Performance Analyses of EGEE-like Grids in Asia and Latin America

Evaluate the status of several EGEE-like infrastructures outside of Europ

The Open Science Commons for the European Research Area

Nowadays, research practice in all scientific disciplines is increasingly, and in many cases exclusively, data driven. Knowledge of how to use tools to manipulate research data, and the availability of e-Infrastructures to support them for data storage, processing, analysis and preservation, is fundamental. In parallel, new types of communities are forming around interests in digital tools, computing facilities and data repositories. By making infrastructure services, community engagement and training inseparable, existing communities can be empowered by new ways of doing research, and new communities can be created around tools and data. Europe is ideally positioned to become a world leader as provider of research data for the benefit of research communities and the wider economy and society. Europe would benefit from an integrated infrastructure where data and computing services for big data can be easily shared and reused. This is particularly challenging in EO given the volumes and variety of the data that make scalable access difficult, if not impossible, to individual researchers and small groups (i.e. to the so-called long tail of science). To overcome this limitation, as part of the European Commission Digital Single Market strategy, the European Open Science Cloud (EOSC) initiative was launched in April 2016, with the final aim to realise the European Research Area (ERA) and raise research to the next level. It promotes not only scientific excellence and data reuse, but also job growth and increased competitiveness in Europe, and results in Europe-wide cost efficiencies in scientific infrastructure through the promotion of interoperability on an unprecedented scale. This chapter analyses existing barriers to achieve this aim and proposes the Open Science Commons as the fundamental principles to create an EOSC able to offer an integrated infrastructure for the depositing, sharing and reuse of big data, including Earth Observation (EO) data, leveraging and enhancing the current e-Infrastructure landscape, through standardization, interoperability, policy and governance. Finally, it is shown how an EOSC built on e-Infrastructures can improve the discovery, retrieval and processing capabilities of EO data, offering virtualised access to geographically distributed data and the computing necessary to manipulate and manage large volumes. Well-established e-Infrastructure services could provide a set of reusable components to accelerate the development of exploitation platforms for satellite data solving common problems, such as user authentication and authorisation, monitoring or accounting

Set up your own bioinformatics server: Chipster in EGI Federated Cloud

Chipster is an easy to use data analysis platform for bioinformatics. It provides an uniform graphical interface for over 360 commonly used bioinformatics tools including several R/Bioconductor-based tools and standalone programs (i.e. BWA, TopHat). Chipster is based on a client-server system where the user runs locally a Chipster-client that submits analysis tasks to a Chipster server. Even though Chipster is an open source tool, there is no public Chipster server that would be open for everybody. Due to that, a researcher needs to have an access to some of the existing Chipster servers to be able to use this platform. Alternatively, a researcher can set up his own Chipster server. In this paper, we describe how a Chipster server can be launched EGI Federated Could environment, that provides resources for all European researchers. With the instructions provided here, any European researcher can launch and manage his own Chipster server, suited for needs of a small research group or a bioinformatics course. The setup described here is based on a collaboration of several European instances. Chipster is developed by CSC – IT Center for Science Ltd. in Finland. European Grid Infrastructure (EGI) has fitted Chipster to cloud environment and provides the cloud computing resources. Finally, Rutherford Appleton Laboratory hosts the CVMFS server that provides the scientific tools and data sets for the Chipster servers running in EGI federated cloud

The EGI Federated Cloud e-Infrastructure

Trabajo presentado al EGI Community Forum, celebrado en Bari (Italia) del 10 al 13 de noviembre de 2015.This work by Parties of the EGI-Engage Consortium is licensed under a Creative Commons Attribution 4.0 International License.Peer reviewe

Federating infrastructure as a service cloud computing systems to create a uniform e-infrastructure for research

This paper details the state of the art, the design, development and deployment of the EGI Federated Cloud platform, an e-infrastructure offering scalable and flexible models of utilization to the European research community. While continuing support for the traditional High Throughput Computing model, the EGI Cloud Platform extends its reach to other models of utilization such as long-lived services and on demand computation. Following a two-year period of development, the EGI Federated Cloud platform was officially launched in May 2014 offering resources provided by trusted academic and research organisations from within the user communities and consistently with their standard funding regime. Since then, the use cases supported have significantly increased both in total number and diversity of model of service required, validating both the choice of enforcing cloud technology agnosticism and of supporting service mobility and portability by means of open standards. These design choices have also allowed for the inclusion of commercial cloud providers into an infrastructure previously supported only by academic institutions. This contributes to a wider goal of funding agencies to create economic and social impact from supported research activities

The EOSC Early Adopter Programme: Experiences from EMSO ERIC

American Geophysical Union (AGU) Fall Meeting, 13-17 December 2021, New OrleansThe European Multidisciplinary Seafloor and water column Observatory (EMSO) aims to explore the oceans and explain the driving factors and the effects of changes they play in the broader earth systems, focusing on climate change, warning signals of biodiversity loss and ecosystem impact, and geo-hazards. A fundamental component of the EMSO cyber-infrastructure that allows integrating multiple ocean variables from EMSO ERIC regional facilities is its data management platform. EMSO engaged with European Grid Infrastructure (EGI) to develop an initial data management platform as part of the EMSODEV H2020 project. The EOSC-hub Early Adopters Programme now supports the transition of the EMSO data management platform to pre-production providing, through its partners, resources, and solutions for the deployment of EMSO ERIC data services. This transition enables data and services to be harmonized and standardized across EMSO observatories. It also increases its interoperability with the marine subdomain according to FAIR principles as part of the ENVRI-FAIR H2020 project, which will ultimately deliver EMSO ERIC added value data services via the EOSC marketplace impacting different communities. This effort also establishes an appropriate workflow for taking stewardship of every stage of the data lifecycle and ensuring long-term preservation and redundancy and additional mechanisms for data, metadata, and data product discovery and delivery based on decentralized approaches and broadly used technologies and tools. The envisioned architecture is based on robustness and fault tolerance, including redundancy and failover capabilities on computing and storage resources, and scalability and security, including a distributed architecture for data access and analysis. EOSC-hub currently provides cloud-based resources from two geo-distributed datacenters in Italy (RECAS-BARI) and Spain (CESGA), delivering over 10TB online storage and in excess of 4M CPU-hours over twelve months, guaranteed by an SLA. Additional critical services are provided, such as support for integrating an Authentication and Authorization Infrastructure based on the EGI Check-In service. User-related information is planned to be managed according to anonymization standards using tools such as OpenAIRE AmnesiaPeer reviewe

The demand for consistent web-based workflow editors

This paper identifies the high value to researchers in many disciplines of having web-based graphical editors for scientific workflows and draws attention to two technological transitions: good quality editors can now run in a browser and workflow enactment systems are emerging that manage multiple workflow languages and support multi-lingual workflows. We contend that this provides a unique opportunity to introduce multi-lingual graphical workflow editors which in turn would yield substantial benefits: workflow users would find it easier to share and combine methods encoded in multiple workflow languages, the common framework would stimulate conceptual convergence and increased workflow component sharing, and the many workflow communities could share a substantial part of the effort of delivering good quality graphical workflow editors in browsers. The paper examines whether such a common framework is feasible and presents an initial design for a web-based editor, tested with a preliminary prototype. It is not a fait accompli but rather an urgent rallying cry to explore collaboratively a generic web-based framework before investing in many divergent individual implementations

e-Infrastructures for e-Science: A Global View

In the last 10 years, a new way of doing science is spreading in the world thank to the development of virtual research communities across many geographic and administrative boundaries. A virtual research community is a widely dispersed group of researchers and associated scientific instruments working together in a common virtual environment. This new kind of scientific environment, usually addressed as a “collaboratory”, is based on the availability of high-speed networks and broadband access, advanced virtual tools and Grid-middleware technologies which, altogether, are the elements of the e-Infrastructures. The European Commission has heavily invested in promoting this new way of collaboration among scientists funding several international projects with the aim of creating e-Infrastructures to enable the European Research Area and connect the European researchers with their colleagues based in Africa, Asia and Latin America. In this paper we describe the actual status of these e- Infrastructures and present a complete picture of the virtual research communities currently using them. Information on the scientific domains and on the applications supported are provided together with their geographic distribution

EOSC IF Interoperability Guideline: Access to content via PID

Bardi A, Manghi P, Gonzalez Lopez JB, et al. EOSC IF Interoperability Guideline: Access to content via PID.An important aspect of Open Science is the possibility to re-use existing research products (e.g. research data), deposited in repositories and accessible via their persistent identifiers (e.g. handle, doi, ark). However, there is no standard way a service can access the actual content behind persistent identifiers, as these typically resolve to the landing pages of the research products. The lack of standard for accessing the actual content identified by persistent identifiers makes the automatic consumption of research products hardly implementable and, when possible, limited to the persistent identifiers issued by a specific repository (e.g. the first prototype of the EGI Data Transfer Service integrated in the EOSC EXPLORE portal supported only DOIs from Zenodo). The EOSC Future Working Group on Research Product Publishing proposes the adoption of the Publication Boundary Pattern of the SignPosting protocol and recomends it for inclusion as interoperability guideline in the EOSC IF

EOSC-IF / Interoperability Guideline: Research Product Deposition

Bardi A, Manghi P, Gonzalez Lopez JB, et al. EOSC-IF / Interoperability Guideline: Research Product Deposition.Open Science calls for researchers to publish as soon as possible any type of research product in such a way their research activity can be transparently assessed, reviewed, reproduced, and rewarded in all its aspects. However, the publishing process has become more and more a burden for scientists, who must, most of the time, spend time to publish their articles, data, software, and other products in the many institutional or thematic repositories of reference. Scenarios include first-time publishing of new resource products or double-publishing of research products, to satisfy institutional mandates and community practices. Such tedious work is often incomplete, with some products ending up unpublished and others showing incomplete or imprecise metadata. Some communities investigated and realised the integration of their research performing services, from research infrastructures and clusters, with repositories for research product deposition. The integration ensures that outcomes of such services are deposited automatically, prior authorization of the users, into a given repository, giving life to an end-to-end scientific workflow, from experimentation to publishing. The limit of existing approaches is to be bound to a specific repository API and format; introducing multiple repositories as potential targets of deposition for the service, multiplies the problem, as bilateral interactions with the respective repository API must be established. For example, the Zenodo deposition API and the B2SHARE API are similar but different in many ways; a service willing to automate publishing into either repositories would require implementing and maintaining two different workflows. For the EOSC to act as enabler for Open Science practices, its Interoperability Framework should guide services of research infrastructures and clusters of the EOSC on how to implement (semi-)automated workflows for the deposition and consumption of research products. To support different integration options, two modalities are supported by these guidelines: SWORD protocol v3 for push mode and a combination of COAR Notify and Signposting for pull mode. The EOSC guidelines for research product onboarding are suggested as metadata exchange format