Relevant bibliographies by topics / Scientific workflow and FAIR protocols

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers
  5. Reports

Academic literature on the topic 'Scientific workflow and FAIR protocols'

Author: Grafiati
Published: 25 May 2024
Last updated: 31 July 2025

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Journal articles on the topic "Scientific workflow and FAIR protocols"

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Celebi, Remzi, Joao Rebelo Moreira, Ahmed A. Hassan, et al. "Towards FAIR protocols and workflows: the OpenPREDICT use case." PeerJ Computer Science 6 (September 21, 2020): e281. http://dx.doi.org/10.7717/peerj-cs.281.

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It is essential for the advancement of science that researchers share, reuse and reproduce each other’s workflows and protocols. The FAIR principles are a set of guidelines that aim to maximize the value and usefulness of research data, and emphasize the importance of making digital objects findable and reusable by others. The question of how to apply these principles not just to data but also to the workflows and protocols that consume and produce them is still under debate and poses a number of challenges. In this paper we describe a two-fold approach of simultaneously applying the FAIR prin
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Yuen, Denis, Louise Cabansay, Andrew Duncan, et al. "The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols." Nucleic Acids Research 49, W1 (2021): W624—W632. http://dx.doi.org/10.1093/nar/gkab346.

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Abstract Dockstore (https://dockstore.org/) is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows. The platform has facilitated large-scale biomedical research collaborations by using cloud technologies to increase the Findability, Accessibility, Interoperability and Reusability (FAIR) of computational resources, thereby promoting the reproducibility of complex bioinformatics analyses. Dockstore supports a variety of source repositories, analysis frameworks, and language technologies to provide a seamless publishing platform for authors to create a
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Soiland-Reyes, Stian, Peter Sefton, Leyla Jael Castro, et al. "Creating lightweight FAIR Digital Objects with RO-Crate." Research Ideas and Outcomes 8 (October 12, 2022): e93937. https://doi.org/10.3897/rio.8.e93937.

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RO-Crate (Soiland-Reyes et al. 2022) is a lightweight method to package research outputs along with their metadata, based on Linked Data principles (Bizer et al. 2009) and W3C standards. RO-Crate provides a flexible mechanism for researchers archiving and publishing rich data packages (or any other research outcome) by capturing their dependencies and context. However, additional measures should be taken to ensure that a crate is also following the FAIR principles (Wilkinson 2016), including consistent use of persistent identifiers, provenance, community standards, clear machine/human-readable
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Mozzherin, Dmitry, Deborah Paul, and Amanda Whitmire. "Can We Standardize Name Reconciliaton via OpenRefine?" Biodiversity Information Science and Standards 8 (August 19, 2024): e134910. https://doi.org/10.3897/biss.8.134910.

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Scientific names in biodiversity represent one of the oldest identifiers used in science. As a result, a common repetitive task is being able to reconcile a list of scientific names against curated data sources. Reconciliation allows one to determine if names in a list are spelled correctly, whether they are currently accepted, and their nomenclatural status. There are several online and local resources that provide reconciliation services. We share here the potential in interoperability across reconciliation tools.Global Names Verifier (GNverifier), Catalogue of Life, Global Biodiversity Info
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Rios, Nelson, Sharif Islam, James Macklin, and Andrew Bentley. "Technical Considerations for a Transactional Model to Realize the Digital Extended Specimen." Biodiversity Information Science and Standards 5 (September 3, 2021): e73812. https://doi.org/10.3897/biss.5.73812.

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Technological innovations over the past two decades have given rise to the online availability of more than 150 million specimen and species-lot records from biological collections around the world through large-scale biodiversity data-aggregator networks. In the present landscape of biodiversity informatics, collections data are captured and managed locally in a wide variety of databases and collection management systems and then shared online as point-in-time Darwin Core archive snapshots. Data providers may publish periodic revisions to these data files, which are retrieved, processed and r
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Penev, Lyubomir, Dimitrios Koureas, Quentin Groom, et al. "The Biodiversity Knowledge Hub (BKH): a crosspoint and knowledge broker for FAIR and linked biodiversity data." Biodiversity Information Science and Standards 7 (August 24, 2023): e111482. https://doi.org/10.3897/biss.7.111482.

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The Biodiversity Knowledge Hub (BKH) is a web platform acting as an integration point and broker of an open, FAIR (Findable, Accessible, Interoperable, Reusable) and interlinked corpora of biodiversity data, services and knowledge. It serves the entire biodiversity research cycle, from specimens and observations to sequences, taxon names and finally to scientific publications. The strategic aim of the BKH is to support a functional and integrated biodiversity knowledge graph and an emerging new community of users. The BKH is aimed at biodiversity researchers in the widest sense, research infra
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Dillen, Mathias, Pieter Huybrechts, Quentin Groom, and Lynn Delgat. "Calculating the Digitization Level of Specimens with the Minimum Information about a Digital Specimen (MIDS) Standard." Biodiversity Information Science and Standards 6 (August 1, 2022): e90879. https://doi.org/10.3897/biss.6.90879.

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Natural history specimens constitute physical evidence for past observations of nature. They hold further value as the backbone of taxonomy and as historical samples that can be subjected to further analysis. Yet, as physical objects scattered across collections around the world, their scientific use cases are limited by an overall lack of FAIRness, i.e. not easily Findable, Accessible, Interoperable or Reusable. Digitization of these specimens through imaging and categorical metadata capture can improve this FAIRness and has been done to some extent for decades already, but only recently have
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Peterseil, Johannes, Alexandre Belleflamme, Alessandro Oggioni, et al. "Advancing Scientific Research through Well-Defined and Standardized Data Products in eLTER." ARPHA Conference Abstracts 8 (May 28, 2025): e151888. https://doi.org/10.3897/aca.8.e151888.

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The scientific community increasingly relies on high-quality data products to drive research, enable cross-disciplinary studies and inform decision-making. The eLTER RI, as a European scale research infrastructure, aims to monitor the key characteristics of ecosystems and biodiversity and their response to global change and provide data streams as one of its services. In this context, the Whole System Approach (WAILS) and the derived eLTER Standard Observations (SOs) provide the scientific framework and protocols not only for data collection but also for integrating legacy data from long-term
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Zulfiqar, Mahnoor, Michael R. Crusoe, Birgitta König-Ries, Christoph Steinbeck, Kristian Peters, and Luiz Gadelha. "Implementation of FAIR Practices in Computational Metabolomics Workflows—A Case Study." Metabolites 14, no. 2 (2024): 118. http://dx.doi.org/10.3390/metabo14020118.

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Scientific workflows facilitate the automation of data analysis tasks by integrating various software and tools executed in a particular order. To enable transparency and reusability in workflows, it is essential to implement the FAIR principles. Here, we describe our experiences implementing the FAIR principles for metabolomics workflows using the Metabolome Annotation Workflow (MAW) as a case study. MAW is specified using the Common Workflow Language (CWL), allowing for the subsequent execution of the workflow on different workflow engines. MAW is registered using a CWL description on Workfl
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Hemani, Yousuf, Kilian Koch, Oscar Mendo-Diaz, Anusch Bachhofner, Simone Baffelli, and Davide Bleiner. "The openBIS Digital Platform for Instrumentation and Data Workflow in the Analytical Laboratory." CHIMIA 79, no. 1-2 (2025): 36–45. https://doi.org/10.2533/chimia.2025.36.

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The management of scientific data plays a key role in all research areas and has increased in importance. Providing researchers with customizable data management tools is crucial for effectively managing data according to the FAIR principles. These principles have been defined by Wilkinson et al. in 2016, which describe how scientific data should be managed.[1] To support the specific needs of researchers at Empa, openBIS[2] was chosen as a FAIR compliant data management platform. OpenBIS is an Electronic Laboratory Notebook (ELN) and Laboratory Information Management System (LIMS) developed a
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Dissertations / Theses on the topic "Scientific workflow and FAIR protocols"

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Djaffardjy, Marine. "Pipelines d'Analyse Bioinformatiques : solutions offertes par les Systèmes de Workflows, Cadre de représentation et Étude de la Réutilisation." Electronic Thesis or Diss., université Paris-Saclay, 2023. http://www.theses.fr/2023UPASG059.

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La bioinformatique est un domaine multidisciplinaire qui combine biologie, informatique et statistiques, permettant de mieux comprendre les mécanismes du vivant.Son fondement repose essentiellement sur l'analyse des données biologiques.L'émergence de nouvelles technologies, en particulier les avancées majeures dans le domaine du séquençage, a entraîné une croissance exponentielle des données, posant de nouveaux défis en matière d'analyse et de gestion des données.Pour exploiter ces données, des pipelines sont utilisés, enchaînant des outils et des processus informatiques pour conduire les anal
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Book chapters on the topic "Scientific workflow and FAIR protocols"

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Li, Yin, Yuyin Ma, and Ziyang Zeng. "A Novel Approach to Location-Aware Scheduling of Workflows Over Edge Computing Resources." In Research Anthology on Edge Computing Protocols, Applications, and Integration. IGI Global, 2022. http://dx.doi.org/10.4018/978-1-6684-5700-9.ch016.

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Edge computing is pushing the frontier of computing applications, data, and services away from centralized nodes to the logical extremes of a network. A major technological challenge for workflow scheduling in the edge computing environment is cost reduction with service-level-agreement (SLA) constraints in terms of performance and quality-of-service requirements because real-world workflow applications are constantly subject to negative impacts (e.g., network congestions, unexpected long message delays, shrinking coverage, range of edge servers due to battery depletion. To address the above c
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Ferreira da Silva, Rafael, Tristan Glatard, and Frédéric Desprez. "Self-Management of Operational Issues for Grid Computing." In Advances in Systems Analysis, Software Engineering, and High Performance Computing. IGI Global, 2015. http://dx.doi.org/10.4018/978-1-4666-8213-9.ch006.

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Science gateways, such as the Virtual Imaging Platform (VIP), enable transparent access to distributed computing and storage resources for scientific computations. However, their large scale and the number of middleware systems involved in these gateways lead to many errors and faults. This chapter addresses the autonomic management of workflow executions on science gateways in an online and non-clairvoyant environment, where the platform workload, task costs, and resource characteristics are unknown and not stationary. The chapter describes a general self-management process based on the MAPE-
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Martínez-García, Alicia, Giorgio Cangioli, Catherine Chronaki, et al. "FAIRness for FHIR: Towards Making Health Datasets FAIR Using HL7 FHIR." In MEDINFO 2021: One World, One Health – Global Partnership for Digital Innovation. IOS Press, 2022. http://dx.doi.org/10.3233/shti220024.

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Medical data science aims to facilitate knowledge discovery assisting in data, algorithms, and results analysis. The FAIR principles aim to guide scientific data management and stewardship, and are relevant to all digital health ecosystem stakeholders. The FAIR4Health project aims to facilitate and encourage the health research community to reuse datasets derived from publicly funded research initiatives using the FAIR principles. The ‘FAIRness for FHIR’ project aims to provide guidance on how HL7 FHIR could be utilized as a common data model to support the health datasets FAIRification proces
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Conference papers on the topic "Scientific workflow and FAIR protocols"

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Menager, H., and Z. Lacroix. "A Workflow Engine for the Execution of Scientific Protocols." In 22nd International Conference on Data Engineering Workshops (ICDEW'06). IEEE, 2006. http://dx.doi.org/10.1109/icdew.2006.24.

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Koderi, Harikrishnan, Vladimirs Šatrevičs, and Irina Voronova. "IDENTIFICATION OF HUMAN FACTORS AND USER EXPERIENCE IN A REMOTE ENVIRONMENT." In 12th International Scientific Conference „Business and Management 2022“. Vilnius Gediminas Technical University, 2022. http://dx.doi.org/10.3846/bm.2022.737.

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The pandemic had caused a worldwide disruption introducing new and extraordinary challenges. Social dis-tancing and new protocols ensuring safety for people derived new models of work environments. Moreover, when we deal with our physical health, introducing new ways to interact and work in this new remote covid workflow it is also essential to take care of our mental health. Globally, due to the new adjusted routines in all aspects had opened a new remote world. The research identified human factors and user experience influencing the remote environments, there is a significant negative relat
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Bakota, Boris. "EUROPEAN COURT OF HUMAN RIGHTS AND THE EUROPEAN GREEN DEAL." In International Scientific Conference “Digitalization and Green Transformation of the EU“. Faculty of Law, Josip Juraj Strossmayer University of Osijek, 2023. http://dx.doi.org/10.25234/eclic/27448.

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The European Green Deal aims to make Europe the first climate-neutral continent by 2050 and maps a new and inclusive growth strategy to boost the economy, improve people’s health and quality of life, care for nature, etc. EU Farm to Fork Strategy for fair, healthy and environmentally- friendly food system, among others, asks for „moving to a more plant-based diet“. Plant-based diet is a diet consisting mostly or entirely of plant-based foods. Plant-based diet does not exclude meat or dietary products totally, but the emphasis should be on plants. Vegetarianism is the practice of abstaining fro
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van Mastrigt, Pieter, and Michael J. Quinn. "Reducing Uncertainties to Shape the Future of Exploration." In International Petroleum Technology Conference. IPTC, 2021. http://dx.doi.org/10.2523/iptc-21339-ms.

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Abstract For any given Exploration oil and gas portfolio and associated opportunities, successful business decisions can only be made on the basis of technically robust estimates of the subsurface risk versus the resource potential and estimate of the associated upside(s). Ideally, these estimates should incorporate the entire spectrum of opportunities for the complete portfolio and they should be made in a consistent and comparable way. However, as Explorers, we are often faced with data that is incomplete, limited, of variable quality, and/or inconsistent. As a result, subsurface evaluation
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Reports on the topic "Scientific workflow and FAIR protocols"

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Kopte, Robert. OSADCP Toolbox. GEOMAR, 2024. http://dx.doi.org/10.3289/sw_2_2024.

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Vessel-mounted Acoustic Doppler Current Profilers (ADCPs) provide velocity profiles of the upper ocean along the ship track. They are a key tool in oceanographic research to study the oceanic circulation and the associated distribution of mass, heat, contaminants and other tracers. In order to obtain high-quality ocean current data from vessel-mounted ADCP measurements, a number of requirements must be met, from system installation and data acquisition measures to certain essential processing steps. Here, we collect key points on ADCP data acquisition in general and on the characteristics and
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