diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml index 289f9bd..40c896a 100644 --- a/.github/workflows/jekyll.yml +++ b/.github/workflows/jekyll.yml @@ -32,24 +32,18 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout - uses: actions/checkout@v4 + uses: actions/checkout@v6 - name: Setup Ruby - uses: ruby/setup-ruby@v1.204.0 + uses: ruby/setup-ruby@v1 with: ruby-version: '3.3' bundler-cache: true cache-version: 1 - name: Install Mermaid build dependencies run: | - # Chrome sudo apt-get update - sudo apt-get install -y google-chrome-stable - # Install Puppeteer Browsers - npx puppeteer browsers install chrome-headless-shell # Install Mermaid - sudo npm install -g @mermaid-js/mermaid-cli # Install Mermaid CLI - # Install Ruby dependencies - bundle install + npm install -g @mermaid-js/mermaid-cli - name: Setup Pages id: pages uses: actions/configure-pages@v5 @@ -66,7 +60,7 @@ jobs: JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }} - name: Upload artifact # Automatically uploads an artifact from the './_site' directory by default - uses: actions/upload-pages-artifact@v3 + uses: actions/upload-pages-artifact@v4 # Deployment job deploy: diff --git a/404.html b/404.html index 086a5c9..324c556 100644 --- a/404.html +++ b/404.html @@ -1,25 +1,13 @@ --- permalink: /404.html -layout: default +layout: page --- - - -
-

404

- -

Page not found :(

-

The requested page could not be found.

+
+

Page not found

+

The requested page could not be found.

+

+ Back to home + Browse metadata sources +

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resource-table-all: " " - -exclude: - - README.md - - .gitignore - - var/ - - vendor - - Gemfile* - - LICENSE diff --git a/_data/CONTRIBUTORS.yml b/_data/CONTRIBUTORS.yml index 6532fa0..7a46c16 100644 --- a/_data/CONTRIBUTORS.yml +++ b/_data/CONTRIBUTORS.yml @@ -42,3 +42,7 @@ Veit Schwämmle: email: veits@bmb.sdu.dk orcid: 0000-0002-9708-6722 affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark +Mihail Anton: + git: mihai-sysbio + orcid: 0000-0002-7753-9042 + affiliation: ELIXIR \ No newline at end of file diff --git a/_data/topnav.yml b/_data/topnav.yml index e528ae6..4bebd1e 100644 --- a/_data/topnav.yml +++ b/_data/topnav.yml @@ -15,7 +15,7 @@ subitems: url: /contributors - title: Contacts url: /contacts - - title: Publications and presentations + - title: Publications url: /publications - title: Credits url: /credits diff --git a/_posts/2024-04-29-welcome-to-jekyll.markdown b/_posts/2024-04-29-welcome-to-jekyll.markdown deleted file mode 100644 index bc30d3c..0000000 --- a/_posts/2024-04-29-welcome-to-jekyll.markdown +++ /dev/null @@ -1,28 +0,0 @@ ---- -title: "Welcome to Jekyll!" -date: 2024-04-29 22:09:46 +0200 -categories: jekyll update ---- -You’ll find this post in your `_posts` directory. Go ahead and edit it and re-build the site to see your changes. You can rebuild the site in many different ways, but the most common way is to run `jekyll serve`, which launches a web server and auto-regenerates your site when a file is updated. - -Jekyll requires blog post files to be named according to the following format: - -`YEAR-MONTH-DAY-title.MARKUP` - -Where `YEAR` is a four-digit number, `MONTH` and `DAY` are both two-digit numbers, and `MARKUP` is the file extension representing the format used in the file. After that, include the necessary front matter. Take a look at the source for this post to get an idea about how it works. - -Jekyll also offers powerful support for code snippets: - -{% highlight ruby %} -def print_hi(name) - puts "Hi, #{name}" -end -print_hi('Tom') -#=> prints 'Hi, Tom' to STDOUT. -{% endhighlight %} - -Check out the [Jekyll docs][jekyll-docs] for more info on how to get the most out of Jekyll. File all bugs/feature requests at [Jekyll’s GitHub repo][jekyll-gh]. If you have questions, you can ask them on [Jekyll Talk][jekyll-talk]. - -[jekyll-docs]: https://jekyllrb.com/docs/home -[jekyll-gh]: https://github.com/jekyll/jekyll -[jekyll-talk]: https://talk.jekyllrb.com/ diff --git a/applications.md b/applications.md index c1b186a..4690c5c 100644 --- a/applications.md +++ b/applications.md @@ -5,4 +5,4 @@ title: Applications page_id: applications --- - +RSEc metadata supports a variety of downstream applications, from workflow catalogues to benchmarking dashboards. Browse the applications below to see how the ecosystem is reused. diff --git a/assets/img/logo-rsec.bmp b/assets/img/logo-rsec.bmp deleted file mode 100644 index 2be6a1b..0000000 Binary files a/assets/img/logo-rsec.bmp and /dev/null differ diff --git a/contributors.md b/contributors.md index 2dbe2d9..a4c981c 100644 --- a/contributors.md +++ b/contributors.md @@ -4,7 +4,7 @@ title: Contributors --- - +The Research Software Ecosystem is built by a community across ELIXIR and collaborating organisations. The list below is generated from `_data/CONTRIBUTORS.yml`. {% include contributor-tiles-all.html %} diff --git a/docs.md b/docs.md index 266e6ea..8e9c6d4 100644 --- a/docs.md +++ b/docs.md @@ -7,6 +7,12 @@ title: Documentation ## Introduction The RSEc version-controlled repository federates metadata for research software, predominantly within the life sciences domain. These metadata cover a wide spectrum of use cases, spanning software discovery, evaluation, deployment, and execution. Centralised in an open and version-controlled repository, these metadata can be used to cross-link multiple services, to facilitate curation, and to provide insights on bioinformatics software through their aggregation and analysis. This page contains the information and links to access and understand the software metadata provided by the Research Software Ecosystem, as well as contribution guidelines and support channels. +## Quick start +- Browse metadata directly in the [RSEc content repository](https://github.com/research-software-ecosystem/content) (see `data` and `imports`). +- Check the [imports workflow](https://github.com/research-software-ecosystem/content/tree/master/.github/workflows/import.yaml) to see when each source is refreshed. +- Use the cross-links in the table below to jump between sources (e.g. bio.tools IDs, Bioconda packages, Galaxy tool IDs). +- Open an issue in the [content repo issue tracker](https://github.com/research-software-ecosystem/content/issues) if you spot a metadata problem. + ## Metadata Repository contents The RSEc metadata can be accessed on [the GitHub dedicated repository](https://github.com/research-software-ecosystem/content). The main folders to access metadata are: the `imports` folder, which contains one subfolder per metadata source, and the `data` folder, which contains one subfolder for each of the bio.tools entries, combining bio.tools tools and metadata files which are directly linked to it. An example of this organisation is illustrated in Figure 1. @@ -41,6 +47,12 @@ The RSEc metadata can be accessed on [the GitHub dedicated repository](https://g

+## How to use the metadata +- **Discover tools**: search `data/` folders to see aggregated metadata across registries. +- **Validate metadata**: compare entries across sources (e.g. bio.tools vs OpenEBench) and file PRs to fix discrepancies. +- **Integrate programmatically**: consume the raw JSON/YAML from the repository or mirror it to your own services. +- **Automate updates**: use the weekly imports as a stable schedule for downstream synchronisation. + ## Supported Formats Details about the specific formats for each of the federated resources can be found in the following places: diff --git a/index.md b/index.md index 535dce7..e14a77e 100644 --- a/index.md +++ b/index.md @@ -1,10 +1,9 @@ --- -# Feel free to add content and custom Front Matter to this file. -# To modify the layout, see https://jekyllrb.com/docs/themes/#overriding-theme-defaults - +title: The Ecosystem ---
+

Discover, trust, and reuse research software metadata

ELIXIR Research Software Ecosystem (RSEc) centralizes and curates high-quality metadata for computational biology software tools, providing a single, trusted resource for researchers. By synchronizing metadata from major software-related services, RSEc enables the discovery, validation and cross-linking of software information. Researchers can use the resource to explore software metadata and improve the consistency and quality of information across the computational biology landscape.

@@ -14,6 +13,10 @@

ELIXIR is a European research infrastructure which manages and safeguards the massive amounts of life science data and tools being generated by publicly-funded research. RSEc has been developed as part of the ELIXIR Tools Platform.

+

+ View metadata sources + Read the documentation +

RSEc diagram diff --git a/licence.md b/licence.md index 3f8679a..8aeb690 100644 --- a/licence.md +++ b/licence.md @@ -1,8 +1,7 @@ --- # Feel free to add content and custom Front Matter to this file. # To modify the layout, see https://jekyllrb.com/docs/themes/#overriding-theme-defaults - +title: License --- - [Code for the Research Software Ecosystem](https://github.com/research-software-ecosystem/utils) is available under the terms of the [MIT license](https://github.com/research-software-ecosystem/utils/blob/main/LICENSE). -- [Contents of the Research Software Ecosystem](https://github.com/research-software-ecosystem/content) is available under the terms of the [Creative Commons Attribution 4.0 International license](https://github.com/research-software-ecosystem/content/blob/master/LICENSE), unless stated otherwise for specific contr -ibutions. +- [Contents of the Research Software Ecosystem](https://github.com/research-software-ecosystem/content) is available under the terms of the [Creative Commons Attribution 4.0 International license](https://github.com/research-software-ecosystem/content/blob/master/LICENSE), unless stated otherwise for specific contributions. diff --git a/sources.md b/sources.md index 09ce142..aff874b 100644 --- a/sources.md +++ b/sources.md @@ -4,3 +4,7 @@ title: Sources page_id: sources --- + +The RSEc aggregates metadata from the registries and services below. Each source is refreshed regularly through the automated import workflows. For technical details on update schedules and formats, see the [Documentation page](/docs). + +Explore the sources below to learn how each registry contributes metadata to the ecosystem.