International Wader Study Group : annual conference 26-29 September 2014 : Haapsalu, Estonia

Full textInternational Wader Study Group : annual conference 26-29 September 2014 : Haapsalu, EstoniaSupported by Environmental Investment Centr

COMP Superscalar, an interoperable programming framework

COMPSs is a programming framework that aims to facilitate the parallelization of existing applications written in Java, C/C++ and Python scripts. For that purpose, it offers a simple programming model based on sequential development in which the user is mainly responsible for identifying the functions to be executed as asynchronous parallel tasks and annotating them with annotations or standard Python decorators. A runtime system is in charge of exploiting the inherent concurrency of the code, automatically detecting and enforcing the data dependencies between tasks and spawning these tasks to the available resources, which can be nodes in a cluster, clouds or grids. In cloud environments, COMPSs provides scalability and elasticity features allowing the dynamic provision of resources.This work has been supported by the following institutions: the Spanish Government with grant SEV-2011-00067 of the Severo Ochoa Program and contract Computacion de Altas Prestaciones VI (TIN2012-34557); by the SGR programme (2014-SGR-1051) of the Catalan Government; by the project The Human Brain Project, funded by the European Commission under contract 604102; by the ASCETiC project funded by the European Commission under contract 610874; by the EUBrazilCloudConnect project funded by the European Commission under contract 614048; and by the Intel-BSC Exascale Lab collaboration.Peer ReviewedPostprint (published version

The Global Impact of Science Gateways, Virtual Research Environments and Virtual Laboratories

Science gateways, virtual laboratories and virtual research environments are all terms used to refer to community-developed digital environments that are designed to meet a set of needs for a research community. Specifically, they refer to integrated access to research community resources including software, data, collaboration tools, workflows, instrumentation and high-performance computing, usually via Web and mobile applications. Science gateways, virtual laboratories and virtual research environments are enabling significant contributions to many research domains, facilitating more efficient, open, reproducible research in bold new ways. This paper explores the global impact achieved by the sum effects of these programs in increasing research impact, demonstrates their value in the broader digital landscape and discusses future opportunities. This is evidenced through examination of national and international programs in this field

Urbanization and health in Africa : exploring the interconnections between poverty, inequality and the burden of disease

There are few changes in the history of human existence comparable to urbanization in scope and potential to bring about biologic change. The transition in the developed world from an agricultural to an industrial-urban society has already produced substantial changes in human health, morphology and growth (Schell, Smith and Bilsborough, 1993, p.1). By the year 2000, about 50% of the world s total population will be living crowded in urban areas and soon thereafter, by the year 2025 as the global urban population reaches the 5 billion mark more of the world s population will be living in urban areas. This has enormous health consequences. By the close of the twenty-first century, more people will be packed into the urban areas of the developing world than are alive on the planet today (UNCHS (Habitat), 1996, p.xxi). Africa presents a particularly poignant example of the problems involved, as it has the fastest population and urban growth in the world as well as the lowest economic development and growth and many of the poorest countries, especially in Tropical Africa. Thus it exemplifies in stark reality many of the worst difficulties of urban health and ecology (Clarke, 1993, p.260). This essay is therefore concerned to analyse the trends of urbanization in Africa. This is followed by an overview of the environmental conditions of Africa s towns and cities. The subsequent section explores the links between the urban environment and health. Although the focus is with physical hazards it is important to note that the social milieu is also vital in the reproduction of health. The paper concludes by providing some policy recommendations

Helmholtz Portfolio Theme Large-Scale Data Management and Analysis (LSDMA)

The Helmholtz Association funded the "Large-Scale Data Management and Analysis" portfolio theme from 2012-2016. Four Helmholtz centres, six universities and another research institution in Germany joined to enable data-intensive science by optimising data life cycles in selected scientific communities. In our Data Life cycle Labs, data experts performed joint R&D together with scientific communities. The Data Services Integration Team focused on generic solutions applied by several communities

Generic Metadata Handling in Scientific Data Life Cycles

Scientific data life cycles define how data is created, handled, accessed, and analyzed by users. Such data life cycles become increasingly sophisticated as the sciences they deal with become more and more demanding and complex with the coming advent of exascale data and computing. The overarching data life cycle management background includes multiple abstraction categories with data sources, data and metadata management, computing and workflow management, security, data sinks, and methods on how to enable utilization. Challenges in this context are manifold. One is to hide the complexity from the user and to enable seamlessness in using resources to usability and efficiency. Another one is to enable generic metadata management that is not restricted to one use case but can be adapted with limited effort to further ones. Metadata management is essential to enable scientists to save time by avoiding the need for manually keeping track of data, meaning for example by its content and location. As the number of files grows into the millions, managing data without metadata becomes increasingly difficult. Thus, the solution is to employ metadata management to enable the organization of data based on information about it. Previously, use cases tended to only support highly specific or no metadata management at all. Now, a generic metadata management concept is available that can be used to efficiently integrate metadata capabilities with use cases. The concept was implemented within the MoSGrid data life cycle that enables molecular simulations on distributed HPC-enabled data and computing infrastructures. The implementation enables easy-to-use and effective metadata management. Automated extraction, annotation, and indexing of metadata was designed, developed, integrated, and search capabilities provided via a seamless user interface. Further analysis runs can be directly started based on search results. A complete evaluation of the concept both in general and along the example implementation is presented. In conclusion, generic metadata management concept advances the state of the art in scientific date life cycle management

A Vision for Science Gateways: Bridging the Gap and Broadening the Outreach

The future for science gateways warrants exploration as we consider the possibilities that extend well beyond science and high performance computing into new interfaces, applications and user communities. In this paper, we look retrospectively at the successes of representative gateways thus far. This serves to highlight existing gaps gateways need to overcome in areas such as accessibility, usability and interoperability, and in the need for broader outreach by drawing insights from technology adoption research. We explore two particularly promising opportunities for gateways - computational social sciences and virtual reality – and make the case for the gateway community to be more intentional in engaging with users to encourage adoption and implementation, especially in the area of educational usage. We conclude with a call for focused attention on legal hurdles in order to realize the full future potential of science gateways. This paper serves as a roadmap for a vision of science gateways in the next ten years

Extending Molecular Docking Desktop Applications with Cloud Computing Support and Analysis of Results

Structure-based virtual screening simulations, which are often used in drug discovery, can be very computationally demanding. This is why user-friendly domain-specific web or desktop applications that enable running simulations on powerful computing infrastructures have been created. This article investigates how domain-specific desktop applications can be extended to use cloud computing and how they can be part of scenarios that require sharing and analysing previous molecular docking results. A generic approach based on interviews with scientists and analysis of existing systems is proposed. A proof of concept is implemented using the Raccoon2 desktop application for virtual screening, WS-PGRADE workflows, gUSE services with the CloudBroker Platform, the structural alignment tool DeepAlign, and the ligand similarity tool LIGSIFT. The presented analysis illustrates that this approach of extending a domainspecific desktop application can use different types of clouds, thus facilitating the execution of virtual screening simulations by life scientists without requiring them to abandon their favourite desktop environment and providing them resources without major capital investment. It also shows that storing and sharing molecular docking results can produce additional conclusions such as viewing similar docking input files for verification or learning

The Past, Present and Future of the ELKH Cloud

This review article summarizes the history the Hungarian Scientific Cloud Infrastructure project. This research infrastructure was launched officially on 1 October 2016, funded by the Hungarian Academy of Sciences. With the support of ELKH, the infrastructure’s capacity has been substantially boosted; the features and workflows that it offers to scientists were significantly expanded to celebrate the arrival of the year 2022. The article reviews the types of work Hungarian researchers implemented on the infrastructure, thereby providing an overview of the state of cloud-computing enabled science in Hungary