Jonathan A Tedds | University of Leicester (original) (raw)

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Papers by Jonathan A Tedds

Zenodo (CERN European Organization for Nuclear Research), Jul 13, 2023

Zenodo (CERN European Organization for Nuclear Research), Jun 17, 2022

This deliverable is the blueprint of the Life Science AAI, a common authentication and authorisat... more This deliverable is the blueprint of the Life Science AAI, a common authentication and authorisation service for the European life science research infrastructures. The Life Science AAI provides a way to coordinate the way how user identity and access is managed in research services and data in the (community-specific) federated Infrastructure. The service will be managed by the life sciences community and operated by the e-infrastructures, such as GEANT, EGI and EUDAT. The requirements of the Life Science AAI were initially developed by CORBEL WP5 and piloted with e-infrastructures in the AARC2 project. This deliverable lays the ground for the production deployment with e-infrastructures during the EOSC-Life project. This deliverable and its appendices first introduces the technical and non-technical requirements for the e-infrastructure service offering and further clarifies how that relates to and integrates to the AAI service components operated by the life sciences research inf...

Zenodo (CERN European Organization for Nuclear Research), Jun 20, 2023

Life Science (LS) communities must increase the sustainability of their data resources, software ... more Life Science (LS) communities must increase the sustainability of their data resources, software tools, and workflows, to allow their long-term re-use by the wider scientific community, especially in future applications involving machine-based analyses. Here, we describe key findings regarding sustainable LS resources, based on experiences from the EOSC-Life project. EOSC-Life involves 13 European LS Research Infrastructures. It lays the foundation for an open, digital and collaborative space for biological and medical research. We describe organisational, technical, financial and legal/ethical challenges that represent the main barriers to sustainability in the LS domain. Using lessons from 27 scientific projects selected via open calls, we demonstrate the efficiency of the EOSC-Life support model for sustainable FAIR data management and explore the complex sustainability needs for sensitive-and industry-related data resources. We describe cross-disciplinary sharing of best practices, and how this contributes to the sustainability of knowledge across communities, through building of training resources. We formulate a set of recommendations, focusing on working with experts, and communicating outcomes, to establish strong credibility and recognition of research projects. Furthermore, demonstrating and practising also permit a more sustainable adoption of reproducible research outputs. Recommended measures include sustainable training methodologies, as well as ensuring high quality metadata to drive the sustainable reusability of scientific objects. Responsibilities and roles to ensure sovereignty, sustainable services and tools must also be attributed. Finally, our analysis demonstrates how data harmonisation facilitates interoperability of tools, data, solutions and a better understanding of concepts, functionalities and semantics in the LSs.

Zenodo (CERN European Organization for Nuclear Research), Sep 28, 2022

The nature of molecular shocks, which play an important role in the processes of momentum and ene... more The nature of molecular shocks, which play an important role in the processes of momentum and energy transfer within starforming molecular clouds (McKee 1989), is still uncertain (Draine & McKee 1993). The Orion molecular cloud is the brightest

We report rst results from a project carried out by the Survey Science Centre of the XMM-Newton s... more We report rst results from a project carried out by the Survey Science Centre of the XMM-Newton satellite aiming at the optical identication and characterisation of serendipitous EPIC sources at low galactic latitudes (jbj S)-log S curves for identied active coronae once the variation of the mean local absorption and biases introduced by the limiting magnitude for optical identication are taken into account. At mid galactic latitudes (jbj< 3 -16 ), a small fraction of the extragalactic population is bright enough in the optical to be detected with our instrumentation. In this range of latitudes, the AGN population dominates X-ray number counts at all energies being most prominent in the hard X-rays. At very low latitudes (b 0), active coronae account for the totality of the soft (0.5-2.0 keV) source counts. In the hard band (2.0-12.0 keV), we nd a clear excess of sources above the expected extragalactic contribution. This galactic population of relatively low X-ray luminosity (LX...

F1000Research, 2019

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now reco... more Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled “An intrinsically disordered protein user community proposal for ELIXIR” held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of prio...

International Journal of Digital Curation, 2016

Software underpins the academic research process across disciplines. To be able to understand, us... more Software underpins the academic research process across disciplines. To be able to understand, use/reuse and preserve data, the software code that generated, analysed or presented the data will need to be retained and executed. An important part of this process is being able to persistently identify the software concerned. This paper discusses the reasons for doing so and introduces a model of software entities to enable better identification of what is being identified. The DataCite metadata schema provides a persistent identification scheme and we consider how this scheme can be applied to software. We then explore examples of persistent identification and reuse. The examples show the differences and similarities of software used in academic research, which has been written and reused at different scales. The key concepts of being able to identify what precisely is being used and provide a mechanism for appropriate credit are important to both of them.

International Journal on Digital Libraries, 2016

We would be very grateful if you would fill in this short survey on your evaluation of the manusc... more We would be very grateful if you would fill in this short survey on your evaluation of the manuscript. It will take about 3 minutes to complete the survey and you don't need a SurveyMonkey account to do it (just close the annoying pop-up window if

Cell Genomics, 2021

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by ena... more The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

F1000Research, 2016

With biomedical research becoming ever more computationally intensive, the challenge is to find s... more With biomedical research becoming ever more computationally intensive, the challenge is to find sophisticated software tools that can keep pace with new requirements, while still being easy to use and secure. We describe a technical implementation of an infrastructure to manage the full research ecosystem from participant management, to data and sample collection, and finally to data storage, interrogation and analysis. This infrastructure, known as the Biomedical Research Infrastructure Software as a Service Kit (BRISSKit http://www.brisskit.le.ac.uk), is built on open source solutions throughout, and demonstrates that it is possible for a biomedical research platform to be supplied as a service.