diff --git a/_config.yml b/_config.yml index 9b0a6ea2690999..9425cbf3181a56 100644 --- a/_config.yml +++ b/_config.yml @@ -27,9 +27,11 @@ small_logo: "assets/images/GTN-60px.png" help_url: https://help.galaxyproject.org/ other_languages: #"fr, ja, es, pt, ar" en: English + de: Deutsch + es: Español + zh-CN: 中文 fr: Français ja: 日本語 - es: Español pt: Português ar: العربية diff --git a/_includes/resource-handson.html b/_includes/resource-handson.html index 673fa3efe79b4b..12c235b94cd6ad 100644 --- a/_includes/resource-handson.html +++ b/_includes/resource-handson.html @@ -19,10 +19,10 @@ Toggle Dropdown diff --git a/_includes/resource-slides.html b/_includes/resource-slides.html index 885a516daf145c..36beb3dae0040c 100644 --- a/_includes/resource-slides.html +++ b/_includes/resource-slides.html @@ -25,23 +25,23 @@ {% endif %}
  • Automatic translations
    • - {% for lang in language %}{% unless lang[0] == 'en' %} -
  • - - {{ lang[1] }} - -
    • + {% for lang in site.other_languages %}{% unless lang[0] == 'en' %} +
  • + + {{ lang[1] }} + +
    • {% endunless %}{% endfor %} -
  • - - More Languages - -
    • +
  • + + More Languages + +
  • - - {% icon text-document aria=false %} Plain text slides - + + {% icon text-document aria=false %} Plain text slides +
    • diff --git a/topics/assembly/images/vgp_assembly/paste_data_to_upload.png b/topics/assembly/images/vgp_assembly/paste_data_to_upload.png new file mode 100644 index 00000000000000..b8be37cb32aae5 Binary files /dev/null and b/topics/assembly/images/vgp_assembly/paste_data_to_upload.png differ diff --git a/topics/assembly/tutorials/vgp_genome_assembly/tutorial.md b/topics/assembly/tutorials/vgp_genome_assembly/tutorial.md index 3ee67350a8a897..56c672b3ab3f87 100644 --- a/topics/assembly/tutorials/vgp_genome_assembly/tutorial.md +++ b/topics/assembly/tutorials/vgp_genome_assembly/tutorial.md @@ -913,19 +913,13 @@ Now that we have looked at our primary assembly with multiple {QC} metrics, we k Before proceeding to purging, we need to carry out some text manipulation operations on the output generated by GenomeScope2 to make it compatible with downstream tools. The goal is to extract some parameters which at a later stage will be used by **purge_dups**. -### Parsing **purge_dups** cutoffs from **GenomeScope2** output +### Getting **purge_dups** cutoffs from **GenomeScope2** output The first relevant parameter is the `estimated genome size`. > Get estimated genome size > ->**Step 1**: Open {% tool [Replace parts of text](toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4) %} ->
    ->**Step 2**: Scroll down to find *"+ Insert Find and Replace"* button and click it. ->
    ->**Step 3**: Scroll down again to find *"+ Insert Find and Replace"* button and click it again. After this you should have *"Find and Replace"* panel repeated three times: *"1: Find and Replace"*, *"2: Find and Replace"*, and *"3: Find and Replace"*. ->
    ->**Step 4**: In {% icon param-file %} *"File to process"*: Select `GenomeScope summary` output (generated during *k*-mer profiling [step](#genome-profiling-with-genomescope2)). The input file should have content that looks like this (it may not be exactly like this): +>**Step 1**: Look at the `GenomeScope summary` output (generated during *k*-mer profiling [step](#genome-profiling-with-genomescope2)). The file should have content that looks like this (it may not be exactly like this): > ``` > GenomeScope version 2.0 > input file = .... @@ -943,23 +937,22 @@ The first relevant parameter is the `estimated genome size`. > Model Fit 92.5159% 96.5191% > Read Error Rate 0.000943206% 0.000943206% >``` +>
    +>**Step 2**: Copy the number value for the maximum Genome Haploid Length to your clipboard (CTRL + C on Windows; CMD + C on MacOS). > ->**Step 5**: In the first Find and Replace panel *"1: Find and Replace"* set the following parameters: -> 1. *"Find pattern"*: `^(?!Genome Haploid Length).*\n` -> 2. *"Find-Pattern is a regular expression"*: Toggle to `Yes` +>**Step 3**: Click on "Upload Data" in the toolbox on the left. > ->
    ->**Step 6**: In the second Find and Replace panel *"2: Find and Replace"* set the following parameters: -> 1. *"Find pattern"*: `Genome Haploid Length\s+(\d{1,3}(?:,\d{3})*\s+bp)\s+(\d{1,3}(?:,\d{3})*)\s+bp` -> 2. *"Replace with"*: `$2` -> 3. *"Find-Pattern is a regular expression"*: Toggle to `Yes` +>**Step 4**: Click on "Paste/Fetch data". > ->
    ->**Step 7**: In the third Find and Replace panel *"3: Find and Replace"* set the following parameters: ->*"Find pattern"*: `,` (Yes, just a comma) +>**Step 5**: Change `New File` to `Estimated genome size`. > ->
    ->**Step 8**: Rename the output as `Estimated genome size`. +>**Step 6**: Paste the maximum Genome Haploid Length into the text box. +> +>**Step 7**: Remove the commas from the number! We only want integers. +> +>**Step 8**: Click "Start". +> +> ![Image showing where to click to upload data as pasted data.](../../images/vgp_assembly/paste_data_to_upload.png "Use the 'paste data' dialog to upload a file with the estimated genome size.") > > > > > diff --git a/topics/dev/tutorials/community-tool-table/images/galaxy_tool_metadata_extractor_pipeline.png b/topics/dev/tutorials/community-tool-table/images/galaxy_tool_metadata_extractor_pipeline.png new file mode 100644 index 00000000000000..40829e66acf489 Binary files /dev/null and b/topics/dev/tutorials/community-tool-table/images/galaxy_tool_metadata_extractor_pipeline.png differ diff --git a/topics/dev/tutorials/community-tool-table/images/microgalaxy_tools.png b/topics/dev/tutorials/community-tool-table/images/microgalaxy_tools.png new file mode 100644 index 00000000000000..d4d5283088f89d Binary files /dev/null and b/topics/dev/tutorials/community-tool-table/images/microgalaxy_tools.png differ diff --git a/topics/dev/tutorials/community-tool-table/tutorial.md b/topics/dev/tutorials/community-tool-table/tutorial.md new file mode 100644 index 00000000000000..cf428ecb4a7dfb --- /dev/null +++ b/topics/dev/tutorials/community-tool-table/tutorial.md @@ -0,0 +1,203 @@ +--- +layout: tutorial_hands_on +title: Creation of an interactive Galaxy tools table for your community +level: Introductory +subtopic: tooldev +questions: +- Is it possible to have an overview of all Galaxy tools for a specific scientific domain? +- How can I create a new overview for a specific Galaxy community or domain? +objectives: +- Create a community reviewed table for Galaxy tools within a specific scientific domain +- Embed an interactive table in a community page +time_estimation: 1H +key_points: +- The Galaxy Tool Metadata Extractor extracts all Galaxy tools to create interactive tables +- The tool tables can be filtered by ToolShed categories and community-reviewed lists of tools to keep or exclude +- The community interactive Galaxy tools table can be embed into any website +tags: +- Community +- SIG +contributions: + authorship: + - bebatut + +--- + +Galaxy offers thousands of tools. They are developed across various GitHub repositories. Furthermore, Galaxy also embraces granular implementation of software tools as sub-modules. In practice, this means that tool suites are separated into Galaxy tools, also known as wrappers, that capture their component operations. Some key examples of suites include [Mothur](https://bio.tools/mothur) and [OpenMS](https://bio.tools/openms), which translate to tens and even hundreds of Galaxy tools. + +While granularity supports the composability of tools into rich domain-specific workflows, this decentralized development and sub-module architecture makes it **difficult for Galaxy users to find and reuse tools**. It may also result in Galaxy tool developers **duplicating efforts** by simultaneously wrapping the same software. This is further complicated by a lack of tool metadata, which prevents filtering for all tools in a specific research community or domain, and makes it all but impossible to employ advanced filtering with ontology terms and operations like [EDAM ontology](https://edamontology.org/page). + +The final challenge is also an opportunity: the global nature of Galaxy means that it is a big community. Solving the visibility of tools across this ecosystem and the potential benefits are far-reaching for global collaboration on tool and workflow development. + +To provide the research community with a comprehensive list of available Galaxy tools, [Galaxy Tool Metadata Extractor](https://github.com/galaxyproject/galaxy_tool_metadata_extractor) was developed to collect Galaxy wrappers from a list of Git repositories and automatically extract their metadata (including Conda version, [bio.tools](https://bio.tools/) identifiers, and EDAM annotations). The workflow also queries the availability of the tools and usage statistics from the three main Galaxy servers (usegalaxy.*). + +![A diagram illustrating the Galaxy Tool Metadata Extractor pipeline, showcasing the various steps involved in creating a community Galaxy tool table.](./images/galaxy_tool_metadata_extractor_pipeline.png "Workflow of the Galaxy Tool Metadata Extractor pipeline. Tool wrappers are parsed from different repositories and additional metadata is retrieved from bio.tools, BioConda, and the main public Galaxy servers. Upon filtering and manual curation of the data for specific scientific communities, the data is transformed into interactive web tables and a tool usage statistic-base word cloud, that can be integrated into any website.") + +The pipeline creates an [interactive table with all tools and their metadata](https://galaxyproject.github.io/galaxy_tool_metadata_extractor/). This table can be **filtered to only include tools that are relevant to a specific research community**. Here is an example for the microbial related tools: + + + +The generated community-specific interactive table can be used as it and/or embedded, e.g. into the respective Galaxy Hub page or Galaxy subdomain. This table allows further filtering and searching for fine-grained tool selection. + +The pipeline is **fully automated** and executes on a **weekly** basis. Any research community can apply the pipeline to create a table specific to their community. + +The aim is this tutorial is to create such table for a community. + +> +> +> In this tutorial, we will cover: +> +> 1. TOC +> {:toc} +> +{: .agenda} + +# Add your community to the Galaxy Tool Metadata Extractor pipeline + +To create a table for a community, you first need to create a new folder in the `data/community` folder within [Galaxy Tool Metadata Extractor code source](https://github.com/galaxyproject/galaxy_tool_metadata_extractor). + +> Create a folder for your community +> +> 1. If not already done, fork the [Galaxy Tool Metadata Extractor repository](https://github.com/galaxyproject/galaxy_tool_metadata_extractor) +> 2. Go to the `data/communities` folder +> 3. Click on **Add file** in the drop-down menu at the top +> 4. Select **Create a new file** +> 5. Fill in the `Name of your file` field with: name of your community + `/categories` +> +> This will create a new folder for your community and add a categories file to this folder. +> +{: .hands_on} + +One of the filters for the main community table is based on the tool categories on the [Galaxy ToolShed](https://toolshed.g2.bx.psu.edu/). Only tools in the selected ToolShed categories will be added to the filtered table. As a result, it is recommended to include broad categories. + +> Select the ToolShed categories +> +> 1. Go to the [Galaxy ToolShed](https://toolshed.g2.bx.psu.edu/) +> 2. On the main page, pick the most obvious categories that represent tools used by your community +> 3. Add the name of these categories in the `categories` file you started above, with 1 ToolShed category per row +> +> For example: +> ``` +> Assembly +> Metagenomics +> ``` +> +> 4. Search on the [Galaxy ToolShed](https://toolshed.g2.bx.psu.edu/) for some of the popular tools in your community +> 5. Open the tool entries on the ToolShed, and note their categories +> 6. Add any new categories to the `categories` file +{: .hands_on} + +Once you have a list of the ToolShed categories that you wish to keep, you can submit this to Galaxy Tool Metadata Extractor. + +> Submit the new community to Galaxy Tool Metadata Extractor +> +> 1. Click on **Commit changes** at the top +> 2. Fill in the commit message with something like `Add X community` +> 3. Click on `Create a new branch for this commit and start a pull request` +> 4. Create the pull request by following the instructions +> +{: .hands_on} + +The Pull Request will be reviewed. Make sure to respond to any feedback. + +Once the Pull Request is merged, the interactive table will be created and made available online at `https://galaxyproject.github.io/galaxy_tool_metadata_extractor/`. + +# Review the generated interactive table + +The interactive table will contain all the tools associated with the ToolShed categories that you selected. However, not all of these tools might be interesting for your community. + +Galaxy Tool Metadata Extractor provides 2 optional filters for tools: +- A list of tools to exclude +- A list of tools that should definitely be kept. + +## Add a list of tools to exclude + +> Add a list of tools to exclude +> +> 1. Open your interactive table +> 2. Search for some tools to exclude +> 3. Go to your community folder on [Galaxy Tool Metadata Extractor repository](https://github.com/galaxyproject/galaxy_tool_metadata_extractor) +> 4. Click on **Add file** drop-down menu on the top +> 5. Select **Create a new file** +> 6. Fill in `tools_to_exclude` in `Name of your file` +> 7. Add the `Galaxy wrapper id` of the tools to exclude, with 1 tool identifier per row +> 8. Submit your changes as before +> 9. Wait for the Pull Request to be merged +> +{: .hands_on} + +## Add a list of tools to keep + +> Add a list of tools to keep +> +> 1. Open your interactive table +> 2. Search for some tools to keep +> 3. Go to your community folder on [Galaxy Tool Metadata Extractor repository](https://github.com/galaxyproject/galaxy_tool_metadata_extractor) +> 4. Click on **Add file** drop-down menu on the top +> 5. Select **Create a new file** +> 6. Fill in `tools_to_keep` in `Name of your file` +> 7. Add the `Galaxy wrapper id` of the tools to keep, with 1 tool identifier per row +> 8. Submit your changes as before +> 9. Wait for the Pull Request to be merged +> +{: .hands_on} + +## Review all tools in your table + +Once the required filters have been implemented, you can review the full list of tools to ensure that you have created an interactive table reflecting the Galaxy tool landscape for your community. + +> Review all tools in your table +> +> 1. Download the `tools.tsv` file in `results/` +> 2. Open `tools.tsv` with a Spreadsheet Software +> 3. Review each line corresponding to a tool +> 1. Change the value in the `Reviewed` column from `False` to `True` +> 2. Add `True` to the `To keep` column if the tool should be kept, and `False` if not +> 4. Extract the list of tools to keep +> 1. Create a sheet for the list of tools to keep to +> 1. Filter on the `To keep` column to keep value `True` +> 2. Keep only the `Galaxy wrapper id` column +> 2. Add this list of `Galaxy wrapper id` to the `tools_to_keep` file +> 5. Extract the list of tools to exclude +> 1. Create a sheet for the list of tools to keep to +> 1. Filter on the `To keep` column to keep value `False` +> 2. Keep only the `Galaxy wrapper id` column +> 2. Add this list of `Galaxy wrapper id` to the `tools_to_exclude` file +> 6. Submit the changes +> 7. Wait for the Pull Request to be merged +> +{: .hands_on} + +You should have now an interactive table reflecting the Galaxy tool landscape for your community. + +# Embed the interactive table in your community page on the Hub + +The interactive table you have created can be embedded in your community page on the Hub, e.g. [microGalaxy](https://galaxyproject.org/community/sig/microbial/#tools). + +> Embed your table as an iframe +> +> 1. If not already done, fork the repository [Galaxy Hub](https://github.com/galaxyproject/galaxy-hub) +> 2. Open or create your community page: `content/community/sig//index.md` +> 3. Add an iframe to embed the interactive table +> +> ``` +> +> ``` +> +> 4. Replace `` by the name of your community in `src` +> 5. Submit the changes +> 7. Wait for the Pull Request to be merged +> +{: .hands_on} + +# Conclusion + +You now have an interactive table with Galaxy tools available for your community, and this table is embedded in a community page. + diff --git a/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.md b/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.md index 0553c1467f230b..5f3008d169f6c2 100644 --- a/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.md +++ b/topics/genome-annotation/tutorials/amr-gene-detection/tutorial.md @@ -22,6 +22,14 @@ tags: - jbrowse1 - microgalaxy subtopic: prokaryote +edam_ontology: +- topic_3673 # Whole genome sequencing +- topic_3305 # Public health and epidemiology +- topic_0622 # Genomics +- topic_3301 # Microbiology +- topic_0080 # Sequence analysis +- topic_3324 # Infectious disease +- topic_4013 # Antimicrobial resistance level: Introductory contributions: diff --git a/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.md b/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.md index 191fe6af0bc4d2..bed7dff2d51053 100644 --- a/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.md +++ b/topics/genome-annotation/tutorials/bacterial-genome-annotation/tutorial.md @@ -22,14 +22,20 @@ tags: - microgalaxy - jbrowse1 subtopic: prokaryote +edam_ontology: +- topic_0622 # Genomics +- topic_3301 # Microbiology +- topic_0623 # Gene and protein families +- topic_0080 # Sequence analysis +- topic_3673 # Whole genome sequencing +- topic_0085 # Functional genomics +- topic_0798 # Mobile genetic elements level: Introductory - contributions: authorship: - bebatut funding: - abromics - follow_up_training: - type: "internal" topic_name: genome-annotation @@ -44,7 +50,6 @@ follow_up_training: topic_name: galaxy-interface tutorials: - history-to-workflow - --- After sequencing and assembly, a genome can be annotated. It is an essential step to describe the genome. diff --git a/topics/microbiome/metadata.yaml b/topics/microbiome/metadata.yaml index 39a6b0bb4458c4..5d30a8b8693bf2 100644 --- a/topics/microbiome/metadata.yaml +++ b/topics/microbiome/metadata.yaml @@ -29,3 +29,17 @@ references: title: "Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences." link: "https://www.ncbi.nlm.nih.gov/pubmed/25118885" summary: "" + +subtopics: + - id: intro + title: "Introduction" + description: "Start here if you are new to microbiome analyses in Galaxy." + - id: metabarcoding + title: "Metabarcoding / Amplicon analyses" + description: "Taxonomic characterisation of mixed samples using a single gene region." + - id: metagenomics + title: "Metagenomics" + description: "Taxonomic and functional characterisation and assembly of mixed samples using whole genome data." + - id: metatranscriptomics + title: "Metatranscriptomics" + description: "Taxonomic and functional characterisation of mixed samples using transcriptome data." \ No newline at end of file diff --git a/topics/microbiome/tutorials/beer-data-analysis/tutorial.md b/topics/microbiome/tutorials/beer-data-analysis/tutorial.md index 52cc0fce2b746c..1fc5db1ef21a00 100644 --- a/topics/microbiome/tutorials/beer-data-analysis/tutorial.md +++ b/topics/microbiome/tutorials/beer-data-analysis/tutorial.md @@ -18,6 +18,7 @@ key_points: - Yeast species but also contamination can be identified and visualized directly from the sequences using several bioinformatics tools - With its graphical interface, Galaxy makes it easy to use the needed bioinformatics tools - Beer microbiome is not just made of yeast and can be quite complex +subtopic: metagenomics tags: - nanopore - beer @@ -34,6 +35,11 @@ contributions: - gallantries redirect_from: - /topics/metagenomics/tutorials/beer-data-analysis/tutorial +edam_ontology: +- topic_3174 # Metagenomics +- topic_3697 # Microbial ecology +- topic_0637 # Taxonomy +- topic_0080 # Sequence analysis --- diff --git a/topics/microbiome/tutorials/general-tutorial/tutorial.md b/topics/microbiome/tutorials/general-tutorial/tutorial.md index 82f8fec7a8ec7f..5e8ea1bb2a4917 100644 --- a/topics/microbiome/tutorials/general-tutorial/tutorial.md +++ b/topics/microbiome/tutorials/general-tutorial/tutorial.md @@ -21,10 +21,17 @@ key_points: contributors: - shiltemann - bebatut +subtopic: intro tags: - microgalaxy redirect_from: - /topics/metagenomics/tutorials/general-tutorial/tutorial +edam_ontology: +- topic_3174 # Metagenomics +- topic_3697 # Microbial ecology +- topic_0637 # Taxonomy +- topic_0080 # Sequence analysis +- topic_4038 # Metabarcoding --- diff --git a/topics/microbiome/tutorials/metagenomics-assembly/tutorial.md b/topics/microbiome/tutorials/metagenomics-assembly/tutorial.md index 8865152585c7c7..aefbd8d0df2b9d 100644 --- a/topics/microbiome/tutorials/metagenomics-assembly/tutorial.md +++ b/topics/microbiome/tutorials/metagenomics-assembly/tutorial.md @@ -35,6 +35,7 @@ contributions: - bebatut funding: - gallantries +subtopic: metagenomics tags: - assembly - metagenomics diff --git a/topics/microbiome/tutorials/metagenomics-binning/tutorial.md b/topics/microbiome/tutorials/metagenomics-binning/tutorial.md index d4e45992fa9fe4..f8f9160b4736a1 100644 --- a/topics/microbiome/tutorials/metagenomics-binning/tutorial.md +++ b/topics/microbiome/tutorials/metagenomics-binning/tutorial.md @@ -26,12 +26,16 @@ contributions: authorship: - npechl - fpsom +subtopic: metagenomics tags: - binning - metagenomics - microgalaxy redirect_from: - /topics/metagenomics/tutorials/metagenomics-binning/tutorial +edam_ontology: +- topic_3174 # Metagenomics +- topic_0196 # Sequence assembly --- Metagenomics is the study of genetic material recovered directly from environmental samples, such as soil, water, or gut contents, without the need for isolation or cultivation of individual organisms. Metagenomics binning is a process used to classify DNA sequences obtained from metagenomic sequencing into discrete groups, or bins, based on their similarity to each other. diff --git a/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.md b/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.md index 5502b28ab51788..e53875a80df35b 100644 --- a/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.md +++ b/topics/microbiome/tutorials/metatranscriptomics-short/tutorial.md @@ -13,6 +13,7 @@ objectives: - Understand where metatranscriptomics fits in 'multi-omic' analysis of microbiomes - Visualise a community structure level: Introductory +subtopic: metatranscriptomics tags: - metatranscriptomics - microgalaxy @@ -34,6 +35,12 @@ contributors: - EngyNasr redirect_from: - /topics/metagenomics/tutorials/metatranscriptomics-short/tutorial +edam_ontology: +- topic_3941 # Metatranscriptomics +- topic_3697 # Microbial ecology +- topic_0637 # Taxonomy +- topic_1775 # Function analysis +- topic_0080 # Sequence analysis --- diff --git a/topics/microbiome/tutorials/metatranscriptomics/tutorial.md b/topics/microbiome/tutorials/metatranscriptomics/tutorial.md index cd6fc154e5cdc8..5e2d3e99f2b572 100644 --- a/topics/microbiome/tutorials/metatranscriptomics/tutorial.md +++ b/topics/microbiome/tutorials/metatranscriptomics/tutorial.md @@ -13,6 +13,7 @@ objectives: - Understand where metatranscriptomics fits in 'multi-omic' analysis of microbiomes - Visualise a community structure level: Introductory +subtopic: metatranscriptomics tags: - metatranscriptomics - microgalaxy @@ -36,6 +37,12 @@ contributors: - EngyNasr redirect_from: - /topics/metagenomics/tutorials/metatranscriptomics/tutorial +edam_ontology: +- topic_3941 # Metatranscriptomics +- topic_3697 # Microbial ecology +- topic_0637 # Taxonomy +- topic_1775 # Function analysis +- topic_0080 # Sequence analysis --- {% include topics/microbiome/tutorials/metatranscriptomics/content.md short=false %} diff --git a/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.md b/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.md index 9cd39f447206ee..480d93b3c8fc81 100644 --- a/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.md +++ b/topics/microbiome/tutorials/mothur-miseq-sop-short/tutorial.md @@ -20,10 +20,18 @@ contributors: - shiltemann - bebatut - tnabtaf +subtopic: metabarcoding tags: + - metabarcoding + - 16S - microgalaxy redirect_from: - /topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial +edam_ontology: +- topic_3697 # Microbial ecology +- topic_0637 # Taxonomy +- topic_0080 # Sequence analysis +- topic_4038 # Metabarcoding --- {% include topics/microbiome/tutorials/mothur-miseq-sop/content.md short=true %} diff --git a/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.md b/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.md index 9416c9141d518a..43356a66d70c81 100644 --- a/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.md +++ b/topics/microbiome/tutorials/mothur-miseq-sop/tutorial.md @@ -20,10 +20,18 @@ contributors: - shiltemann - bebatut - tnabtaf +subtopic: metabarcoding tags: + - metabarcoding + - 16S - microgalaxy redirect_from: - /topics/metagenomics/tutorials/mothur-miseq-sop/tutorial +edam_ontology: +- topic_3697 # Microbial ecology +- topic_0637 # Taxonomy +- topic_0080 # Sequence analysis +- topic_4038 # Metabarcoding --- {% include topics/microbiome/tutorials/mothur-miseq-sop/content.md short=false %} diff --git a/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.md b/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.md index a4315f4a981dfe..83c074bf168172 100644 --- a/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.md +++ b/topics/microbiome/tutorials/nanopore-16S-metagenomics/tutorial.md @@ -16,11 +16,19 @@ key_points: - We preprocessed Nanopore sequences in order to improve their quality contributors: - gallardoalba +subtopic: metabarcoding tags: + - metabarcoding + - 16S - nanopore - microgalaxy redirect_from: - /topics/metagenomics/tutorials/nanopore-16S-metagenomics/tutorial +edam_ontology: +- topic_3697 # Microbial ecology +- topic_0637 # Taxonomy +- topic_0080 # Sequence analysis +- topic_4038 # Metabarcoding --- diff --git a/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md b/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md index 466a22a540489f..e373a2ace85b8a 100644 --- a/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md +++ b/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md @@ -2,6 +2,7 @@ layout: tutorial_hands_on title: "Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition" +subtopic: metagenomics tags: - microgalaxy - Nanopore data analysis diff --git a/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.md b/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.md index 7fd3ff23246594..ade73bff58d10a 100644 --- a/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.md +++ b/topics/microbiome/tutorials/plasmid-metagenomics-nanopore/tutorial.md @@ -22,6 +22,7 @@ key_points: contributors: - willemdek11 - shiltemann +subtopic: metabarcoding tags: - nanopore - plasmids @@ -30,6 +31,14 @@ tags: - microgalaxy redirect_from: - /topics/metagenomics/tutorials/plasmid-metagenomics-nanopore/tutorial +edam_ontology: +- topic_3837 # Metagenomic sequencing +- topic_3305 # Public health and epidemiology +- topic_3174 # Metagenomics +- topic_3301 # Microbiology +- topic_3324 # Infectious disease +- topic_0080 # Sequence analysis +- topic_4013 # Antimicrobial resistance --- # Overview diff --git a/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.md b/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.md index 6c8e1113a81438..e50608428bfbf9 100644 --- a/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.md +++ b/topics/microbiome/tutorials/qiime2-cancer-microbiome-intervention/tutorial.md @@ -4,12 +4,19 @@ title: QIIME 2 Cancer Microbiome Intervention hands_on: external hands_on_url: "https://docs.qiime2.org/jupyterbooks/cancer-microbiome-intervention-tutorial/index.html#" time_estimation: 10H +subtopic: metabarcoding tags: -- metagenomics +- metabarcoding +- 16S - taxonomic profiling - diversity - microgalaxy contributions: authorship: - qiime2 ---- \ No newline at end of file +edam_ontology: +- topic_3697 # Microbial ecology +- topic_0637 # Taxonomy +- topic_0080 # Sequence analysis +- topic_4038 # Metabarcoding +--- diff --git a/topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.md b/topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.md new file mode 100644 index 00000000000000..db03f0b3a49695 --- /dev/null +++ b/topics/microbiome/tutorials/qiime2-moving-pictures/tutorial.md @@ -0,0 +1,21 @@ +--- +layout: tutorial_hands_on +title: QIIME 2 Moving Pictures +hands_on: external +hands_on_url: "https://docs.qiime2.org/2024.2/tutorials/moving-pictures-usage" +time_estimation: 10H +tags: +- metagenomics +- taxonomic profiling +- diversity +- microgalaxy +subtopic: metabarcoding +edam_ontology: +- topic_3697 # Microbial ecology +- topic_0637 # Taxonomy +- topic_0080 # Sequence analysis +- topic_4038 # Metabarcoding +contributions: + authorship: + - qiime2 +--- \ No newline at end of file diff --git a/topics/microbiome/tutorials/taxonomic-profiling/tutorial.md b/topics/microbiome/tutorials/taxonomic-profiling/tutorial.md index 2ecd79f260c3f8..2ce33a274d8c03 100644 --- a/topics/microbiome/tutorials/taxonomic-profiling/tutorial.md +++ b/topics/microbiome/tutorials/taxonomic-profiling/tutorial.md @@ -26,12 +26,18 @@ contributions: - paulzierep funding: - gallantries +subtopic: metagenomics tags: - metagenomics - taxonomic profiling - microgalaxy redirect_from: - /topics/metagenomics/tutorials/taxonomic-profiling/tutorial +edam_ontology: +- topic_3174 # Metagenomics +- topic_3697 # Microbial ecology +- topic_0637 # Taxonomy +- topic_0080 # Sequence analysis --- diff --git a/topics/proteomics/tutorials/metaproteomics/tutorial.md b/topics/proteomics/tutorials/metaproteomics/tutorial.md index 72a7b00c128ad7..d52bee477055d6 100644 --- a/topics/proteomics/tutorials/metaproteomics/tutorial.md +++ b/topics/proteomics/tutorials/metaproteomics/tutorial.md @@ -23,6 +23,11 @@ contributors: - subinamehta subtopic: multi-omics tags: [microgalaxy] +edam_ontology: +- topic_0121 # Proteomics +- topic_3922 # Proteogenomics +- topic_3050 # Biodiversity +- topic_0637 # Taxonomy --- In this metaproteomics tutorial we will identify expressed proteins from a complex bacterial community sample. diff --git a/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md b/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md index 482e96f88762a1..1bf488a772ae13 100644 --- a/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md +++ b/topics/proteomics/tutorials/metaquantome-data-creation/tutorial.md @@ -32,6 +32,11 @@ follow_up_training: subtopic: multi-omics tags: [microgalaxy] +edam_ontology: +- topic_0121 # Proteomics +- topic_3922 # Proteogenomics +- topic_3050 # Biodiversity +- topic_0637 # Taxonomy --- diff --git a/topics/proteomics/tutorials/metaquantome-function/tutorial.md b/topics/proteomics/tutorials/metaquantome-function/tutorial.md index 1f59d1156f782f..dd8262d4cf85fc 100644 --- a/topics/proteomics/tutorials/metaquantome-function/tutorial.md +++ b/topics/proteomics/tutorials/metaquantome-function/tutorial.md @@ -39,6 +39,12 @@ requirements: - metaquantome-data-creation subtopic: multi-omics tags: [microgalaxy] +edam_ontology: +- topic_0121 # Proteomics +- topic_3922 # Proteogenomics +- topic_3941 # Metatranscriptomics +- topic_3697 # Microbial ecology +- topic_3174 # Metagenomics --- diff --git a/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md b/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md index f5cbee103a5e89..05245ed8c78bc9 100644 --- a/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md +++ b/topics/proteomics/tutorials/metaquantome-taxonomy/tutorial.md @@ -36,6 +36,13 @@ requirements: subtopic: multi-omics tags: [microgalaxy] +edam_ontology: +- topic_0121 # Proteomics +- topic_3922 # Proteogenomics +- topic_3941 # Metatranscriptomics +- topic_3697 # Microbial ecology +- topic_3174 # Metagenomics +- topic_0637 # Taxonomy --- diff --git a/topics/variant-analysis/tutorials/microbial-variants/tutorial.md b/topics/variant-analysis/tutorials/microbial-variants/tutorial.md index 60647239bd4c20..096534c4e23d9e 100644 --- a/topics/variant-analysis/tutorials/microbial-variants/tutorial.md +++ b/topics/variant-analysis/tutorials/microbial-variants/tutorial.md @@ -25,6 +25,13 @@ contributors: - annasyme - slugger70 - tseemann +edam_ontology: +- topic_0622 # Genomics +- topic_0196 # Sequence assembly +- topic_2885 # DNA polymorphism +- topic_3301 # Microbiology +- topic_0080 # Sequence analysis +- topic_0199 # Genetic variation --- diff --git a/topics/variant-analysis/tutorials/non-dip/tutorial.md b/topics/variant-analysis/tutorials/non-dip/tutorial.md index 49a3a07f29ff53..316c6eb9da3d63 100644 --- a/topics/variant-analysis/tutorials/non-dip/tutorial.md +++ b/topics/variant-analysis/tutorials/non-dip/tutorial.md @@ -20,6 +20,13 @@ key_points: contributors: - nekrut - astrovsky01 +edam_ontology: +- topic_0622 # Genomics +- topic_0196 # Sequence assembly +- topic_2885 # DNA polymorphism +- topic_3301 # Microbiology +- topic_0080 # Sequence analysis +- topic_0199 # Genetic variation --- diff --git a/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.md b/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.md index 2889ac58320c06..504b4f2198db10 100644 --- a/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.md +++ b/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.md @@ -24,6 +24,13 @@ tags: - prokaryote - one-health - microgalaxy +edam_ontology: +- topic_0622 # Genomics +- topic_3301 # Microbiology +- topic_0196 # Sequence assembly +- topic_0199 # Genetic variation +- topic_3305 # Public health and epidemiology +- topic_3324 # Infectious disease ---