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D4.2: Science Demonstrator Selection Process [article]

Montserrat Gonzalez, Steven Newhouse, Hermann Lederer, Brian Matthews, Gergely Sipos, Dario Vianello
2017 Zenodo  
The selected Science Demonstrators will represent a broad range of scientific activities that will provide requirements for the infrastructure and will help in evaluating the services offered by the EOSCpilot. Five initial Science Demonstrators were selected during the preparation of the EOSCpilot project proposal. The objective of this deliverable is to define a process and criteria that will be used to select the ten additional Science Demonstrators that will be run within the project. To
more » ... ne the selection process and criteria, we considered the objectives of the Science Demonstrators, the principles in which the selection process will be based and the minimum necessary staff to run the selection process. The selection process is formed by 13 different steps: open the call for proposals, review the compliance of the applications received, assign reviewers for all the applications, develop a scientific review, develop a technical review, prioritize the proposals, do the final selection, communicate the results to the EOSCpilot project consortium, communicate the results to the applicants, allocate resources to the selected projects, provide an appeal process and answer questions, and develop a general assessment on the selection procedure. As complement to the selection process, we have specified the selection criteria that will be used during the selection process and provided to the applicants.
doi:10.5281/zenodo.3387592 fatcat:khjj7ntoxfdelij4ilz3iwdgpq

Report: Updated Elixir Technical Services Roadmap

Tommi Nyrönen, Ludek Matyska, Steven Newhouse, Compute Platform Community
2018 Zenodo  
This version of the ELIXIR Technical Services Roadmap (ELIXIR-EXCELERATE deliverable D4.2) has been written at the end of PY2 of the ELIXIR-EXCELERATE project (August 2017) and represents an update to the previous version that was established in August 2016 ( Deliverable D4.1 ). It will be updated again in Summer 2018 following the 3rd Annual meeting of the ELIXIR Compute Platform (ECP). The ELIXIR Technical Services Roadmap is a living document that provides advice as to the current and future
more » ... implementation activities, and is subject to change between versions that is publicly accessible and commentable. This version contains information relating to the technical work undertaken primarily within the ELIXIR Compute Platform during PY2, an assessment of the Platform's capability that was defined through a number of Technical Use Cases (TUCs), and an assessment of the ability of the ELIXIR Compute Platform (through these TUCs) to support user-driven use cases. Overall, the ELIXIR Compute Platform will need to support these TUCs directly through services hosted by the ELIXIR Nodes or indirectly in partnership with European e-Infrastructure providers. These integrated services - the ELIXIR Compute Platform - will be available to bioinformatics experts for use to analyse globally significant data resources. Progress in PY2 has been extensive with a range of services now becoming available for end-users to consider adopting. The ELIXIR AAI allows a user to create 1 an ELIXIR identity based on a pre-existing identity (e.g. Google, ORCID or the researcher's home university as an attribute and an identity provider) and for that individual to be enrolled into the ELIXIR Virtual Organisation, and potentially into groups within this Virtual Organisation (using Perun2). This organisational information has then been exposed through the ELIXIR Proxy IdP to identified relying parties to use this information for authentication and authorisation decisions. These include the ELIXIR Intranet, other ELIXIR service [...]
doi:10.5281/zenodo.1321698 fatcat:ztdzpknsizdevfveemsid557ta

D3.3 and D4.4: Consolidated Science Demonstrator progress and evaluation reports [article]

Hermann Lederer, Steven Newhouse
2018 Zenodo  
The Science Demonstrators play an essential role as early adopters of EOSC from a range of science areas. Their input is used to drive and prioritize the integration of the EOSC services in a common homogeneous platform. To achieve this goal, a selection process for Science Demonstrators through Open Calls has been developed, followed by the execution of two Open Calls. Following five initial pre-selected Science Demonstrators, ten additional Science Demonstrators have been selected through two
more » ... rounds of scientific and technical review processes. An Engagement Model for Science Demonstrators has been developed and applied. Science Demonstrators have been introduced into their roles, and continuous shepherding of Science Demonstrators during their 12 months project execution has been carried out. Shepherding activities and project progress has been monitored in regular meetings. Feedback was collected in reports which are available for all work packages.
doi:10.5281/zenodo.3387596 fatcat:7svhwma7xrhyfch4qiqeaquruu

D4.1: Science Demonstrator Engagement Model [article]

Hermann Lederer, Dario Vianello, Montserrat González, John Kennedy, Thomas Zastrow, Steven Newhouse, Matthew Viljoen, Brian Matthews
2017 Zenodo  
Modification of 3.2 (monitoring of data handling risks). 0.4 03/03/2017 Hermann Lederer (MPG) General content, extension of Annex C Steven Newhouse (EMBL-EBI) 0.5 07/03/2017 Dario Vianello (EMBL-EBI) General  ... 
doi:10.5281/zenodo.3387589 fatcat:6jepabybqrg7dkvdxgpalruhdu

Computational Communities: A Marketplace for Federated Resources [chapter]

Steven Newhouse, John Darlington
2001 Lecture Notes in Computer Science  
doi:10.1007/3-540-48228-8_76 fatcat:2fyg6ysbtrci3kcbn5qaur4j24

Building Computational Communities from Federated Resources [chapter]

Nathalie Furmento, Steven Newhouse, John Darlington
2001 Lecture Notes in Computer Science  
We describe the design and the implementation in Java and Jini of a Computational Community, which supports the federation of resources from different organisations. Resources from the local Administrative Domain are published in a Jini space to form a Computational Community. Different access control policies can be applied to the same resource in different Computational Communities. We show how this architecture can be extended through the addition of an Application Mapper and Resource Broker to build a computational economy.
doi:10.1007/3-540-44681-8_119 fatcat:pmpn3lobtjdsza2y335otvrj2a

EOSC-Life Final EOSC-LS Cloud Observatory Report

Steven Newhouse, Harald Wagener, Marius Dieckmann, Ania Niewielska, Justin Clark-Casey, Santiago Insua
2022 Zenodo  
Activities on Cloud Resource Planning and Integration Task 7.1 is led by Steven Newhouse (EMBL-EBI) with contributions from the team at EMBL-EBI (Susheel Varma, Montse Gonzalez, Oihane Fano-Bilbao and  ... 
doi:10.5281/zenodo.6555208 fatcat:rdwwejl4lbdzzblpbxjql42bba

IT Service management system for EMBL's European Bioinformatics Institute's IT department

Montserrat González Ferreiro, Steven Newhouse
2022 F1000Research  
EMBL-EBI, Europe's biomolecular data hub, is a world leader in managing and analysing big data in biology and making it freely available to scientists worldwide. Research infrastructures (RI) like EMBL-EBI rely extensively on information technology (IT) services to conduct research and support the delivery of scientific services. These IT services are complex and diverse and IT service management (ITSM) has been shown in other domains to help to improve efficiency and productivity. ITSM is a
more » ... lection of standards that help organisations develop a process-based approach for managing the full lifecycle of IT services, while keeping their users' needs at the forefront and promoting continuous improvement. However, many organisations struggle with the design and implementation of an ITSM system as it involves the need for organisational change, and because the process approach can seem rigid and bureaucratic on the surface. This article aims to share the experience of the EMBL-EBI IT department in designing and implementing an ITSM system. ITSM implementation steps, benefits, challenges, opportunities, and practices are highlighted, critically analysed, and discussed.
doi:10.12688/f1000research.118082.1 fatcat:hahjor3ou5eojkxfzkq3mxh6ju

A Component Framework for HPC Applications [chapter]

Nathalie Furmento, Anthony Mayer, Stephen McGough, Steven Newhouse, John Darlington
2001 Lecture Notes in Computer Science  
We describe a general component software framework designed for demanding grid environments that provides optimal performance for the assembled component application. This is achieved by separating the high level abstract description of the composition from the low level implementations. These implementations are chosen at run time by performance analysis of the composed application on the currently available resources. We show through the solution of a simple linear algebra problem that the
more » ... mework introduces minimal overheads while always selecting the most effective implementation.
doi:10.1007/3-540-44681-8_78 fatcat:qjd6wkvw4bbylo3okzahe65gza

User Priorities for Data: Results from SUPER

Jennifer M. Schopf, Steven Newhouse
2008 International Journal of Digital Curation  
A full list is available (Newhouse, Schopf, Richards, & Atkinson, 2007, Appendix A) .  ...  Details for the complete survey results can be found in the final SUPER report (Newhouse, Schopf, Richards, & Atkinson, 2007 ).  ... 
doi:10.2218/ijdc.v2i1.23 fatcat:qc2vyniucrdtxezfuthepahkx4

EOSC-Life Initial EOSC-LS Cloud Observatory Report

Steven Newhouse, Harald Wagener, Montserrat González Ferrero, Oihane Fano-Bilbao, Tony Wildish, Marius Dieckmann, Ania Niewielska, Shubham Kapoor, Tommi Nyrönen
2020 Zenodo  
To do so, we analyse the activities carried on to date within the WP7 tasks.Activities on Cloud Resource Planning and IntegrationTask 7.1 is led by Steven Newhouse (EMBL-EBI) with contributions from the  ... 
doi:10.5281/zenodo.4010420 fatcat:nf52or3nxndv5e3jioklfoq6wq

Federated OmicsDI: Cloud-based architecture for omics data discovery

Gaurhari Dass, Manh-Tu Vu, Pablo Moreno, David Ocana, Pan Xu, Weimin Zhu, Steven Newhouse, Henning Hermjakob, Yasset Perez-Riverol
2021 Zenodo  
Motivation: Omics Discovery Index (OmicsDI - www.omicsdi.org) is an integrated and open-source platform to facilitate the discovery and dissemination of omics datasets metadata. It provides a unique infrastructure to integrate datasets coming from multiple omics studies, including at present proteomics, genomics, transcriptomics, metabolomics, and systems biology. The OmicsDI architecture was originally implemented and deployed in a dedicated high-performance computing cluster, limiting
more » ... ity and dynamic allocation of resources by the data processing pipelines. In addition, the original OmicsDI resource could not be reused by independent laboratories and research groups to share and disseminate their data. Results: Here, we present a new version of OmicsDI that can be easily deployed in cloud architectures and local infrastructures enabling the development of a Federated OmicsDI. The new architecture can be automatically synchronized with the main OmicsDI resource, increasing the integration with other omics data providers. Also, the proposed Cloud-based architecture is more scalable, providing better capabilities to manage the increase of data providers and datasets.
doi:10.5281/zenodo.4478424 fatcat:qyft35gcxfcdhm5x4e45pnlpve

Meaning and Behaviour in Grid Oriented Components [chapter]

Anthony Mayer, Stephen McGough, Murtaza Gulamali, Laurie Young, Jim Stanton, Steven Newhouse, John Darlington
2002 Lecture Notes in Computer Science  
The ICENI middleware utilises information captured within a component based application in order to facilitate Grid-based scheduling. We describe a system of application related meta-data that features a separation of concerns between meaning, behaviour and implementation, which allows for both communication and implementation selection at run-time, while providing the user with a flow-based programming model. It is shown that this separation enables a flexible approach to scheduling, and eases
more » ... the integration of components with disparate control flow patterns or data types, by means of converters and tees for collective communication. By explicitly recording application information and supporting multiple scheduling approaches, communication protocols and component applications, while retaining OGSA compatibility, the ICENI component model is ideally suited to Grid computing. Meta-data In previous works [1,2], we have made the observation that information is key to the successful exploitation of the Grid -information about the resources them-M.
doi:10.1007/3-540-36133-2_10 fatcat:a7pjk72qazaqhog56tcoaxwapi

A Componentized Approach to Grid Enabling Seismic Wave Modeling Application [chapter]

Dheeraj Bhardwaj, Jeremy Cohen, Steve McGough, Steven Newhouse
2004 Lecture Notes in Computer Science  
Seismic modeling is an integral part of the seismic data processing for oil and gas exploration, as it provides us the seismic response for a given earth model. Grid enabled seismic wave modeling can facilitate users in the area of geophysics to calculate synthetic seismograms using federated HPC resources and complex solution algorithms without knowing their complexities. The present paper is about componentization of the wave equation based seismic modeling algorithm and its implement using
more » ... perial College e-Science Networked Infrastructure (ICENI) Grid Middleware.
doi:10.1007/978-3-540-30501-9_23 fatcat:a7hxoljncngajbudbgyip4jina

ICENI: Optimisation of component applications within a Grid environment

Nathalie Furmento, Anthony Mayer, Stephen McGough, Steven Newhouse, Tony Field, John Darlington
2002 Parallel Computing  
doi:10.1016/s0167-8191(02)00187-4 fatcat:bo7oslhdjnagvly657ph4cooqe
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