The slides used for a lecture given at the University of York, where I introduced the FAIR principles and FAIRsharing, and put them in the context of ELIXIR and ELIXIR UK. FAIRsharing is an informative and educational resource on interlinked standards, databases and policies, three key elements of the FAIR ecosystem. FAIRsharing is adopted by funders, publishers and communities across all research disciplines. It promotes the existence and value of these resources to aid data discovery, interoperability and sharing across all of our stakeholder groups. Here we discuss how FAIRsharing can be searched and updated by our user community, and how you can make the best use out of it as part of a broader data management infrastructure.
AgBioData and FAIRsharing: FAIRsharing: promoting the discovery of data stand...Allyson Lister
Video of this presentation: https://www.youtube.com/watch?v=nNl1oUvWYJE&t=240s
FAIRsharing is an informative and educational resource on interlinked standards, repositories and policies, three key elements of the FAIR ecosystem. FAIRsharing promotes the existence and value of these standards, repositories and policies, fostering a culture change within the research community into one where the use of these resources for FAIRer data is pervasive and seamless. This is achieved by guiding consumers to discover, select and use these resources with confidence, and helping producers to make their resources more visible, more widely adopted and cited. This presentation will highlight key collaborative, successful activities as well as next steps within FAIRsharing. It will also provide information on how to become a recommended repository in FAIRsharing and how to use FAIRsharing to engage with your stakeholders as well as with journal publishers and their data policies.
2021 04 Introduction to FAIRsharing - cinecaAllyson Lister
Part of the The “How FAIR are you” webinar series and hackathon, which aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.
More information at
* the webinar page: https://www.cineca-project.eu/news-events-all/how-fair-are-you-hackathon
* the recording of the talk: https://www.youtube.com/watch?v=UdGZOynyuGo
FAIRsharing: curating an ecosystem of research standards and databasesAllyson Lister
FAIRsharing is an informative and educational resource on interlinked standards, databases and policies, three key elements of the FAIR ecosystem. FAIRsharing is adopted by funders, publishers and communities across all research disciplines. It promotes the existence and value of these resources to aid data sharing and consequently requires a high standard of curation to ensure accurate and timely information is provided for all of our stakeholder groups. Here we discuss the methods employed and challenges faced during curation and maintenance of existing content as well as the introduction of new features. We will describe how our curation team uses a blend of manual and semi-automated curation to work on individual records and across large subsets of the registry. We also will discuss the benefits of both in-house curation and community-driven curation provided by our stakeholder groups.
FAIRsharing: discover and curate an ecosystem of research standards and datab...Allyson Lister
FAIRsharing helps many user communities to enhance discoverability of both their resources (databases, standards, policies) and the data they produce. Find out how FAIRsharing can help enable FAIR data as well as findability of resources for the multi-omics domain as part of a presentation for ECCB 2022 (NTB W02) at the "FAIRification of multi-omics metadata" workshop.
2022-11-09 National Biodiversity Network Conference - FAIRsharing and Biodive...Allyson Lister
FAIRsharing (https://fairsharing.org/) works closely with its user community to aid discoverability of their data resources and to help enable FAIR data. The relationships we build (both at a social and a data level) are at the core of FAIRsharing, making it an essential part of FAIR research data management. Our collaboration with the biodiversity community is a prime example of the success of such community engagement.
The role of FAIRsharing in assessing FAIRness of digital objects: we assist, not assess. The workshop brought together a number of FAIR evaluation tools to discuss and design common FAIR tests to ensure tools deliver consistet results. Our presentation illustrates how FAIRsharing's content helps and how FAIRsharing's service contributes. The work will contribute to the work of the EOSC FAIR Metrics Task Force.
Presentation to the EOSC workshop on policies (https://www.google.com/url?q=https://eoscfuture.eu/eventsfuture/monitoring-eosc-readiness-fair-data-policies) on what FAIRsharing does for policies, including providing registration, discovery, flexible and clearer descriptions, relationships, machine readability and comparability.
AgBioData and FAIRsharing: FAIRsharing: promoting the discovery of data stand...Allyson Lister
Video of this presentation: https://www.youtube.com/watch?v=nNl1oUvWYJE&t=240s
FAIRsharing is an informative and educational resource on interlinked standards, repositories and policies, three key elements of the FAIR ecosystem. FAIRsharing promotes the existence and value of these standards, repositories and policies, fostering a culture change within the research community into one where the use of these resources for FAIRer data is pervasive and seamless. This is achieved by guiding consumers to discover, select and use these resources with confidence, and helping producers to make their resources more visible, more widely adopted and cited. This presentation will highlight key collaborative, successful activities as well as next steps within FAIRsharing. It will also provide information on how to become a recommended repository in FAIRsharing and how to use FAIRsharing to engage with your stakeholders as well as with journal publishers and their data policies.
2021 04 Introduction to FAIRsharing - cinecaAllyson Lister
Part of the The “How FAIR are you” webinar series and hackathon, which aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.
More information at
* the webinar page: https://www.cineca-project.eu/news-events-all/how-fair-are-you-hackathon
* the recording of the talk: https://www.youtube.com/watch?v=UdGZOynyuGo
FAIRsharing: curating an ecosystem of research standards and databasesAllyson Lister
FAIRsharing is an informative and educational resource on interlinked standards, databases and policies, three key elements of the FAIR ecosystem. FAIRsharing is adopted by funders, publishers and communities across all research disciplines. It promotes the existence and value of these resources to aid data sharing and consequently requires a high standard of curation to ensure accurate and timely information is provided for all of our stakeholder groups. Here we discuss the methods employed and challenges faced during curation and maintenance of existing content as well as the introduction of new features. We will describe how our curation team uses a blend of manual and semi-automated curation to work on individual records and across large subsets of the registry. We also will discuss the benefits of both in-house curation and community-driven curation provided by our stakeholder groups.
FAIRsharing: discover and curate an ecosystem of research standards and datab...Allyson Lister
FAIRsharing helps many user communities to enhance discoverability of both their resources (databases, standards, policies) and the data they produce. Find out how FAIRsharing can help enable FAIR data as well as findability of resources for the multi-omics domain as part of a presentation for ECCB 2022 (NTB W02) at the "FAIRification of multi-omics metadata" workshop.
2022-11-09 National Biodiversity Network Conference - FAIRsharing and Biodive...Allyson Lister
FAIRsharing (https://fairsharing.org/) works closely with its user community to aid discoverability of their data resources and to help enable FAIR data. The relationships we build (both at a social and a data level) are at the core of FAIRsharing, making it an essential part of FAIR research data management. Our collaboration with the biodiversity community is a prime example of the success of such community engagement.
The role of FAIRsharing in assessing FAIRness of digital objects: we assist, not assess. The workshop brought together a number of FAIR evaluation tools to discuss and design common FAIR tests to ensure tools deliver consistet results. Our presentation illustrates how FAIRsharing's content helps and how FAIRsharing's service contributes. The work will contribute to the work of the EOSC FAIR Metrics Task Force.
Presentation to the EOSC workshop on policies (https://www.google.com/url?q=https://eoscfuture.eu/eventsfuture/monitoring-eosc-readiness-fair-data-policies) on what FAIRsharing does for policies, including providing registration, discovery, flexible and clearer descriptions, relationships, machine readability and comparability.
FAIRsharing consists of three registries: data standards, databases and data policies. This short talk focuses on the FAIRsharing data policy registry, and how including your institutional, funder, publisher, journal, society, project in FAIRsharing can improve findability and machine readability of your policy
A presentation on FAIR, FAIRsharing and the FAIR ecosystem for the ENVRI-FAIR community on the 13th December 2019. This presentation covers the basics of what FAIR is, how FAIRsharing can help 'FAIRify' standards, repositories, knowledgebases and data policies, and then the connections FAIRsharing has with other initiatives, such as the FAIR Evaluator, Data Stewardship Wizard, our RDA WG, GO-FAIR and EOSC-Life.
A 10 minute presentation for the virtual ELIXIR All Hands Meeting 2020 - FAIRification mini symposium. In this presentation I talk about some of the community work we do in FAIRsharing, from sharing our metadata with other resources to research on data policy repository criteria.
FAIRsharing as a content provider for maDMPAllyson Lister
How FAIRsharing can help provide content for the creation of machine-actionable Data Management Plans.
Part of the DCC's "Machine Actionable DMP Workshop" co-located at the RDA Plenary, March 2023 (https://www.dcc.ac.uk/events)/RDAcolocated_machine_actionable_DMPs
FAIRsharing: curation and governance of an ecosystem of research standards an...Allyson Lister
FAIRsharing is an informative and educational resource on interlinked standards (including terminologies), databases and policies, three key elements of the FAIR ecosystem. FAIRsharing is adopted by funders, publishers and communities across all research disciplines. It promotes the existence and value of these resources to aid data sharing and consequently requires a high standard of curation to ensure accurate and timely information is provided across all of our stakeholder groups. Here I discuss the methods employed and challenges faced during curation and maintenance of existing content, as well as the introduction of new features. I will cover how we store machine- and human-accessible metadata, including governance information, and the methods we use to determine what common metadata we should describe. I also will discuss the benefits of both in-house curation and community-driven curation by our stakeholder groups.
EOSC-Life AGM 2022 Publishing FAIR RI data resources in EOSC.pdfAllyson Lister
FAIRsharing uses collections to create community-specific views of the resource descriptions we store and the relationships among them. This talk describes the work by EOSC-Life Work Package 1 to update and enrich the EOSC-Life collection, which groups together all resources created by EOSC-Life partners. Part of the EOSC-Life AGM 2022 (https://www.eosc-life.eu/news/3rd-agm/).
FAIRsharing and DataCite: Data Repository Selection- Criteria That MatterSusanna-Assunta Sansone
Through a collaboration with Datacite, FAIRsharing is working with a number of journal publishers (PLOS, Springer Nature, F1000, Wiley, Taylor and Francis, Elsevier, EMBO Press, eLife, GigaScience and Cambridge University Press) to identify a common set of criteria for selecting and recommending data repositories (and associated standards) that will be implemented in FAIRsharing. Details of this work and participants at https://osf.io/m2bce
Making Repositories FAIR (via metadata in FAIRsharing.orgPeter McQuilton
A 10 minute presentation on how we can make repositories FAIR, primarily through storing their metadata on FAIRsharing.org. Presented at the FAIRsFAIR FAIR Semantics & FAIR Repositories pre-RDA P14 meeting in Helsinki, Finland on the 22nd October 2019. FAIRsharing can be used to edit and store metadata on repositories from across the natural sciences, engineering sciences, social sciences and humanities. This metadata is marked-up in schema.org and bioschemas (where relevant) and is given a citable DOI. This metadata can be used to power DMP tools and wizards and can also be used to perform FAIR assessments, such as through the FAIR evaluator or FAIRshake.
Connecting communities to promote FAIR resources: perspectives from an RDA / ...Allyson Lister
Connecting communities to promote FAIR resources: perspectives from an RDA / EOSC Future Domain Ambassador
https://www.rd-alliance.org/connecting-communities-promote-fair-resources-perspectives-rda-eosc-future-domain-ambassador
As part of Allyson Lister's RDA / EOSC Future Ambassadorship, she has launched the FAIRsharing Content & Community Programme, which brings together discipline experts to curate FAIRsharing content and create FAIR educational material. In return, they are attributed for their efforts, gain expertise and become a part of a network of like-minded data enthusiasts that, as a result of the will continue for years to come. This event will highlight the work of these enthusiastic domain experts, and how they have worked to connect their communities with the material and resources they need. This event will summarise the importance of and challenges facing the RDA and EOSC future in effective community building as well as dissemination of outputs.
These slides were presented at the RDA webinar of the same name on November 22, 2023.
A 10 minute presentation given at the RDA UK meeting in London (Jan 2019). This presentation covers FAIRsharing work as part of the RDA/Force11 FAIRsharing WG.
Brief introduction to FAIRsharing work with industry (publishers, pharmas) and the FAIR Cookbook (for the Life Science): https://www.opensciencefair.eu/2021/workshops/applying-fair-principles-to-open-science-and-industry-to-drive-innovation-challenges-and-opportunities
RDA Data Innovation Forum: FAIRsharing.org, an output of the joint RDA/Force ...Peter McQuilton
A 15 minute presentation at the RDA Data Innovation Forum in Brussels on the 20th January. This presentation covers the RDA/Force11 WG and FAIRsharing, mapping the landscape of data standards, databases and data policies.
A short presentation I use within my STEM Ambassador work as a simple explanation of DNA, genes and genetics to KS1-KS2. Notes are provided to help with accompanying text for the presentation.
This presentation accompanies my practical for kids where they build sweetie DNA with jelly babies, toothpicks and licorice laces.
Working with Genes: Introduction to DNA, Genes and GeneticsAllyson Lister
A short presentation I use within my STEM Ambassador work as a simple explanation of DNA, genes and genetics to KS1-KS2. Notes are provided to help with accompanying text for the presentation.
More Related Content
Similar to A Whirlwind tour of the FAIR Principles, ELIXIR, and FAIRsharing in the context of research data management (RDM)
FAIRsharing consists of three registries: data standards, databases and data policies. This short talk focuses on the FAIRsharing data policy registry, and how including your institutional, funder, publisher, journal, society, project in FAIRsharing can improve findability and machine readability of your policy
A presentation on FAIR, FAIRsharing and the FAIR ecosystem for the ENVRI-FAIR community on the 13th December 2019. This presentation covers the basics of what FAIR is, how FAIRsharing can help 'FAIRify' standards, repositories, knowledgebases and data policies, and then the connections FAIRsharing has with other initiatives, such as the FAIR Evaluator, Data Stewardship Wizard, our RDA WG, GO-FAIR and EOSC-Life.
A 10 minute presentation for the virtual ELIXIR All Hands Meeting 2020 - FAIRification mini symposium. In this presentation I talk about some of the community work we do in FAIRsharing, from sharing our metadata with other resources to research on data policy repository criteria.
FAIRsharing as a content provider for maDMPAllyson Lister
How FAIRsharing can help provide content for the creation of machine-actionable Data Management Plans.
Part of the DCC's "Machine Actionable DMP Workshop" co-located at the RDA Plenary, March 2023 (https://www.dcc.ac.uk/events)/RDAcolocated_machine_actionable_DMPs
FAIRsharing: curation and governance of an ecosystem of research standards an...Allyson Lister
FAIRsharing is an informative and educational resource on interlinked standards (including terminologies), databases and policies, three key elements of the FAIR ecosystem. FAIRsharing is adopted by funders, publishers and communities across all research disciplines. It promotes the existence and value of these resources to aid data sharing and consequently requires a high standard of curation to ensure accurate and timely information is provided across all of our stakeholder groups. Here I discuss the methods employed and challenges faced during curation and maintenance of existing content, as well as the introduction of new features. I will cover how we store machine- and human-accessible metadata, including governance information, and the methods we use to determine what common metadata we should describe. I also will discuss the benefits of both in-house curation and community-driven curation by our stakeholder groups.
EOSC-Life AGM 2022 Publishing FAIR RI data resources in EOSC.pdfAllyson Lister
FAIRsharing uses collections to create community-specific views of the resource descriptions we store and the relationships among them. This talk describes the work by EOSC-Life Work Package 1 to update and enrich the EOSC-Life collection, which groups together all resources created by EOSC-Life partners. Part of the EOSC-Life AGM 2022 (https://www.eosc-life.eu/news/3rd-agm/).
FAIRsharing and DataCite: Data Repository Selection- Criteria That MatterSusanna-Assunta Sansone
Through a collaboration with Datacite, FAIRsharing is working with a number of journal publishers (PLOS, Springer Nature, F1000, Wiley, Taylor and Francis, Elsevier, EMBO Press, eLife, GigaScience and Cambridge University Press) to identify a common set of criteria for selecting and recommending data repositories (and associated standards) that will be implemented in FAIRsharing. Details of this work and participants at https://osf.io/m2bce
Making Repositories FAIR (via metadata in FAIRsharing.orgPeter McQuilton
A 10 minute presentation on how we can make repositories FAIR, primarily through storing their metadata on FAIRsharing.org. Presented at the FAIRsFAIR FAIR Semantics & FAIR Repositories pre-RDA P14 meeting in Helsinki, Finland on the 22nd October 2019. FAIRsharing can be used to edit and store metadata on repositories from across the natural sciences, engineering sciences, social sciences and humanities. This metadata is marked-up in schema.org and bioschemas (where relevant) and is given a citable DOI. This metadata can be used to power DMP tools and wizards and can also be used to perform FAIR assessments, such as through the FAIR evaluator or FAIRshake.
Connecting communities to promote FAIR resources: perspectives from an RDA / ...Allyson Lister
Connecting communities to promote FAIR resources: perspectives from an RDA / EOSC Future Domain Ambassador
https://www.rd-alliance.org/connecting-communities-promote-fair-resources-perspectives-rda-eosc-future-domain-ambassador
As part of Allyson Lister's RDA / EOSC Future Ambassadorship, she has launched the FAIRsharing Content & Community Programme, which brings together discipline experts to curate FAIRsharing content and create FAIR educational material. In return, they are attributed for their efforts, gain expertise and become a part of a network of like-minded data enthusiasts that, as a result of the will continue for years to come. This event will highlight the work of these enthusiastic domain experts, and how they have worked to connect their communities with the material and resources they need. This event will summarise the importance of and challenges facing the RDA and EOSC future in effective community building as well as dissemination of outputs.
These slides were presented at the RDA webinar of the same name on November 22, 2023.
A 10 minute presentation given at the RDA UK meeting in London (Jan 2019). This presentation covers FAIRsharing work as part of the RDA/Force11 FAIRsharing WG.
Brief introduction to FAIRsharing work with industry (publishers, pharmas) and the FAIR Cookbook (for the Life Science): https://www.opensciencefair.eu/2021/workshops/applying-fair-principles-to-open-science-and-industry-to-drive-innovation-challenges-and-opportunities
RDA Data Innovation Forum: FAIRsharing.org, an output of the joint RDA/Force ...Peter McQuilton
A 15 minute presentation at the RDA Data Innovation Forum in Brussels on the 20th January. This presentation covers the RDA/Force11 WG and FAIRsharing, mapping the landscape of data standards, databases and data policies.
A short presentation I use within my STEM Ambassador work as a simple explanation of DNA, genes and genetics to KS1-KS2. Notes are provided to help with accompanying text for the presentation.
This presentation accompanies my practical for kids where they build sweetie DNA with jelly babies, toothpicks and licorice laces.
Working with Genes: Introduction to DNA, Genes and GeneticsAllyson Lister
A short presentation I use within my STEM Ambassador work as a simple explanation of DNA, genes and genetics to KS1-KS2. Notes are provided to help with accompanying text for the presentation.
An introduction to DNA for kids aged about 8, as I originally aimed it at Year 3 (Key Stage 2). This ties to two short practicals: making sweetie DNA and drawing their own chalk masterpiece of "fluorescent bacteria"
Systems Biology Model Semantics and IntegrationAllyson Lister
A short description of my research experiences using OWL to perform semantic data integration and, ultimately, the addition of annotation for systems biology models.
Saint: A Lightweight Model Annotation and Data Integration ToolAllyson Lister
A talk given by Allyson Lister at BioSysBio (http://conferences.theiet.org/biosysbio/) in March 2009. Describes Saint, a lightweight model annotation and data integration tool. You can find out more at http://saint-annotate.sourceforge.net. CellML support is coming soon.
Annotation of SBML Models Through Rule-Based Semantic IntegrationAllyson Lister
This talk was given on June 28, 2009 at the Bio-Ontologies SIG as part of ISMB/ECCB 2009. You can download the paper this presentation is about from http://hdl.handle.net/10101/npre.2009.3286.1. More information on the ISMB conference is available at http://www.iscb.org/ismbeccb2009/ and http://friendfeed.com/ismbeccb2009
Working with Genes: A Presentation for Children (Key Stages 1 and 2)Allyson Lister
This is a presentation I gave in the Fall of 2008 as part of the Teacher Scientist Network at a grammar school in the UK. The slides were used with both Key Stages 1 and 2, with the audio content (i.e. what I said) varying between the two age groups. For non-UK people, Key Stages 1 and 2 cover ages 5-11. For more info, see my post: http://themindwobbles.wordpress.com/2008/11/07/scientist-meets-small-children-and-doesnt-stop-talking-and-listening-all-day/
And for notes on each slide, see http://themindwobbles.wordpress.com/2009/05/20/slides-and-notes-available-on-working-with-genes-presentation-for-kids/
SyMBA (http://symba.sf.net) is a data archive and integrator based on Version 1 of the Functional Genomics Experiment (FuGE, http://fuge.sf.net) Object Model (FuGE-OM), and which archives, stores, and retrieves raw high-throughput data. Until now, few published systems have successfully integrated multiple omics data types and information about experiments in a single database. SyMBA includes a database back-end, expert and standard interfaces, and a Life Science Identifier (LSID) Resolution and Assigning service to identify objects and provide programmatic access to the database. Having a central data repository prevents deletion, loss, or accidental modification of primary data, while giving convenient access to the data for publication and analysis. It also provides a central location for storage of metadata for the high-throughput data sets, and will facilitate subsequent data integration strategies.
We encourage the use, installation and development of SyMBA by other groups. Please let us know if you are interested in using or evaluating SyMBA for use at your own Centre. Contact us: symba-devel at lists.sourceforge.net
BREEDING METHODS FOR DISEASE RESISTANCE.pptxRASHMI M G
Plant breeding for disease resistance is a strategy to reduce crop losses caused by disease. Plants have an innate immune system that allows them to recognize pathogens and provide resistance. However, breeding for long-lasting resistance often involves combining multiple resistance genes
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
Abnormal or anomalous secondary growth in plants. It defines secondary growth as an increase in plant girth due to vascular cambium or cork cambium. Anomalous secondary growth does not follow the normal pattern of a single vascular cambium producing xylem internally and phloem externally.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
A Whirlwind tour of the FAIR Principles, ELIXIR, and FAIRsharing in the context of research data management (RDM)
1. CC BY-SA 4.0 International
An ecosystem of research standards and databases
for effective RDM
University of York: 26 April 2022
@FAIRsharing_org
contact@fairsharing.org
10.25504/FAIRsharing.2abjs5
datareadiness.eng.ox.ac.uk
Allyson Lister, PhD
FAIRsharing - Content and Community Coordinator
Senior Knowledge Engineer
ORCiD: 0000-0002-7702-4495
2. CC BY-SA 4.0 International
Metadata is a love
note to the future
Jason Scott https://twitter.com/textfiles/status/119403173436850176 (2011)
3. CC BY-SA 4.0 International
The FAIR Principles:
What they are and why we’re
interested
4. CC BY-SA 4.0 International
Discoveries are made using shared data and this requires data that are:
• Retrievable and structured in standard format(s)
• Self-described so that third parties can make sense of it
The challenge
Forbes article on 2016 Data Scientist Report
https://www.forbes.com/sites/gilpress/2016/03/23/data-preparat
ion-most-time-consuming-least-enjoyable-data-science-task-surve
y-says/#276a35e6f637
Data preparation accounts for about 80% of the work of data scientists
5. CC BY-SA 4.0 International
doi.org/10.2777/02999
The cost of not having FAIR research data
Impact on innovation
6. CC BY-SA 4.0 International
The scholarly publishing
ecosystem is changing
Data-relates mandates by
funders and institutions are
growing
Researchers need
recognition and credit
theconversation.com/how-robots-can-help-us-embrace-a-more-human-view-of-disability-76
815
Human-machine collaboration is the future
o 21% pharmacology data (doi.org/10.1038/nrd3439-c1)
o 11% cancer data (doi.org/10.1038/483531a)
o unsatisfactory in ML (openreview.net/pdf?id=By4l2PbQ-)
towardsdatascience.com/scientific-data-analysis-pipelines-and-reproducibility-75ff9df5b4c5
Reproducibility of published studies is still problematic
Responding to needs
7. CC BY-SA 4.0 International
“Most metadata field names and their values are not standardized
or controlled. Even simple binary or numeric fields are often
populated with inadequate values of different data types”
Standardised description - does it matter? YES
https://doi.org/10.1038/sdata.2019.21
8. CC BY-SA 4.0 International
A set of principles to enhance the
value of all digital resources and its
reuse by humans and machines
Data that is discoverable and reusable at scale
9. CC BY-SA 4.0 International
Findable Accessible Interoperable Reusable
The FAIR Principles in a nutshell
10. CC BY-SA 4.0 International
Globally unique,
resolvable, and
persistent identifiers
To retrieve and
connect data
Community-defined
descriptive metadata
To enhance
discoverability and
interpretability
Community-defined
terminologies
To use the same term
and mean the
same thing
Findable Accessible Interoperable Reusable
11. CC BY-SA 4.0 International
Globally unique,
resolvable, and
persistent identifiers
To retrieve and
connect data
Community-defined
descriptive metadata
To enhance
discoverability and
interpretability
Community-defined
terminologies
To use the same term
and mean the
same thing
Detailed provenance
and workflows
To contextualize the
data and facilitate use in
applications
Terms of access “as
open as possible, as
closed a necessary”
To understand how data
can be accessed
Terms of use and clear
licenses
To enable innovation
and reuse, ensuring
credit as needed
Findable Accessible Interoperable Reusable
12. CC BY-SA 4.0 International
Findable
Accessible
Interoperable
Reusable
Providing for a continuum of features, attributes
and behaviours
FAIR: aspirational guidance
13. CC BY-SA 4.0 International
FAIR: just principles, not practice
14. CC BY-SA 4.0 International
ELIXIR and ELIXIR-UK:
Bringing together life science resources
from across Europe into a single
infrastructure
15. CC BY-SA 4.0 International
ELIXIR –
a sustainable infrastructure for biological data
16. CC BY-SA 4.0 International
https://elixiruknode.org/welcome-to-elixir-uk/about/member-organisations-2/
17. CC BY-SA 4.0 International
Resources to make data FAIR
• ELIXIR’s Recommended Interoperability
Resources.
• These are resources that:
• Establish connections between resources
• Acquire and expose metadata of different
resources
• Create the infrastructure needed to build
integratable data collections
• They will help you translate your data
across databases or resources or find the
best standards for your data.
18. CC BY-SA 4.0 International
FAIR service framework
Ontologies,
formats, reporting
guidelines,
Identifier
Authorities
Metadata
Annotation
&Validation
Citation
Harvesting,
Indexing,
Search
Ontology
Mapping
Identifier
Mapping
Ontology
Lookup
Identifier
resolution
Ontology
Management
Identifier
minting
Standards &
databases
Ontologies Tools Workflows
Identifiers
Registries
Type specific
Mapping &
resolution
Extract-
Transform-Load
APIs
Standard
s
Services Type specific KBs,
integration &
aggregation
Knowledge
19. CC BY-SA 4.0 International
FAIR service framework
Ontologies,
formats, reporting
guidelines,
Identifier
Authorities
Metadata
Annotation
&Validation
Citation
Harvesting,
Indexing,
Search
Ontology
Mapping
Identifier
Mapping
Ontology
Lookup
Identifier
resolution
Ontology
Management
Identifier
minting
Standards &
databases
Ontologies Tools Workflows
Identifiers
Registries
Type specific
Mapping &
resolution
Extract-
Transform-Load
APIs
Standard
s
Services Type specific KBs,
integration &
aggregation
Knowledge
20. CC BY-SA 4.0 International
FAIRsharing in a nutshell:
scope and mission
21. CC BY-SA 4.0 International
Users, adopters, communities and working groups
Including:
An endorsed output of the
FAIRsharing WG
(since 2015):
A WG (since 2015) in:
Researchers in academia,
industry and government
Developers & curators of
resources and tools
Research data facilitators,
librarians, trainers
Society, unions
and community alliances
Journal publishers and
organisations with data policies
Funders and data
policy makers
A recommended resource in EOSC reports
Used by all stakeholder groups
https://fairsharing.org/communities
22. CC BY-SA 4.0 International
Guides consumers to discover, select and use these resources with confidence
Helps producers to make their resources more visible, more widely adopted and cited
Promoting use and value of databases, standards, policies
Total of
over 3584
resources
(Feb 2022)
repositories
standards
policie
s
23. CC BY-SA 4.0 International
Search by subject
Powered by our Subject Ontology of 436 terms
https://fairsharing.org/browse/subject
https://github.com/FAIRsharing/subject-ontology
https://www.ebi.ac.uk/ols/ontologies/srao
24. CC BY-SA 4.0 International
Search by subject
Powered by our Subject Ontology of 436 terms
https://fairsharing.org/browse/subject
https://github.com/FAIRsharing/subject-ontology
https://www.ebi.ac.uk/ols/ontologies/srao
25. CC BY-SA 4.0 International
Search by subject
Powered by our Subject Ontology of 436 terms
https://fairsharing.org/browse/subject
https://github.com/FAIRsharing/subject-ontology
https://www.ebi.ac.uk/ols/ontologies/srao
26. CC BY-SA 4.0 International
Search by subject
Powered by our Subject Ontology of 436 terms
https://fairsharing.org/browse/subject
https://github.com/FAIRsharing/subject-ontology
https://www.ebi.ac.uk/ols/ontologies/srao
27. CC BY-SA 4.0 International
Search by subject
Powered by our Subject Ontology of 436 terms
https://fairsharing.org/browse/subject
https://github.com/FAIRsharing/subject-ontology
https://www.ebi.ac.uk/ols/ontologies/srao
28. CC BY-SA 4.0 International
A repository record:
at-a-glance view
29. CC BY-SA 4.0 International
How to get an account and create/update a record with us:
https://fairsharing.gitbook.io/fairsharing/
30. CC BY-SA 4.0 International
Record page
and general
information
> 40 descriptors including:
● Subject(s) coverage
● Maintainer(s)
● Funder(s)
● Organization(s)
● Access
● Licence(s)
● Publication(s)
● Related resources
https://doi.org/10.25504/FAIRsharing.wkggtx
31. CC BY-SA 4.0 International
Maintainer
Actions
New login options
via our trusted
status with
and also via
36. CC BY-SA 4.0 International
All records have
relationship graphs
https://fairsharing.org/graph/1998
Dryad’s graph, for example, shows the
• standards it implements
• repositories it shares data or code
with
• policies that recommend it
• collections that contain it
37. CC BY-SA 4.0 International
Data
Conditions
and Access
38. CC BY-SA 4.0 International
Data
Conditions
and Access
42. CC BY-SA 4.0 International
Evolution is monitored and reasons provided
43. CC BY-SA 4.0 International
Evolution is monitored and reasons provided
44. CC BY-SA 4.0 International
• Every edit is checked by the in-house
curation team
• Maintainers are notified via email when
their record is updated
In-house curation
and the ‘life cycle
status’ tags
Life cycle tags:
45. CC BY-SA 4.0 International
How do consumers and producers
of standards, repositories and policies
use FAIRsharing and benefit from it?
46. CC BY-SA 4.0 International
Research data facilitators,
librarians, trainers
Use FAIRsharing to provide a
foundation for lectures, training
and teaching material; to plug
into data management planning
tools and other FAIR-supporting
resources.
Funders and data
policy makers
Recommend FAIRsharing to
your awardees or community
to inform development of their
data management plan; select
the appropriate resources to
recommend in your data policy.
Researchers in academia,
industry, government
Use FAIRsharing to identify and
cite the resources that exist for
your discipline when creating a
data management plan,
releasing data or submitting a
manuscript to a journal.
A closer look at our community
47. CC BY-SA 4.0 International
Developers and curators
of resources
Make your standard, database
or repository discoverable by
adding or claiming it in
FAIRsharing; increase exposure
outside your community and
promote adoption.
Journal publishers and
data policy developers
Create personalised
inter-related lists of citable
resources relevant to your
authors, users or their
community; maintain and revise
your recommendation over time.
Learned societies, unions
and associations
Collaborate with FAIRsharing
to raise awareness of your
resource; mobilize your
community to take action to
promote registration, use and
citation of key resources.
A closer look at our community
48. CC BY-SA 4.0 International
Tailored views for education and promotion
Collections are are branded pages that group selected standards and/or repositories
Initiatives and projects have created them for several purposes, e.g. to list resources:
URL: https://fairsharing.org/CrosswalkOfMostUsedMetadataSchemesAndGuidelines
Maintainers
Subjects
Mapped to each other
URL: https://fairsharing.org/RDACovid19WG
Maintainers
Subjects
Recommended by a community
URL: https://fairsharing.org/IVOA
Maintainers
Subjects
Developed by the community
URL: https://fairsharing.org/CDISC
Maintainers
Subjects
Developed by a SDO
49. CC BY-SA 4.0 International
To discover and search the 230 related standards part
of the specification developed by the
ISO Technical Committee on Biotechnology Processes
URL: https://fairsharing.org/ISO20691
Researchers: knowledge graphs to complement lists
URL: https://committee.iso.org/standard/68848.html
50. CC BY-SA 4.0 International
A growing number of FAIR-enabling Services access
FAIRsharing API, and use it as look-up and select
service for standards and repositories for:
● data management plans and guidelines
● FAIR assessment
A new, in-development Data Discovery Service, part
of ELIXIR-driven EOSC-Life and BY-COVID projects:
● register repositories’ access methodologies, e.g.
schema.org, bioschemas, OAI-PMH
● enable (meta)data harvesting
Services: curated content to power 3rd party tools
ds-wizard.org
dmponline.dcc.ac.uk
w3id.org/AmIFAIR
openaire.eu
fairshake.cloud
51. CC BY-SA 4.0 International
How FAIRsharing helps in FAIR evaluation and
RDM / DMP applications
52. CC BY-SA 4.0 International
1. For FAIR evaluation, DMP and other tools/services
it provides a look-up service (via the API) for standards and repositories
2. For developers and users of FAIRness tests and indicators
it provides a searchable registry to describe and discover them
3. For community, organizations and projects
it enables creation of profiles to declare and visual the standards and repositories
they use
4. (future?) For standards, repositories and policies’ owners/maintainer
it could enable them to display a FAIRness level on their record page; along with
the name of the tool used to measure it, a time stamp, and improvement tracking
Ways in which FAIRsharing assists others with FAIRness
53. CC BY-SA 4.0 International
1. For FAIR evaluation, DMP and other
tools/services it provides a look-up service
(via the API) for standards: name, types and
other metadata
To help with questions like:
● what are the types of PID schemas?
● Is SpectralDM the right community
standard data model to describe the
structure of spectrophotometric
datasets?
As a look-up service for standards
Identifiers
Terminologies Guidelines
Formats
830
507
232
21
1590 data and metadata
standards and growing
54. CC BY-SA 4.0 International
1. For FAIR evaluation, DMP and other
tools/services it provides a look-up service
(via the API) for standards: name, types and
other metadata
To help with questions like:
● what are the types of PID schemas?
● Is SpectralDM the right community
standard data model to describe the
structure of spectrophotometric
datasets?
As a look-up service for standards
➔ Be aware: checking ‘compliance’ against standards is not
easy, or even possible for many, due to their narrative
form (checklists) and/or absence of canonical validators;
these challenges are the focus of our pre-print
doi.org/10.5281/zenodo.5596465
55. CC BY-SA 4.0 International
1. For FAIR evaluation, DMP and other
tools/services it provides a look-up service
(via the API) for standards: name, types and
other metadata
To help with questions like:
● what are the types of PID schemas?
● Is SpectralDM the right community
standard data model to describe the
structure of spectrophotometric
datasets?
As a look-up service for standards
➔ Be aware: checking ‘compliance’ against standards is not
easy, or even possible for many, due to their narrative
form (checklists) and/or absence of canonical validators;
these challenges are the focus of our pre-print
doi.org/10.5281/zenodo.5596465
56. CC BY-SA 4.0 International
1. For FAIR evaluation, DMP and other
tools/services it provides a look-up service (via
the API) for repositories: name, types and
other metadata
To help collecting information (at data resource
level), such as the presence and type of:
● licence or terms of use
● datasets accessibility/openness
● accessibility mechanism
● policies (e.g. curation, preservation)
● PIDs schema
● data and metadata standards
● and many others…
As a look-up service for repositories
57. CC BY-SA 4.0 International
1. For FAIR evaluation, DMP and other
tools/services it provides a look-up service (via
the API) for repositories: name, types and
other metadata
To help collecting information (at data resource
level), such as the presence and type of:
● licence or terms of use
● datasets accessibility/openness
● accessibility mechanism
● policies (e.g. curation, preservation)
● PIDs schema
● data and metadata standards
● and many others…
As a look-up service for repositories
58. CC BY-SA 4.0 International
1. For FAIR evaluation, DMP and other
tools/services it provides a look-up service (via
the API) for repositories: name, types and
other metadata
To help collecting information (at data resource
level), such as the presence and type of:
● licence or terms of use
● datasets accessibility/openness
● accessibility mechanism
● policies (e.g. curation, preservation)
● PIDs schema
● data and metadata standards
● and many others…
As a look-up service for repositories
59. CC BY-SA 4.0 International
2. For developers and users of FAIRness tests
and indicators it provides a searchable
registry to describe and discover them
To complement their storage in e.g. GitHub,
and help to make them to be:
● discoverable
● citable (via record’s DOI)
● unique
○ ensuring community ‘sees’ what
exists and adds/extends as needed
● usable in community profiles
As a registry for FAIRness tests and indicators
➔ This functionality is in a testing phase
60. CC BY-SA 4.0 International
3. For community, organizations and projects
it enables the creation of profiles to declare and
visualise standards and repositories they use
This is done through collections, connecting the
standards used to the FAIR indicators fulfilled
As a place to compare profiles, fostering FAIRness
Translational
Medicine
Clinical Developments
URL: https://fairsharing.org/PistoiaAllianceFIPs
(work in progress!)
A collaboration with the FAIR Implementation WG
➔ This is an explorative work, which may be
improved as the tests and indicators
mature and are globally agreed!
61. CC BY-SA 4.0 International
3. For community, organizations and projects
it enables the creation of profiles to declare and
visualise standards and repositories they use
This is done through collections, connecting the
standards used to the FAIR indicators fulfilled
As a place to compare profiles, fostering FAIRness
Disclaimer: These profiles speak for a limited community and do not represent any company standards
Clinical Developments
➔ This is an explorative work, which may be
improved as the tests and indicators
mature and are globally agreed!
62. CC BY-SA 4.0 International
Clinical Developments
Disclaimer: These profiles speak for a limited community and do not represent any company standards
URL: https://fairsharing.org/PistoiaAllianceFIPs
(work in progress!)
Comparing the use of standards and
promoting convergence
63. CC BY-SA 4.0 International
The FAIR Cookbook:
A collection of recipes that cover the operation
steps of FAIR data management
64. The FAIR Cookbook
What is it?
An online, ‘live’
resource for the life
sciences
A collection of
recipes that cover
the operation steps
of FAIR data
management
Who is it for?
Who developed it?
Researchers and
data managers
professionals in the
life sciences, from
academia and
industry
Including ELIXIR
members
Email: fairplus-cookbook@elixir-europe.org
Online resource:
https://faircookbook.elixir-europe.org
65. Learning objectives
Learn how to improve the FAIRness with exemplar datasets
Understand the levels and indicators of FAIRness
Discover open source technologies, tools and services
Find out the required skills
Acknowledge the challenges
Email: fairplus-cookbook@elixir-europe.org
Online resource:
https://faircookbook.elixir-europe.org
66.
67. Creators and contributors to date
+50 life sciences professionals, researchers and data managers
FARIplus
partners
Industry
+
Academia
ELIXIR
Nodes
represented
Email: fairplus-cookbook@elixir-europe.org
Online resource:
https://faircookbook.elixir-europe.org
68. CC BY-SA 4.0 International
Stakeholder Advisors
● Amye Kenall, VP of Publishing and Product, Research Square
● Adam Leary, Oxford University Press
● Catriona MacCallum, Hindawi
● Dagmar Meyer, European Research Council, Executive Agency
● Dominic Fripp, JISC, UK
● Emma Ganley, Protocols.io
● Geraldine Clement-Stoneham, Medical Research Council
● Helena Cousijn, DataCite
● Iain Hrynaszkiewicz, PLoS
● Imma Subirats, FAO of the United Nations
● Kiera McNiece, Cambridge University Press
● Luiz Olavo Bonino, GO-FAIR
● Marina Soares E Silva and Sarah Callaghan, Elsevier
● Michael Ball, Biotechnology and Biological Sciences Research Council
● Mike Huerta, NIH National Library of Medicine
● Molly Cranston and Guillaume Wright, F1000Research
● Nick Everitt and Matthew Cannon, Taylor and Francis
● Scott Edmunds, GigaScience, Oxford University Press
● Simon Hodson, CODATA
● Theo Bloom, British Medical Journal
● Thomas Lemberger, EMBO Press
● Wei-Mun Chan, eLife
● Sowmya Swaminathan, Springer Nature
Current Operational Team
● Allyson Lister, Content and Community Lead
● Milo Thurston, Technical Lead
● Ramon Granell, Data Enrichment & Quality Manager
● Delphine Dauga, Data Curator Manager
● Hiring in progress, Web Developer
● Dominique Batista, Research Software Engineer
● Philippe Rocca-Serra, Co-Founder
● Susanna-Assunta Sansone, PI and Founder
● and many collaborators and contributors!
Executive Advisors
● Varsha Khodiyar, HDRUK
● David Carr, Independent expert
● Chris Graf, Springer Nature
● Marta Teperek, Data Stewardship Coordinator, TUDelft
● Robert Hanisch, Director, NIST Office of Data & Informatics
● Peter McQuilton, FAIRsharing Founding Member, GSK
Early Adopter Community Curators
● Kyle Copas, GBIF
● Annie Elkjær Ørum-Kristensen, GBIF
● Lindsey Anderson, PNNL
● Joe Miller, GBIF
Thank you!
SAS and AL contributed to these slides.