57 research outputs found
Leveraging FAIR Signposting & RO-Crate for the Norwegian Research Data Archive
Get PDFLightning talk given during the 1st workshop organised by FAIR-Impact on the framework on the half day virtual workshop on "Enabling FAIR Signposting and RO-Crate".
This presentation briefly explains what our goals are and what support we need to fulfil our task
Galaxy: A Decade of Realising CWFR Concepts
Get PDFDespite recent encouragement to follow the FAIR principles, the day-to-day research practices have not changed substantially. Due to new developments and the increasing pressure to apply best practices, initiatives to improve the efficiency and reproducibility of scientific workflows are becoming more prevalent. In this article, we discuss the importance of well-annotated tools and the specific requirements to ensure reproducible research with FAIR outputs. We detail how Galaxy, an open-source workflow management system with a web-based interface, has implemented the concepts that are put forward by the Canonical Workflow Framework for Research (CWFR), whilst minimising changes to the practices of scientific communities. Although we showcase concrete applications from two different domains, this approach is generalisable to any domain and particularly useful in interdisciplinary research and science-based applications.publishedVersio
Improving the reproducibility in geoscientific papers: lessons learned from a Hackathon in climate science
Get PDFIn this paper, we explore the crucial role and challenges of computational reproducibility in geosciences, drawing insights from the Climate Informatics Reproducibility Challenge (CICR) in 2023. The competition aimed at (1) identifying common hurdles to reproduce computational climate science; and (2) creating interactive reproducible publications for selected papers of the Environmental Data Science journal. Based on lessons learned from the challenge, we emphasize the significance of open research practices, mentorship, transparency guidelines, as well as the use of technologies such as executable research objects for the reproduction of geoscientific published research. We propose a supportive framework of tools and infrastructure for evaluating reproducibility in geoscientific publications, with a case study for the climate informatics community. While the recommendations focus on future CIRCs, we expect they would be beneficial for wider umbrella of reproducibility initiatives in geosciences
Ontological Analysis of FAIR Supporting Resources
Get PDFAligning with the FAIR Principles is a key requirement for European-funded research. However, different interpretations of the FAIR Principles lead to diverging evaluations of how to implement them. Previous research introduced the FAIR Implementation Profile (FIP) as a driver to accelerate broad community convergence on FAIR implementation options. To scale FIP creation and analysis, we established a decentralised socio-technical ecosystem, supported by a lightweight FIP ontology including a typology of FAIR Supporting Resources (FSRs). However, categorising FSR instances is sometimes challenging, suggesting that there are unclarities in the FSR type definitions. This paper presents an ontological analysis of the FSR typology, aiming to improve its accuracy in supporting the peer-reviewed curation process of FSR descriptions provided by a wide community of FIP users. Using the Unified Foundational Ontology (UFO) as a reference, we analysed class definitions and demonstrated UFO’s capability to resolve controversies leading to disambiguation of FSRs of type FAIR Specification and FAIR Practice.</p
Climate–ecosystem modelling made easy: The Land Sites Platform
Get PDFDynamic Global Vegetation Models (DGVMs) provide a state-of-the-art process-based approach to study the complex interplay between vegetation and its physical environment. For example, they help to predict how terrestrial plants interact with climate, soils, disturbance and competition for resources. We argue that there is untapped potential for the use of DGVMs in ecological and ecophysiological research. One fundamental barrier to realize this potential is that many researchers with relevant expertize (ecology, plant physiology, soil science, etc.) lack access to the technical resources or awareness of the research potential of DGVMs. Here we present the Land Sites Platform (LSP): new software that facilitates single-site simulations with the Functionally Assembled Terrestrial Ecosystem Simulator, an advanced DGVM coupled with the Community Land Model. The LSP includes a Graphical User Interface and an Application Programming Interface, which improve the user experience and lower the technical thresholds for installing these model architectures and setting up model experiments. The software is distributed via version-controlled containers; researchers and students can run simulations directly on their personal computers or servers, with relatively low hardware requirements, and on different operating systems. Version 1.0 of the LSP supports site-level simulations. We provide input data for 20 established geo-ecological observation sites in Norway and workflows to add generic sites from public global datasets. The LSP makes standard model experiments with default data easily achievable (e.g., for educational or introductory purposes) while retaining flexibility for more advanced scientific uses. We further provide tools to visualize the model input and output, including simple examples to relate predictions to local observations. The LSP improves access to land surface and DGVM modelling as a building block of community cyberinfrastructure that may inspire new avenues for mechanistic ecosystem research across disciplines.publishedVersio
annefou/DSD_FAIR: version 1.0.0 Workshop delivered at the Digital Scholarship Days 2024
No full text<p>Workshop delivered on Wednesday, January 10th, 2024 for Digital Scholarship Days 2024.</p>
<p><strong>FAIR: More Than Just a Buzzword – A Framework for Data Excellence</strong></p>
<p><em>Learn to make your research work more Findable, Accessible, Interoperable and Reusable (FAIR) using ROHub, an online and free Research Objects Management Platform.</em></p>
<p>Join our workshop to learn about the FAIR principles and get to know ROHub, a platform tailored for Research Objects (ROs). With ROHub, you can manage, share, and preserve your research materials more efficiently. It even has a built-in tool to guide you in improving the quality of your research. We'll walk you through real-world examples of how FAIR and ROHub can benefit you. Key points: ROHub organizes your research into one accessible spot, making it easier to manage. Plus, it uses clear labels so both you and computers can make sense of your work.</p>
<p><strong>Objectives:</strong></p>
<p>Introduction to the FAIR principles and how we can put them in practice.- Introduction to RoHub: Participants will gain a comprehensive understanding of RoHub's capabilities and how it facilitates collaborative research.
RO Model Exploration: The workshop delves into the Research Object model, explaining how RoHub adheres to its principles.</p>
<p><em>Hands-On session</em>: Attendees will have the opportunity to explore and experience for themselves RoHub's features through practical demonstrations.</p>
<p><em>Collaborative Research</em>: The workshop emphasises the benefits of collaborative research and how RoHub can speed it up.
FAIR Principles: Discussion on how RoHub aligns with the FAIR principles, ensuring research work is easily discoverable, accessible, and reusable.</p>
<p><strong>Learning outcomes</strong></p>
<ul>
<li>Understand the FAIR principles and how to interpret them to put them in practice.- Get a better understanding of the concept of FAIR Digital Objects (FDOs) and Research Objects (RO-Crate).</li>
<li>Get to know <a href="https://www.rohub.org/">ROHub</a> (an online and freely available Research Object Management Platform).</li>
<li>Be able to explore existing Research Objects in ROHub.</li>
<li>Understand how to use the ROHub's integrated FAIR assessment tool to check the FAIRness of your Research Objects and guide end-users to improve the FAIRness of their own research work.</li>
<li>Understand how to create ROs and their lifecycle (live ROs, snapshots, archives) when aggregating diverse research artefacts.By the end of this workshop, you will understand the capabilities of Research Objects and how to harness them for more effective research management and collaboration, and for increasing the FAIRness of your research outputs e.g. data, software, workflows, etc.</li>
</ul>
<p><strong>Prerequisites</strong></p>
<p>You do not need to be familiar with the FAIR principles prior to the workshop. This workshop is hands-on and attendees who need to make their data, software and/or workflows FAIR will most benefit from this workshop.</p>
<p><strong>Target audience</strong></p>
<p>This workshop is designed for researchers, research engineers, and research software engineers who want to learn how to apply the FAIR principles in practice to their research artefacts, including data, software, and workflows.</p>
<p><strong>Required Materials</strong></p>
<p>You need to bring your laptop with a modern browser and good humour!</p>
<p><strong>Organizer</strong></p>
<p><a href="https://annefou.github.io/">Anne Fouilloux</a> and <a href="https://www.usit.uio.no/english/about/organisation/rde/scs/staff/jeani/index.html">Jean Iaquinta</a></p>
Data Carpentry Dataset: Working with Spatio-temporal data in Python
No full textThis dataset contains netCDF, HDF, GeoTIFF, shapefiles, GEOJSON files used for the Data Carpentry lesson we have developed at the Department of Geosciences, University of Oslo, Norway.
The corresponding lessons are available at https://annefou.github.io/metos_python
annefou/DSD_EOSC: version 1.0.0 Workshop delivered at the Digital Scholarship Days 2024
No full text<p>Workshop delivered on Friday, January 12th, 2024 for Digital Scholarship Days 2024.</p>
<p><strong>Unlocking the Power of EOSC: Navigating Services for Research Visibility and Impact</strong></p>
<p><em>The European Open Science Cloud (EOSC) in a nutshell</em></p>
<p>In today's dynamic research landscape, visibility and impact are paramount for researchers seeking to share their research work, foster collaboration, and drive innovation. The European Open Science Cloud (EOSC) stands as a transformative platform, offering an array of services and resources to empower researchers on their journey to Open Science for greater recognition and influence.Join us in this hands-on workshop, where we will demystify the EOSC ecosystem and guide you through the practical steps to make the most of its offerings. Our emphasis is on equipping you with actionable insights to navigate the jungle of EOSC services effectively, all with the aim of increasing your research visibility and impact.Duration 3 hours.</p>
<p><strong>Learning outcomes</strong></p>
<p>Understanding EOSC: Acquire a comprehensive overview of EOSC's role and significance within the open science paradigm. Recognize its pivotal function in facilitating seamless interactions between researchers, data, and services.
Exploring EOSC Services: Navigate the diverse array of EOSC services designed to cater to the multifaceted requirements of the research community, encompassing domains such as data management, collaboration, and data sharing.
Enhancing Research Visibility: Equip yourself with tactical approaches to augment the reach and visibility of your research through EOSC. Explore the myriad avenues available for disseminating data, publications, and projects within the EOSC framework.
Citation Insights: Comprehend the intrinsic advantages of integrating EOSC services for bolstering citations and overall research recognition. Delve into established practices for effectively citing EOSC resources.</p>
<p><em>Practical Application</em>: Engage in hands-on activities designed to instill a robust understanding of how to adeptly utilize EOSC services, including the nuances of the enrollment process.</p>
<p><em>Engagement with the EOSC Community</em>: Initiate meaningful dialogues with the EOSC community, fostering collaborative ventures and gleaning insights from researchers who have adeptly leveraged EOSC.</p>
<p><em>Connecting with the EOSC Community</em>: Engage with the EOSC community and seize collaborative opportunities. Gain insights from peers who've effectively used EOSC in their research. By the workshop's end, you'll be equipped with the proficiency to adeptly navigate EOSC. Regardless of your research experience, this session will bolster your research's visibility and impact. Join us to harness EOSC's potential and amplify your research's recognition.</p>
<p><strong>Prerequisites</strong></p>
<p>You do not need to be familiar with the European Open Science Cloud prior to the workshop. We will guide you through the process of registering and enrolling in EOSC services, focusing on those that are widely used and relevant to the majority of participants. We understand that some of these services may not be directly integrated into your current daily work practices</p>
<p><strong>Target audience</strong></p>
<p>This workshop is designed for researchers, scholars, and academicians looking at harnessing the full potential of the European Open Science Cloud (EOSC) to enhance the visibility and impact of their research work.</p>
<p><strong>Required Materials</strong></p>
<p>You need to bring your laptop with a modern browser. You will be required to register and connect to EOSC services, so you may want to bring your personal laptop if your organisation's policies forbid such access.</p>
<p><strong>Organizer</strong></p>
<p><a href="https://annefou.github.io/">Anne Fouilloux</a> and <a href="https://www.usit.uio.no/om/organisasjon/ffu/bt/ansatte/jeani/index.html">Jean Iaquinta</a></p>
Teaching ML in Compact Courses
No full textThis talk summarizes the experiences made with teaching Machine Learning within compact events that stretch over several days to a week maximum. Both speakers explain pitfalls they were caught in as well as solutions they found.
This talk was given at the Teaching Machine Learning workshop at ECML-PKDD 2020. For more details and information see https://teaching-ml.github.io/2020/The talk was created in a collaborative fashion on hackmd.io Therefor this contains the final pdf of the slides and the markdown file
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