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CMR248 committed Nov 27, 2023
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81 changes: 81 additions & 0 deletions ...s/2023-10-24-published-paper-streamlining-research-data-management-in-plant-sciences.html
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nfdi4plants - News
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Published paper - Streamlining Research Data Management in Plant Sciences
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24 Oct 2023
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<p>DataPLANT aims to support fundamental plant researchers in data management in various ways. Planning is a crucial component especially in the grant application and setup period of projects. Plant sciences present specific RDM needs, with unique data types and challenges. For this purpose the TA1 team developed a specialized tool: <a href="phttps://plan.nfdi4plants.org/">DataPLAN</a>. It addresses challenges in Research Data Management (RDM) specific to plant sciences. DataPLAN, an open-source tool, incorporates prewritten Data Management Plan (DMP) content to facilitate the creation of multiple DMPs. Compatible with Horizon 2020, Horizon Europe, and DFG-funded projects, DataPLAN aims to standardize RDM practices, reduce workload, and enhance collaboration by offering customizable templates.</p>
<p>A Data Management Plan (DMP) outlines procedures for handling research data throughout a project's lifecycle, contributing to efficient RDM. DMPs ensure the findability, accessibility, interoperability, and reusability (FAIR-ness) of data, addressing requirements set by major funding bodies such as Horizon Europe, DFG, NIH, NSF, and SNSF. DMPs involve challenges due to diverse requirements from funding bodies, leading to the development of multiple tools. These tools assist in creating comprehensive DMPs but vary in their support for specific funding bodies, domain-specific RDM approaches, and relevant regulations. Built on the maDMP standard, which facilitates information exchange among these tools, DataPLAN merges the reusable content across various funding contexts and different projects. By linking to minimum information standards and DataPLANT tools such as PlantDataHub, Swate, ARCcommander and ARCitect, DataPLAN enables the accommodation of plant-specific aspects, such as organ-specific growth parameters, high-throughput phenotyping, and plant taxonomy. As DataPLAN provides comprehensive and tailored DMPs in plant sciences, the workload of the users can be reduced by using DataPLAN.</p>
<p><strong>Further Links</strong><br />
<a href="phttps://plan.nfdi4plants.org/">DataPLAN - Application</a><br />
<a href="https://doi.org/10.3390/data8110159">DataPLAN - Publication</a><br />
<a href="https://github.com/nfdi4plants/dataplan">DataPLAN - Source Code</a></p>
<p><img src="../../images/News-Items/DataPLAN-2.png" width="60%" alt="DataPLAN Cover" /></p>

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82 changes: 82 additions & 0 deletions ...-advances-on-bioinformatics-tools-and-international-exchange-of-dataplant-developers.html
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<link rel="icon" type="image/png" sizes="32x32" href="/images/favicon.png"/>
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nfdi4plants - News
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<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css"/>
<link rel="stylesheet" type="text/css" href="/style/style.css"/>
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thead tr th, strong {
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BioHackathon Europe in Barcelona Fostered Collaborative Advances on Bioinformatics Tools and International Exchange of (DataPLANT) Developers
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10 Nov 2023
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<p>Last week, from October 30th to November 3rd, ELIXIR organized the <a href="https://biohackathon-europe.org/">BioHackathon Europe</a> in Barcelona, drawing international participants, including Timo Mühlhaus, Jonathan Bauer, Lukas Weil, Xiaoran Zhou, and Björn Grüning from the DataPLANT team. The event fostered collaboration, discussions, and shared experiences among 150 participants from across Europe and even Australia.</p>
<p><strong><a href="https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/20">Genome Annotation and Post-Assembly Workflows for the Tree of Life</a></strong><br />
One standout project focused on assessing the performance of various Genome Annotation tools and workflows for diverse organisms, including Human chromosome 19 (HG38), Drosophila melanogaster, Sponge (Phakellia ventilabrum), Butterfly (Helleie helle), Shamrock (Trifolium dubium), Snail (Melampus), and Coral (Pocillopora meandrina). Utilizing tools such as Braker3, Maker, Busco, Funannotate, Helixer, RepeatModeller, Eggnog, InterproScan, and integrating annotations into a shareable JBrowse instance, the team addressed the evolving needs, incorporating RepeatExplorer into Galaxy.</p>
<p><strong><a href="https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/25">Increasing Galaxy Tool Visibility for Specialized Scientific Communities</a></strong><br />
Another noteworthy project led by Galaxy aimed at enhancing the findability, visibility, and impact of Galaxy tools for specialized scientific communities. Collaborating with Nicola Soranzo and Johan Gustafsson, the team, including online participant Bérénice and support from Matúš Kalaš, successfully implemented a pipeline. This pipeline collects Galaxy tool wrappers, incorporates metadata from various sources, and filters tools for specific Galaxy communities, contributing to the broader accessibility and impact of Galaxy tools.</p>
<p>The BioHackathon Europe exemplified the spirit of cross-country and cross-project collaboration and innovation in the bioinformatics community, pushing the boundaries of genome annotation and bioinformatics tool development for the benefit of scientific research worldwide.<br />
The mentioned tools are made available to the DataPLANT community through the <a href="https://nfdi4plants.org/content/news/2023-09-04-step-by-step-integration-of-dataplant-workflows.html">Galaxy workflow integration</a>.</p>
<!--Noch das ARC Project einbringen (https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/14)-->

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89 changes: 89 additions & 0 deletions ...ve-workshop-strengthens-interconnection-of-fdm-helpdesks-across-consortia-and-beyond.html
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<link rel="icon" type="image/png" sizes="32x32" href="/images/favicon.png"/>
<title>
nfdi4plants - News
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<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.7.0/css/font-awesome.min.css"/>
<link rel="stylesheet" type="text/css" href="/style/style.css"/>
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thead tr th, strong {
color: var(--accent-text-color) !important
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color: var(--link-color, #4FB3D9) !important;
}

a:hover {
color: var(--link-hover-color, #3A3A3A) !important;
}

thead {
font-size: 1.2rem;
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Collaborative Workshop Strengthens Interconnection of FDM Helpdesks Across Consortia and Beyond
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22 Nov 2023
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<p>In a collaborative effort to enhance the landscape of research data management (RDM), a <a href="https://www.nfdi.de/community-workshop-helpdesk-vernetzung/">two-day workshop on networking FDM helpdesks</a> took place on November 20th and 21st, 2023, at the University of Duisburg-Essen. The event, which included participants beyond the DataPLANT Consortium, saw the gathering of professionals from institutional FDM contact points, NFDI helpdesks, and support initiatives from FDM state initiatives.</p>
<p>Many universities have already established local FDM service points that provide on-site assistance to researchers with FDM-related queries. The National Research Data Infrastructure (NFDI) consortia are currently establishing a nationwide FDM infrastructure with support services focused on specific disciplines or methodologies. Additionally, several federal states have FDM state initiatives or regional networks offering complementary services or supporting the development of cross-location offerings.</p>
<p>The workshop aimed to explore optimal ways of interconnecting existing FDM helpdesks. The objective was to enhance awareness of existing offerings within consortia and at various locations while developing opportunities to network support services. Data and ideas gathered during the workshop will serve as a basis for developing concrete measures and further steps.</p>
<p>The event, attended by the manager Cristina Rodrigues, proved to be highly productive and will be intensified the foundation for regular meetings in the form of a bi-monthly Jour Fixe.</p>
<p>However, collaboration extends beyond forging connections with related domain consortia such as <a href="https://www.nfdi4biodiversity.org/de/">NFDI4Biodiversity</a> and <a href="https://fairagro.net/">FAIRagro</a>. Joint efforts have already been showcased at CoRDI through a <a href="https://zenodo.org/doi/10.5281/zenodo.8356210">poster</a> created in collaboration with NFDI4Biodiversity.</p>
<p>The future agenda promises further exciting developments, including a planned in-person meeting next year involving additional consortia like <a href="https://nfdi4microbiota.de/">NFDI4Microbiota</a> and <a href="https://www.nfdi4earth.de/">NFDI4Earth</a>. These strategic collaborations will contribute to creating synergies and strengthening the NFDI.</p>
<p>This initiative underscores the importance of collaboration among different consortia to successfully address challenges in RDM and sustainably support the scientific community.</p>
<p><strong>Further Links</strong><br />
<a href="https://www.nfdi.de/community-workshop-helpdesk-vernetzung/">Community Workshop - Vernsetzung der FDM-Helpdesks</a><br />
<a href="https://zenodo.org/doi/10.5281/zenodo.8356210">Poster - Optimizing User Support through Synergistic Integration of Helpdesk Systems</a><br />
<a href="https://www.nfdi4biodiversity.org/de/">Website - NFDI4Biodiversity</a><br />
<a href="https://fairagro.net/">Website - FAIRagro</a><br />
<a href="https://nfdi4microbiota.de/">Website - NFDI4Microbiota</a><br />
<a href="https://www.nfdi4earth.de/">Website - NFDI4Earth</a><br />
<a href="https://helpdesk.nfdi4plants.org/">Helpdesk - DataPLANT</a></p>

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