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workflow4metabolomics community resources update
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‎communities/workflow4metabolomics/lab/README.md‎

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# Community subdomain/Lab

‎communities/workflow4metabolomics/lab/conclusion.html‎

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{% load markdown %}
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<!-- <section class="my-5">
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{% if help_links %}
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<h4 class="mb-3">{{ lab_name }} community support</h4>
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<ul>
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{% for link in help_links %}
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<li>
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<a href="{{ link.url }}" target="_blank">{{ link.title }}</a>
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</li>
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{% endfor %}
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</ul>
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{% endif %}
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</section>
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<section>
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<h4 class="mb-3">News and Events</h4>
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<div class="row justify-content-center">
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<div class="col">
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<iframe width="400px" height="600px" src="https://training.galaxyproject.org/training-material/topics/microbiome/feed.w.xml"></iframe>
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</div>
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<div class="col">
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<iframe width="400px" height="600px" src="https://training.galaxyproject.org/training-material/feeds/microbiome-month.w.xml"></iframe>
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</div>
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</div>
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</section> -->
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{% if feedback_email %}
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<section class="my-5">
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<h4 class="my-3">What do you think of the {{ lab_name }}?</h4>
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<button
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class="ga-btn"
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data-bs-toggle="modal"
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data-bs-target="#feedbackModal"
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>
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Give feedback
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</button>
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</section>
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{% endif %}
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<section class="my-5">
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<h4 class="mb-3">Cite Us</h4>
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</section>
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<section class="my-5">
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If you find the {{ lab_name }} Lab and the effort of the {{ lab_name }} community useful for your research, please cite us using this webpage.
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<!-- If you find the {{ lab_name }} Lab and the effort of the {{ lab_name }} community useful for your research, please cite us using our <a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1" target="_blank" rel="noopener noreferrer">preprint</a>-->
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</section>
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<section id="conclusionExtra">
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{{ conclusion_extra_md|safe }}
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</section>

‎communities/workflow4metabolomics/lab/intro.html‎

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<section class="my-5" id="tagline">
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<p>
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Welcome to the Galaxy {{ site_name }} {{ lab_name }} by the {{ lab_name }} community!
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</p>
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<p>
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#Here include an intro to your page, see the ex mple below from the microgalaxy community
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# Whether you're working with microbiome samples or bacterial isolates, long or short reads, shotgun or 16S sequencing, genomics, transcriptomics, proteomics, metabolomics, or integrative multi-omics analysis—this is the place for you! Learn more about the Microbiology Lab and the effort of the microGalaxy community in our <a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1" target="_blank" rel="noopener noreferrer">preprint</a>. </p>
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<p>
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<a
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href="#"
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data-bs-toggle="modal"
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data-bs-target="#infoModal">
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How does this page relate to Galaxy {{ site_name }}?
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</a>
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</p>
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{{ intro_extra_md }}
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<div class="modal fade" id="infoModal" tabindex="-1">
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<div class="modal-dialog modal-lg">
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<div class="modal-content">
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<div class="modal-header">
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<h5 class="modal-title">Galaxy {{ site_name }}</h5>
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<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
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</div>
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<div class="modal-body">
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<p>
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This site <em>{{ subdomain }}.{{ root_domain }}</em> is connected to the same server as <em>{{ root_domain }}</em>, but with an interface dedicated to helping our {{ analysis_name }} researchers. Your history, jobs and data quota are shared with the "Base" Galaxy {{ site_name }} website.
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</p>
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<p><a class="ga-btn" href="https://{{ root_domain }}" target="_blank">Take me back to Galaxy {{ site_name }}</a></p>
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<p><a class="ga-btn" href="https://{{ root_domain }}/about">What is Galaxy {{ site_name }}?</a></p>
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<p><a class="ga-btn" href="{{support}}">Galaxy {{ site_name }} support</a></p>
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</div>
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<div class="modal-footer">
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<button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
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</div>
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</div>
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</div>
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</div>
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</section>

‎communities/workflow4metabolomics/lab/sections/2_tools.yml‎

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id: tools
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title: Community curated tools
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tabs: []

‎communities/workflow4metabolomics/lab/sections/3_workflows.yml‎

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‎communities/workflow4metabolomics/lab/sections/4_tutorials.yml‎

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id: tutorials
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title: Community curated tutorials
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tabs:
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- id: fair_data
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title: FAIR Data
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heading_md: 'Top 10 most visited tutorials for the Topic : FAIR Data. <br/> Visitors
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: Number of unique visitors automatically calculated using Plausible.'
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content:
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- title_md: "DataPLANT ARCs\n (Visitors: 1829116)"
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description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/fair/tutorials/dataplant-arcs/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "FAIR in a nutshell\n (Visitors: 1107)"
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description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/fair/tutorials/fair-intro/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "FAIR data management solutions\n (Visitors: 486)"
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description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/fair/tutorials/data-management/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Making clinical datasets FAIR\n (Visitors: 441)"
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description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/fair/tutorials/fair-clinical/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "FAIRification of an RNAseq dataset\n (Visitors: 394)"
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description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/fair/tutorials/fair-rna/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Persistent Identifiers\n (Visitors: 377)"
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description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/fair/tutorials/fair-persistent-identifiers/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Exporting Workflow Run RO-Crates from Galaxy\n (Visitors: 374)"
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description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/fair/tutorials/ro-crate-in-galaxy/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Metadata\n (Visitors: 324)"
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description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/fair/tutorials/fair-metadata/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "FAIR and its Origins\n (Visitors: 236)"
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description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/fair/tutorials/fair-origin/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "FAIR Galaxy Training Material\n (Visitors: 233)"
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description_md: Tutorial stored in FAIR Data, Workflows, and Research topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/fair/tutorials/fair-gtn/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- id: introduction_to_galaxy_analyses
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title: Introduction to Galaxy Analyses
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heading_md: 'Top 10 most visited tutorials for the Topic : Introduction to Galaxy
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Analyses. <br/> Visitors : Number of unique visitors automatically calculated
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using Plausible.'
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content:
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- title_md: "Galaxy Basics for genomics\n (Visitors: 55998)"
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description_md: Tutorial stored in Introduction to Galaxy Analyses topic on
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the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-101/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Data Manipulation Olympics\n (Visitors: 7006)"
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description_md: Tutorial stored in Introduction to Galaxy Analyses topic on
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the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/introduction/tutorials/data-manipulation-olympics/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "How to reproduce published Galaxy analyses\n (Visitors: 2442)"
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description_md: Tutorial stored in Introduction to Galaxy Analyses topic on
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the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-reproduce/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Best Practices for Citing Galaxy\n (Visitors: 367)"
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description_md: Tutorial stored in Introduction to Galaxy Analyses topic on
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the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-cite/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Introduction to Galaxy as an RDM platform\n (Visitors: 365)"
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description_md: Tutorial stored in Introduction to Galaxy Analyses topic on
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the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/introduction/tutorials/galaxy-intro-rdm/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- id: metabolomics
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title: Metabolomics
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heading_md: 'Top 10 most visited tutorials for the Topic : Metabolomics. <br/> Visitors
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: Number of unique visitors automatically calculated using Plausible.'
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content:
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- title_md: "Mass spectrometry: LC-MS preprocessing with XCMS\n (Visitors: 3995038)"
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description_md: Tutorial stored in Metabolomics topic on the Galaxy Training
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Network and covering topics related to Metabolomics
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button_link:
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https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Predicting EI+ mass spectra with QCxMS\n (Visitors: 1867817)"
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description_md: Tutorial stored in Metabolomics topic on the Galaxy Training
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Network and covering topics related to Metabolomics
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button_link:
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https://training.galaxyproject.org//topics/metabolomics/tutorials/qcxms-predictions/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Mass spectrometry: LC-MS analysis\n (Visitors: 14099)"
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description_md: Tutorial stored in Metabolomics topic on the Galaxy Training
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Network and covering topics related to Metabolomics
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button_link:
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https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Mass spectrometry: LC-MS data processing\n (Visitors: 3455)"
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description_md: Tutorial stored in Metabolomics topic on the Galaxy Training
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Network and covering topics related to Metabolomics
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button_link:
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https://training.galaxyproject.org//topics/metabolomics/tutorials/lcms-dataprocessing/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Mass spectrometry imaging: Examining the spatial distribution of analytes\n\
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\ (Visitors: 3431)"
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description_md: Tutorial stored in Metabolomics topic on the Galaxy Training
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Network and covering topics related to Metabolomics
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button_link:
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https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-analyte-distribution/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner,
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and matchms)\n (Visitors: 3313)"
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description_md: Tutorial stored in Metabolomics topic on the Galaxy Training
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Network and covering topics related to Metabolomics
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button_link:
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https://training.galaxyproject.org//topics/metabolomics/tutorials/gc_ms_with_xcms/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Mass spectrometry imaging: Finding differential analytes\n (Visitors:
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2250)"
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description_md: Tutorial stored in Metabolomics topic on the Galaxy Training
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Network and covering topics related to Metabolomics
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button_link:
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https://training.galaxyproject.org//topics/metabolomics/tutorials/msi-finding-nglycans/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Mass spectrometry: GC-MS analysis with the metaMS package\n (Visitors:
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1988)"
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description_md: Tutorial stored in Metabolomics topic on the Galaxy Training
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Network and covering topics related to Metabolomics
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button_link:
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https://training.galaxyproject.org//topics/metabolomics/tutorials/gcms/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Molecular formula assignment and mass recalibration with MFAssignR
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package\n (Visitors: 348)"
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description_md: Tutorial stored in Metabolomics topic on the Galaxy Training
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Network and covering topics related to Metabolomics
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button_link:
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https://training.galaxyproject.org//topics/metabolomics/tutorials/mfassignr/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- id: using_galaxy_and_managing_your_data
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title: Using Galaxy and Managing your Data
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heading_md: 'Top 10 most visited tutorials for the Topic : Using Galaxy and Managing
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your Data. <br/> Visitors : Number of unique visitors automatically calculated
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using Plausible.'
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content:
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- title_md: "Using dataset collections\n (Visitors: 17415)"
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description_md: Tutorial stored in Using Galaxy and Managing your Data topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/galaxy-interface/tutorials/collections/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Creating, Editing and Importing Galaxy Workflows\n (Visitors: 6557)"
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description_md: Tutorial stored in Using Galaxy and Managing your Data topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-editor/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Understanding Galaxy history system\n (Visitors: 6073)"
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description_md: Tutorial stored in Using Galaxy and Managing your Data topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Rule Based Uploader\n (Visitors: 6040)"
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description_md: Tutorial stored in Using Galaxy and Managing your Data topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Extracting Workflows from Histories\n (Visitors: 3258)"
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description_md: Tutorial stored in Using Galaxy and Managing your Data topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/galaxy-interface/tutorials/history-to-workflow/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Automating Galaxy workflows using the command line\n (Visitors: 3251)"
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description_md: Tutorial stored in Using Galaxy and Managing your Data topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-automation/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Using Workflow Parameters\n (Visitors: 2160)"
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description_md: Tutorial stored in Using Galaxy and Managing your Data topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-parameters/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Workflow Reports\n (Visitors: 1026)"
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description_md: Tutorial stored in Using Galaxy and Managing your Data topic
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on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-reports/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Rule Based Uploader: Advanced\n (Visitors: 935)"
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description_md: Tutorial stored in Using Galaxy and Managing your Data topic
257+
on the Galaxy Training Network and covering topics related to nan
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button_link:
259+
https://training.galaxyproject.org//topics/galaxy-interface/tutorials/upload-rules-advanced/tutorial.html
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button_tip: View tutorial
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button_icon: tutorial
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- title_md: "Annotate, prepare tests and publish Galaxy workflows in workflow registries\n\
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\ (Visitors: 475)"
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description_md: Tutorial stored in Using Galaxy and Managing your Data topic
265+
on the Galaxy Training Network and covering topics related to nan
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button_link:
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https://training.galaxyproject.org//topics/galaxy-interface/tutorials/workflow-fairification/tutorial.html
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button_tip: View tutorial
269+
button_icon: tutorial

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