European e-Infrastructures Research Articles

Open Source Framework for Enabling HPC and Cloud Geoprocessing Services

Geoprocessing is a set of tools that can be used to efficiently address several pressing chal-lenges for the global economy ranging from agricultural productivity, the design of transport networks, to the prediction of climate change and natural disasters. This paper describes an Open Source Framework developed, within three European projects, for Ena-bling High-Performance Computing (HPC) and Cloud geoprocessing services applied to agricultural challenges. The main goals of the European Union projects EUXDAT (EUro-pean e-infrastructure for eXtreme Data Analytics in sustainable developmenT), CYBELE (fostering precision agriculture and livestock farming through secure access to large-scale HPC-enabled virtual industrial experimentation environment empowering scalable big data analytics), and EOPEN (opEn interOperable Platform for unified access and analysis of Earth observatioN data) are to enable the use of large HPC systems, as well as big data management, user-friendly access and visualization of results. In addition, these projects focus on the development of software frameworks, and fuse Earth-observation data, such as Copernicus data, with non-Earth-observation data, such as weather, environmental and social media information. In this paper, we describe the agroclimatic-zones pilot used to validate the framework. Finally, performance metrics collected during the execution (up to 182 times speedup with 256 MPI processes) of the pilot are presented.

Use of European Open Science Cloud and National e-Infrastructures for the Long-Term Storage of Digitised Assets from Natural History Collections

Digitisation of Natural History Collections (NHC) has evolved from transcription of specimen catalogues in databases to web portals providing access to data, digital images, and 3D models of specimens. These portals increase global accessibility to specimens and help preserve the physical specimens by reducing their handling. The size of the NHC requires developing high-throughput digitisation workflows, as well as research into novel acquisition systems, image standardisation, curation, preservation, and publishing. Nowadays, herbarium sheet digitisation workflows (and fast digitisation stations) can digitise up to 6,000 specimens per day. Operating those digitisation stations in parallel, can increase the digitisation capacity. The high-resolution images obtained from these specimens, and their volume require substantial bandwidth, and disk space and tapes for storage of original digitised materials, as well as availability of computational processing resources for generating derivatives, information extraction, and publishing. While large institutions have dedicated digitisation teams that manage the whole workflow from acquisition to publishing, other institutions cannot dedicate resources to support all digitisation activities, in particular long-term storage. National and European e-infrastructures can provide an alternative solution by supporting different parts of the digitisation workflows. In the context of the Innovation and consolidation for large scale digitisation of natural heritage (ICEDIG Project 2018), three different e-infrastructures providing long-term storage have been analysed through three pilot studies: EUDAT-CINES, Zenodo, and National Infrastructures. The EUDAT-CINES pilot centred on transferring large digitised herbarium collections from the National Museum of Natural History France (MNHN) to the storage infrastructure provided by the Centre Informatique National de l’Enseignement Supérieur (CINES 2014), a European trusted digital repository. The upload, processing, and access services are supported by a combination of services provided by the European Collaborative Data Infrastructure (EUDAT CDI 2019) and CINES . The Zenodo pilot included the upload of herbarium collections from Meise Botanic Garden (APM) and other European herbaria into the Zenodo repository (Zenodo 2019). The upload, processing and access services are supported by Zenodo services, accessed by APM. The National Infrastructures pilot facilitated the upload of digital assets derived from specimens of herbarium and entomology collections held at the Finnish Museum of Natural History (LUOMUS) into the Finnish Biodiversity Information Facility (FinBIF 2019). This pilot concentrates on simplifying the integration of digitisation facilities to Finnish national e-infrastructures, using services developed by LUOMUS to access FinBIF resources. The data models employed in the pilots allow defining data schemas according to the types of collection and specimen images stored. For EUDAT-CINES, data were composed of the specimen data and its business metadata (those the institution making the deposit, in this case MNHN, considers relevant for the data objects being stored), enhanced by archiving metadata, added during the archiving process (institution, licensing, identifiers, project, archiving date, etc). EUDAT uses ePIC identifiers (ePIC 2019) to identify each deposit. The Zenodo pilot was designed to allow defining specimen data and metadata supporting indexing and access to resources. Zenodo uses DataCite Digital Object Identifiers (DOI) and the underlying data types as the main identifiers for the resources, augmented with fields based on standard TDWG vocabularies. FinBIF compiles Finnish biodiversity information to one single service for open access sharing. In FinBIF, HTTP URI based identifiers are used for all data, which link the specimen data with other information, such as images. The pilot infrastructure design reports describe features, capacities, functions and costs for each model, in three specific contexts are relevant for the implementation of the Distributed Systems of Scientific Collections (DiSSCo 2019) research infrastructure, informing the options for long-term storage and archiving digitised specimen data. The explored options allow preservation of assets and support easy access. In a wider context, the results provide a template for service evaluation in the European Open Science Cloud (EOSC 2019) which can guide similar efforts.

West-Life: A Virtual Research Environment for structural biology

The West-Life project (https://about.west-life.eu/) is a Horizon 2020 project funded by the European Commission to provide data processing and data management services for the international community of structural biologists, and in particular to support integrative experimental approaches within the field of structural biology. It has developed enhancements to existing web services for structure solution and analysis, created new pipelines to link these services into more complex higher-level workflows, and added new data management facilities. Through this work it has striven to make the benefits of European e-Infrastructures more accessible to life-science researchers in general and structural biologists in particular.

Community engagement: The ‘last mile’ challenge for European research e-infrastructures

Europe is building its Open Science Cloud; a set of robust and interoperable e-infrastructures with the capacity to provide data and computational solutions through cloud-based services. The development and sustainable operation of such e-infrastructures are at the forefront of European funding priorities. The research community, however, is still reluctant to engage at the scale required to signal a Europe-wide change in the mode of operation of scientific practices. The striking differences in uptake rates between researchers from different scientific domains indicate that communities do not equally share the benefits of the above European investments. We highlight the need to support research communities in organically engaging with the European Open Science Cloud through the development of trustworthy and interoperable Virtual Research Environments. These domain-specific solutions can support communities in gradually bridging technical and socio-cultural gaps between traditional and open digital science practice, better diffusing the benefits of European e-infrastructures.

An Approach to Analyzing Working Practices of Research Communities in the Humanities

The need for a firm understanding of the working practices of researchers in the humanities emerges as a prerequisite for the development of effective digital research infrastructures. This paper will focus on the rationale behind the design and implementation of two related studies conducted in the context of two European e-Infrastructures projects, DARIAH and EHRI. Within DARIAH the challenge involved conducting, analysing and understanding research practices of arts and humanities researchers, a largely ill-defined community encompassing a wide spectrum of disciplines. Each of them deals with a variety of objects employing an extensive number of methods. In the context of EHRI, the challenge is slightly different, due to the involvement of a better-defined research community. Holocaust researchers share well-identified objects, common ground on methods, and handle similar setbacks. In this paper we discuss the approach adopted for designing and implementing qualitative user-centric studies aimed at capturing activities, methods, and types of information objects employed by researchers grounded in identified research goals and questions. It addresses both generic and specific entities and processes, and supports the understanding of researchers’ working practices in settings as diverse and wide as DARIAH, or as specialized as EHRI. The outcomes of the analysis of working practices are used in determining user requirements for digital infrastructures to serve the respective research communities.

Distributed Multiscale Simulations of Clay-Polymer Nanocomposites

ABSTRACTThe mechanical enhancement of polymers when clay nanoparticles are dispersed within it depends on factors over various length scales; for example, the orientation of the clay platelets in the polymer matrix will affect the mechanical resistance of the composite, while at the shortest scale the molecular arrangement and the adhesion energy of the polymer molecules in the galleries and the vicinity of the clay-polymer interface will also affect the overall mechanical properties.In this paper, we address the challenge of creating a hierarchal multiscale modelling scheme to traverse a sufficiently wide range of time and length scales to simulate clay-polymer nanocomposites effectively. This scheme varies from the electronic structure (to capture the polymer – clay interactions, especially those of the reactive clay edges) through classical atomistic molecular dynamics to coarse-grained models (to capture the long length scale structure).Such a scenario is well suited to distributed computing with each level of the scheme allocated to a suitable computational resource. We describe how the e-infrastructure and tools developed by the MAPPER (Multiscale Applications on European e-Infrastructures) project facilitates our multiscale scheme. Using this new technology, we have simulated clay-polymer systems containing up to several million atoms/particles. This system size is firmly within the mesoscopic regime, containing several clay platelets with the edges of the platelets explicitly resolved. We show preliminary results of a “bottom-up” multiscale simulation of a clay platelet dispersion in poly(ethylene) glycol.

Understanding the Information Requirements of Arts and Humanities Scholarship

This paper reports on research of scholarly research practices and requirements conducted in the context of the Preparing DARIAH European e-Infrastructures project, with a view to ensuring current and future fitness for purpose of the planned digital infrastructure, services and tools. It summarises the findings of earlier research, primarily from the field of human information behaviour as applied in scholarly work, it presents a conceptual perspective informed by cultural-historical activity theory, it introduces briefly a formal conceptual model for scholarly research activity compliant with CIDOC CRM, it describes the plan of work and methodology of an empirical research project based on open-questionnaire interviews with arts and humanities researchers, and presents illustrative examples of segmentation, tagging and initial conceptual analysis of the empirical evidence. Finally, it presents plans for future work, consisting, firstly, of a comprehensive re-analysis of interview segments within the framework of the scholarly research activity model, and, secondly, of the integration of this analysis with the extended digital curation process model we presented in earlier work.

CERIF-CRIS for the European e-Infrastructure

The European e-infrastructure is the ICT support for research although the infrastructure will be extended for commercial/business use. It supports the research process across funding agencies to research institutions to innovation. It supports experimental facilities, modelling and simulation, communication between researchers, and workflow of research processes and research management. We propose the core should be CERIF: an EU recommendation to member states for exchanging research information and for homogeneous access to heterogeneous information. CERIF can also integrate associated systems (such as finance, human resource, project management, and library services) and provides interoperation among research institutions, research funders, and innovators.