader scientific community to critique it.

Software for Distributed Systems - The EMI Product Portfolio

The European Middleware Initiative (EMI) brings together ARC, dCache, gLite, and UNICORE to provide a harmonised set of products and streamlined releases to the DCI community. While there are many technical solutions around, EMI is one of the key players in providing software for large-scale distributed systems that are operated around the world today. Having products and solutions in various technical areas such as compute, data, information, and security, it is interesting to understand that these products also implement many of the principles and paradigms of distributed systems. This contribution will provide an overview of the EMI product portfolio focusing on its key features and their role in distributed systems based on comparisons with known literature such as books offered by Tanenbaum.