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

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# Community subdomain/Lab

‎communities/proteomics/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/proteomics/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/proteomics/lab/sections/1_data_import_and_preparation.yml‎

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id: data
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title: Getting started
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tabs:
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- id: data-import
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title: Data import
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heading_md: >
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Common tools that allow for data import.
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content:
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- title_md: Import data to Galaxy
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description_md: >
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Standard upload of data to Galaxy, from your computer or from the web.
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button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1"
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button_tip: Upload Data
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- title_md: Download data from NCBI GenBank/RefSeq
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description_md: >
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Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API
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button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fncbi_acc_download%2Fncbi_acc_download"
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button_tip: Download Data from NCBI
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- title_md: Download raw reads from NCBI SRA
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description_md: >
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Faster Download and Extract Reads in FASTQ format from NCBI SRA
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button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffasterq_dump"
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button_tip: Download raw reads from NCBI SRA
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- title_md: Download run data from EBI SRA
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description_md: >
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ENA data can be searched and retrieved interactively and programmatically and visualized using this ENA Browser tool
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button_link: "https://www.ebi.ac.uk/ena/browser/search"
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button_tip: Download run data from EBI SRA
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- title_md: Download run data from UCSC
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description_md: >
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Use this tool to retrieve and export data from the Genome Browser annotation track database
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button_link: "https://genome.ucsc.edu/cgi-bin/hgTables"
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button_tip: Download run data from UCSC
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# - id: highlight-tools
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# title: Highlight tools
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# heading_md: >
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# Flagship tools for <your-community>
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# content:
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# - title_md: <code>Bakta</code> - Rapid and standardized annotation of bacterial genomes, MAGs and plasmids
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# description_md: >
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# A tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and Metagenomic Assembled Genomes (MAGs).
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# inputs:
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# - datatypes:
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# - fasta
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# button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta"
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# - id: interactive-tools
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# title: Interactive tools
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# heading_md: >
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# Interactive tools for <your-community>
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# content:
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# - title_md: <code>Pavian</code> - Interactive analysis of metagenomics data
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# description_md: >
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# An interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as Kraken, KrakenUniq, Kraken 2, Centrifuge and MetaPhlAn. Pavian also provides an alignment viewer for validation of matches to a particular genome.
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# inputs:
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# - datatypes:
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# - Kraken report
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# - MetaPhlAn report
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# button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_pavian"
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# - id: learning-pathways
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# title: Learning pathways
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# heading_md: >
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# Connected tutorials to train you to perform microbial data analysis.
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# content:
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# - title_md: Introduction to Galaxy and Sequence analysis
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# description_md: >
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# New to Galaxy and/or the field of genomics? In this learning pathway, you will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences.
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# button_link: https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-genomics.html
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# button_icon: tutorial
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# button_tip: Open Learning Pathway
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# heading_md: >
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# Connected tutorials to train you to perform microbial data analysis.

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

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id: workflows
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title: Community curated workflows
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tabs:
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- id: iwc
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content: []
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- id: other_workflowhub
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content: []
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- id: gtn
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content: []
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- id: public
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content: []

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

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

‎communities/proteomics/lab/sections/5_support_and_help.yml‎

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id: support
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title: Support & Help
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tabs:
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- id: help
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title: Help
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heading_md: >
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You can request help through different channels. If you think your problem might help other users as well,
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please post it in the Galaxy Help Forum. Please report tool bugs through our
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[support channel]({{ support_url }})
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and for specific questions feel free to reach out via the matrix chat.
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content:
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- title_md: Troubleshooting
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description_md: >
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Find specific advice for
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{gtn modal}[troubleshooting Galaxy errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html)
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on the GTN.
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- title_md: Galaxy Support
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description_md: >
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Any user of Galaxy {{ site_name }} can request support online!
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button_md: Request support
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button_link: "{{ support_url }}"
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button_icon: help
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button_tip: Request support
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# - title_md: microGalaxy chat room
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# description_md: >
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# Chat with members of the microGalaxy community on Matrix
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# button_link: "{{ microgalaxy_matrix }}"
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# button_md: Matrix channel
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# button_icon: social
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# button_tip: Join the chat
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- id: faq
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title: FAQ
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content:
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- title_md: How can I increase my storage quota?
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description_md: >
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Please submit a quota request if your Galaxy account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request.
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button_md: Request
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button_link: "{{ quota_request_url }}"
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button_tip: Request quota
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button_icon: help
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- title_md: Can I upload sensitive data?
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description_md: >
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No, please do not upload personal or sensitive, such as human health or clinical data. Please see our
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[Privacy Policy]({{ data_policy_url }})
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page for definitions of sensitive and health-related information.
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Please also make sure you have read our
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[Terms of Service]({{ terms_url }}),
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which covers hosting and analysis of research data.
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- title_md: Is my data private?
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description_md: >
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Please read our
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[Privacy Policy]({{ data_policy_url }})
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for information on your personal data and any data that you upload.

‎communities/proteomics/lab/sections/6_community.yml‎

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id: community
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title: Community
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tabs:
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- id: participate
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title: Participate
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content:
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- title_md: Join our community!
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description_md: >
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This Galaxy space is the result of hard, collaborative work by many contributors.
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# It is maintained by the microGalaxy Community of Practice.
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# This group unites scientists like yourself with software developers and bioinformaticians to create, share, and test resources to make microvial data analysis easier.
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# Check out our site and join our community via [microGalaxy mailing list](https://lists.galaxyproject.org/lists/microgalaxy@lists.galaxyproject.org)!
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# - title_md: Chat with others!
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# description_md: >
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# Use our matrix channel to chat with others from microGalaxy community
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# button_link: "{{ microgalaxy_matrix }}"
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# button_md:
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# button_tip: Visit microGalaxy
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# button_icon: social
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- id: governance
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title: How is the Galaxy Community organised?
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heading_md: >
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Learn about the
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{gtn modal}[governance structure of Galaxy communities](https://training.galaxyproject.org/training-material/topics/community/faqs/governance_structure.html) on the GTN.
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content: []
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- id: links
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title: Galaxy Community support links
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content:
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- title_md: "For general Galaxy support"
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description_md: "General Galaxy support"
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button_link: "{{ general_support }}"
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button_tip: Galaxy Support
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button_icon: help
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- title_md: "General Help Forum"
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description_md: "Access general Galaxy help"
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button_link: "{{ galaxy_help_url }}"
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button_tip: Help forum
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button_icon: help
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- title_md: "Galaxy Training Network Slack Workspace"
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description_md: "Join the GTN Slack community"
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button_link: "{{ gtn_slack_url }}"
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button_tip: Slack channel - Join the GTN Slack community.
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button_icon: social
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- title_md: "Galaxy Training Network Community Chat Room"
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description_md: "Connect on the GTN Matrix chat"
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button_link: "{{ gtn_matrix_channel }}"
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button_tip: Matrix channel - Connect on the GTN Matrix chat.
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button_icon: social
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# - title_md: "microGalaxy User Community Chat Room"
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# description_md: "Join the microGalaxy Matrix chat"
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# button_link: "{{ microgalaxy_matrix }}"
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# button_tip: Matrix channel - Join the microGalaxy Matrix chat.
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# button_icon: social
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- title_md: "General Galaxy Project Chat Room"
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description_md: "Join the Galaxy project chat"
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button_link: "{{ galaxy_matrix_channel }}"
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button_tip: Matrix channel - Join the Galaxy project chat.
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button_icon: social
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- title_md: "European Galaxy Server Chat Room"
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description_md: "Join the usegalaxy.eu chat"
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button_link: "{{ european_server_matrix_channel }}"
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button_tip: Matrix channel - Join the usegalaxy.eu chat.
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button_icon: social
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exclude_from:
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- usegalaxy.org.au

‎communities/proteomics/metadata/tool_status.tsv‎

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@@ -5,6 +5,7 @@ bed_to_protein_map galaxyp Converts a BED file to a tabular list of exon locatio
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bioconductor-msnbase recetox MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. False False
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bioconductor_mzr recetox Galaxy wrapper for the Bioconductor mzR package, enabling conversion between common mass spectrometry data formats (mzML, mzXML, netCDF) within Galaxy workflows.
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bioconductor_scp recetox scp is a package for the single cell proteomics data processing. False False
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biosigner workflow4metabolomics [W4M][Metabolomics][LC-MS][GC-MS][NMR] Discovery of significant signatures from omics data.
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bumbershoot galaxyp
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calisp galaxyp Calgary approach to isotopes in proteomics False False
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cardinal galaxyp Statistical and computational tools for analyzing mass spectrometry imaging datasets
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fragpipe galaxyp Data analysis for mass spectrometry-based proteomics. False False
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freqsap recetox Get frequencies of single amino-acid polymorphisms based on nucleid-acid polymorphism for different populations from UniProt and DbSNP.
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hardklor galaxyp Hardklör False False
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heatmap ethevenot [W4M][Metabolomics][LC-MS][GC-MS][NMR] Heatmap of the data matrix.
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hirieftools galaxyp HiRIEF tools False False
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idconvert galaxyp Convert mass spectrometry identification files on linux or MacOSX False False
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lfq_protein_quant galaxyp Enable protein summarisation and quantitation False False
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pmd_fdr galaxyp Calculate Precursor Mass Discrepancy (PMD) for MS/MS False False
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prot_scriber iuc Protein annotation of short human readable descriptions False False
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protease_prediction bgruening This tool can learn the cleavage specificity of a given class of proteases.
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protein_mosaic_q galaxyp Calculate the Mosaic Q descriptor and visualise amino acid clustering in protein structures
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proteinortho iuc Proteinortho is a tool to detect orthologous proteins/genes within different species. False False
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proteomics_improviser bgruening Visualisation of PepXML files
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proteomics_moff galaxyp moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. False False
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psm_validation galaxyp Validate PSM from Ion Fragmentation False False
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psortb bgruening PSORTb — protein subcellular localization prediction for prokaryotes
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ptxqc galaxyp Quality control reports for MaxQuant results
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pybaselines recetox Baseline correction of extracted ion chromatograms using pybaselines
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pyprophet galaxyp Semi-supervised learning and scoring of OpenSWATH results.
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pyteomics galaxyp Tools using the pyteomics library False False
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quantp galaxyp Correlation between protein and transcript abundance False False
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quantwiz_iq galaxyp Isobaric Quantitation using QuantWiz-IQ False False
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rawtools galaxyp Raw Tools False False
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reactome_pathwaymatcher galaxyp Reactome Pathway Matcher False False
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scop3p iuc Fetch post-translational modifications (PTMs) from Scop3P database
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sipros ufz Labeled protein identification
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sixgill galaxyp Six-frame Genome-Inferred Libraries for LC-MS/MS False False
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sopa iuc sopa – Spatial-omics pipeline and analysis
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spectrast2spectrast_irt galaxyp Filter from spectraST files to swath input files False False
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spectrast2tsv galaxyp Filter from spectraST files to swath input files False False
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swissmodel_modelling_api iuc Fully automated protein structure homology-modelling

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