mkdocs overtaken with quarto

.github/workflows/render_page.yml

@@ -1,17 +1,36 @@
-name: render page
-on:
+on: 
   push:
-    branches:
-      - main
+    branches: main
+  workflow_dispatch:
+
+name: Quarto Publish
+
 jobs:
-  deploy:
+  build-deploy:
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - name: Install libcurl on Linux
+        if: runner.os == 'Linux'
+        run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev
+
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
         with:
-          python-version: 3.x
-      - run: |
-          pip install mkdocs-material mkdocs-table-reader-plugin mkdocs-bibtex neoteroi-mkdocs mkdocs-video mkdocs-minify-plugin mkdocs-jupyter mkdocs-git-revision-date-localized-plugin
-          mkdocs gh-deploy --force
- 
+          version: '1.3.450' 
+          tinytex: true
+
+#      - name: Install R
+#        uses: r-lib/actions/setup-r@v2
+
+#      - name: Install R Dependencies
+#        uses: r-lib/actions/setup-renv@v2
+
+      - name: Render and Publish
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages

.gitignore

@@ -39,4 +39,6 @@ vignettes/*.pdf
 .Renviron
 
 # Other
-*.DS_Store
+*.DS_Store
+/.quarto/
+_site

_quarto.yml

@@ -0,0 +1,44 @@
+project:
+  type: website
+
+website:
+  title: 'Health Data Science Sandbox'
+  navbar:
+    logo: /img/logo.png
+    left:
+      - href: index.qmd
+        text: Home
+      - href: news.qmd
+        text: News
+      - href: access/index.qmd
+        text: HPC access
+      - href: modules/index.qmd
+        text: Modules
+      - text: Datasets
+        menu:
+          - href: datasets/datapolicy.qmd
+          - href: datasets/synthdata.qmd
+      - href: about/about.qmd
+        text: About
+#      - href: contact/contact.qmd
+#        text: Contact
+
+    right: 
+      - icon: github
+        href: https://github.com/hds-sandbox
+        aria-label: GitHub
+      - icon: linkedin
+        href: https://www.linkedin.com/company/ucph-heads
+        aria-label: LinkedIn
+      - icon: twitter
+        href: https://twitter.com/ucph_heads
+        aria-label: Twitter   
+
+format:
+  html:
+    theme: 
+      light: [materia, css/materialight.scss]
+      dark: darkly
+    toc: true
+#    include-in-header:
+#      - file: "resources/bioschema.html"

develop/about/about.md → about/about.md

@@ -1,33 +1,50 @@
----
-permalink: /about/
-hide:
-  - navigation
-  - toc
-  - footer
----
-
-<h1 align=center style="margin:0px">About the Sandbox</h1>
-<h3 align=center style="margin:0px">an infrastructure project for <br>health data science training and research in Denmark</h3>
-
-The National Health Data Science Sandbox project kicked off in 2021 with 5 years of funding via the Data Science Research Infrastructure initiative from the Novo Nordisk Foundation. Health data science experts at five Danish universities are contributing to the Sandbox with coordination from the Center for Health Data Science under lead PI Professor Anders Krogh. [Data scientists](https://hds-sandbox.github.io/contact/contact.html) hosted in the research groups of each PI are building infrastructure and training modules on Computerome and UCloud, the primary academic high performance computing (HPC) platforms in Denmark. 
-
-<figure markdown>
-  ![workflow](../assets/images/Sandbox_PIs.png){ width="60%" }
-</figure>
-
-Our computational 'sandbox' allows data scientists to explore datasets, tools and analysis pipelines in the same high performance computing environments where real research projects are conducted. Rather than a single, hefty environment, we're deploying modularized topical environments tailored for independent use on each HPC platform. We aim to support three key user groups based at Danish universities:
-
-- trainees: use our training modules to learn analysis techniques with some guidance and guardrails - for your data type of interest AND for general good practices for HPC environments     
-- researchers: prototype your tools and algorithms with an array of good quality datasets that are GDPR compliant and free to access
-- educators: develop your next course with computational assignments in the HPC environment your students will use for their research
-
-Activity developing independent training modules and hosting workshops has centered on UCloud, while collaborative construction of a flexible Course Platform has been completed on Computerome for use by the Sandbox and independent educators. Publicly sourced datasets are being used in training modules on UCloud, while generation of synthetic data is an ongoing project at Computerome. Sandbox resources are under active construction, so check out our other pages for the current status on [HPC Access](https://hds-sandbox.github.io/access/index.html), [Datasets](https://hds-sandbox.github.io/datasets/datapolicy.html), and [Modules](https://hds-sandbox.github.io/modules/index.html). We run workshops using completed training modules on a regular basis and provide active support for Sandbox-hosted courses through a slack workspace. See our [Contact](https://hds-sandbox.github.io/contact/contact.html) page for more information.
-
----
-
-<center> **Partner with the Sandbox** </center> 
-The Sandbox welcomes proposals for new courses, modules, and prototyping projects from researchers and educators. We'd like to partner with lecturers engaged with us in developing needed materials collaboratively - we would love to have input from subject experts or help promote exciting new tools and analysis methods via modules! Please contact us with your ideas at [nhds_sandbox@sund.ku.dk](mailto:nhds_sandbox@sund.ku.dk).
-
----
-
-**We thank the Novo Nordisk Foundation for funding support. If you use the Sandbox for research or reference it in text or presentations, please acknowledge the Health Data Science Sandbox project and its funder the Novo Nordisk Foundation (grant number NNF20OC0063268).**
+---
+title: "About the Sandbox"
+listing:
+  fields: [image, title, description]
+  contents: ../cards/*.qmd
+  type: default
+  sort:
+    - "date desc"
+---
+
+**An infrastructure project for health data science training and research in Denmark**
+
+The National Health Data Science Sandbox project kicked off in 2021 with 5 years of funding via the Data Science Research Infrastructure initiative from the Novo Nordisk Foundation. Health data science experts at five Danish universities are contributing to the Sandbox with coordination from the Center for Health Data Science under lead PI Professor Anders Krogh. [Data scientists](../contact/contact.qmd) hosted in the research groups of each PI are building infrastructure and training modules on Computerome and UCloud, the primary academic high performance computing (HPC) platforms in Denmark. 
+
+
+![](../images/Sandbox_PIs.png){fig-align="center" width="60%"}
+
+Our computational 'sandbox' allows data scientists to explore datasets, tools and analysis pipelines in the same high performance computing environments where real research projects are conducted. Rather than a single, hefty environment, we're deploying modularized topical environments tailored for independent use on each HPC platform. We aim to support three key user groups based at Danish universities:
+
+- trainees: use our training modules to learn analysis techniques with some guidance and guardrails - for your data type of interest AND for general good practices for HPC environments     
+- researchers: prototype your tools and algorithms with an array of good quality datasets that are GDPR compliant and free to access
+- educators: develop your next course with computational assignments in the HPC environment your students will use for their research
+
+Activity developing independent training modules and hosting workshops has centered on UCloud, while collaborative construction of a flexible Course Platform has been completed on Computerome for use by the Sandbox and independent educators. Publicly sourced datasets are being used in training modules on UCloud, while generation of synthetic data is an ongoing project at Computerome. Sandbox resources are under active construction, so check out our other pages for the current status on [HPC Access](../access/index.qmd), [Datasets](../datasets/datapolicy.qmd), and [Modules](../modules/index.qmd). We run workshops using completed training modules on a regular basis and provide active support for Sandbox-hosted courses through a slack workspace. See our [Contact](../contact/contact.qmd) page for more information.
+
+---
+
+# Partner with the Sandbox
+
+The Sandbox welcomes proposals for new courses, modules, and prototyping projects from researchers and educators. We'd like to partner with lecturers engaged with us in developing needed materials collaboratively - we would love to have input from subject experts or help promote exciting new tools and analysis methods via modules! Please contact us with your ideas at [nhds_sandbox@sund.ku.dk](mailto:nhds_sandbox@sund.ku.dk).
+
+---
+
+**We thank the Novo Nordisk Foundation for funding support. If you use the Sandbox for research or reference it in text or presentations, please acknowledge the Health Data Science Sandbox project and its funder the Novo Nordisk Foundation (grant number NNF20OC0063268).**
+
+# Contact the sandbox team
+
+The Health Data Science Sandbox is coordinated by the [Center for Health Data Science](https://heads.ku.dk/)
+at the University of Copenhagen (KU).  Sandbox data scientists are also placed in collaborating groups at
+the Technical University of Denmark (DTU), University of Southern Denmark (SDU), Aarhus University (AU),
+and Aalborg University (AAU).
+
+To get in touch with the Sandbox or be connected with Sandbox staff at your university,
+please [email us](mailto:nhds_sandbox@sund.ku.dk). To obtain module material for use in your
+own compute environment, see our GitHub organization page
+at [hds-sandbox](https://github.com/hds-sandbox/).
+
+We appreciate the contributions of previous team members José Alejandro Romero Herrera (KU), Conor O'Hare (KU), Sander Boisen Valentin (AAU) and Peter Husen (SDU).
+
+You can find all the team members and their contacts below:

develop/access/Computerome.md → access/Computerome.qmd

@@ -11,7 +11,7 @@ hide:
 
 # Accessing the Sandbox on Computerome
 
-<b>We do not currently support independent use of Sandbox materials on Computerome</b>. Access is supported via courses collaborating with the Sandbox and run on Computerome's [Course Platform](https://computerome.dk/solutions/course-platform). Check [here](https://hds-sandbox.github.io/access/index.html) for more info. 
+<b>We do not currently support independent use of Sandbox materials on Computerome</b>. Access is supported via courses collaborating with the Sandbox and run on Computerome's [Course Platform](https://computerome.dk/solutions/course-platform). Check [here](index.qmd) for more info. 
 
 *The below instructions are provided as reference for course participants.*
 

access/genomedk.qmd

@@ -0,0 +1 @@
+sss

develop/access/index.md → access/index.qmd

@@ -1,31 +1,44 @@
----
-layout: default
-title: HPC Access
-has_children: true
-nav_order: 3
-permalink: /access
-hide:
-  - footer
-  - toc
----
-
-<h1 align="center" style="margin:0px">HPC Access</h1>
-
-The Sandbox is collaborating with the two major academic high performance computing platforms in Denmark. Computerome is located at the Technical University of Denmark (and co-owned by the University of Copenhagen) while UCloud is owned by the University of Southern Denmark. These HPC platforms each have their own strengths which we leverage in the Sandbox in different ways.
-
----
-
-<h3 align="center" style="margin:0px">Computerome</h3>
-
-[Computerome](https://computerome.dk/) is the home of many sensitive health datasets via collaborations between DTU, KU, Rigshospitalet, and other major health sector players in the Capital Region of Denmark. Computerome has recently launched their secure cloud platform, [DELPHI](https://computerome.dk/solutions/delphi), and in collaboration with the Sandbox has built a [Course Platform](https://computerome.dk/solutions/course-platform) on the same backbone such that courses and training can be conducted in the same environment as real research would be performed in the secure cloud. The Sandbox is supporting courses in the Course Platform, but it is also available for independent use by educators at Danish universities. Please see their website for more information on independent use and pricing, and [contact us](mailto:nhds_sandbox@sund.ku.dk) if you'd like to collaborate on hosting a course on Computerome. We can help with tool installation, environment testing, and user support (ranging from using the environment to course content if we have Sandbox staff with matching expertise).
-
-Participants in courses co-hosted by the Sandbox can check [here](https://hds-sandbox.github.io/access/Computerome.html) for access instructions. 
-
---- 
-
-<h3 align="center" style="margin:0px">UCloud</h3>
-
-[UCloud](https://cloud.sdu.dk/app/login) is a relatively new HPC platform that can be accessed by students at Danish universities (via a WAYF university login). It has a user friendly graphical user interface that supports straightforward project, user, and resource management. UCloud provides access to many tools via selectable Apps matched with a range of flexible compute resources, and the Sandbox is deploying training modules in this form such that any UCloud user can easily access Sandbox materials independently. The Sandbox is also hosting workshops and training events on UCloud in conjunction with in-person training. 
-
-Check out UCloud's extensive user docs [here](https://docs.cloud.sdu.dk/index.html) and instructions for how to access Sandbox apps [here](https://hds-sandbox.github.io/access/UCloud.html).
-
+---
+title: "HPC access"
+format: html
+date-modified: last-modified
+date-format: long
+date: 2024-01-01
+---
+
+
+The Sandbox is collaborating with the two major academic high performance computing platforms in Denmark. Computerome is located at the Technical University of Denmark (and co-owned by the University of Copenhagen) while UCloud is owned by the University of Southern Denmark. These HPC platforms each have their own strengths which we leverage in the Sandbox in different ways.
+
+---
+
+## Computerome
+
+[Computerome](https://computerome.dk/) is the home of many sensitive health datasets via collaborations between DTU, KU, Rigshospitalet, and other major health sector players in the Capital Region of Denmark. Computerome has recently launched their secure cloud platform, [DELPHI](https://computerome.dk/solutions/delphi), and in collaboration with the Sandbox has built a [Course Platform](https://computerome.dk/solutions/course-platform) on the same backbone such that courses and training can be conducted in the same environment as real research would be performed in the secure cloud. The Sandbox is supporting courses in the Course Platform, but it is also available for independent use by educators at Danish universities. Please see their website for more information on independent use and pricing, and [contact us](mailto:nhds_sandbox@sund.ku.dk) if you'd like to collaborate on hosting a course on Computerome. We can help with tool installation, environment testing, and user support (ranging from using the environment to course content if we have Sandbox staff with matching expertise).
+
+Participants in courses co-hosted by the Sandbox can check [here](Computerome.qmd) for access instructions. 
+
+--- 
+
+## Ucloud
+
+[UCloud](https://cloud.sdu.dk/app/login) is a relatively new HPC platform that can be accessed by students at Danish universities (via a WAYF university login). It has a user friendly graphical user interface that supports straightforward project, user, and resource management. UCloud provides access to many tools via selectable Apps matched with a range of flexible compute resources, and the Sandbox is deploying training modules in this form such that any UCloud user can easily access Sandbox materials independently. The Sandbox is also hosting workshops and training events on UCloud in conjunction with in-person training. 
+
+Check out UCloud's extensive user docs [here](https://docs.cloud.sdu.dk/index.html) and instructions for how to access Sandbox apps [here](UCloud.qmd).
+
+--- 
+
+## GenomeDK
+
+TBA soon
+
+--- 
+
+## Any other computing cluster
+
+TBA soon
+
+---
+
+## Your local PC
+
+TBA soon

access/other.qmd

@@ -0,0 +1 @@
+sss

cards/AlbaMartinez.qmd

@@ -0,0 +1,14 @@
+---
+title: "Alba Refoyo Martinez"
+description: "Data Scientist, Copenhagen University"
+#https://emojidb.org/quarto-emojis for emojis copypaste
+---
+
+![](alba.jpg){width=300}
+
+
+[![](LinkedIN.png){width=50}](https://dk.linkedin.com/in/albarefoyo)   [![](Github_black.png){width=50}](https://github.com/albarema)   [![](Outlook.png){width=50}](alba.martinez@sund.ku.dk?subject=Test)   [![](mapPin.png){width=50}](https:heads.ku.dk)
+
+
+Alba is a Sandbox data scientist based at the University of Copenhagen. During her academic background as a PhD and Postdoc she has developed a solid expertise in large-scale genomics and pipelines development on computing clusters.
+

cards/JacobHansen.qmd

@@ -0,0 +1,15 @@
+---
+title: "Jacob Fredegaard Hansen"
+description: "Data Scientist, Southern Denmark University"
+#https://emojidb.org/quarto-emojis for emojis copypaste
+---
+
+![](jaCob.jpg){width=300}
+
+
+[![](LinkedIN.png){width=50}](https://www.linkedin.com/in/jacobfh)   [![](Github_black.png){width=50}](https://github.com/jacobfh1)   [![](Outlook.png){width=50}](jfredegaard@bmb.sdu.dk?subject=Test)   [![](mapPin.png){width=50}](https://www.sdu.dk/en/forskning/biomedical-ms)   [![](www.png){width=50}](https://jacobfh.com/)   
+
+
+Jacob is a Sandbox data scientist based at the university of Southern Danmark in Odense, and he is specialized in the proteomics applications. 
+
+

cards/JakobSkelmose.qmd

@@ -0,0 +1,13 @@
+---
+title: "Jakob Skelmose"
+description: "Data Scientist, Aalborg University"
+#https://emojidb.org/quarto-emojis for emojis copypaste
+---
+
+![](jaKob.jpg){width=300}
+
+
+[![](Github_black.png){width=50}](https://github.com/tzuV)   [![](Outlook.png){width=50}](mailto:jbks@dcm.aau.dk?subject=Test)   [![](mapPin.png){width=50}](https://www.klinisk.aau.dk/forskning/forskningsenheder-og-centre/center-for-clinical-data-science)   [![](www.png){width=50}](https://vbn.aau.dk/da/persons/148971)   
+
+
+Jakob is a Sandbox data scientist based at the university of Aalborg. His work is mainly focused on applications related to synthetic data, both for reserch and teaching purposes.

cards/JenniferBartell.qmd

@@ -0,0 +1,12 @@
+---
+title: "Jennifer Bartell"
+description: "Data Scientist and Project coordinator, Copenhagen University"
+#https://emojidb.org/quarto-emojis for emojis copypaste
+---
+
+![](jennie.jpg){width=300}
+
+
+[![](LinkedIN.png){width=50}](https://dk.linkedin.com/in/jagbartell)   [![](Outlook.png){width=50}](mailto:bartell@sund.ku.dk?subject=Test)   [![](mapPin.png){width=50}](https://heads.ku.dk/)   
+
+Jenifer is the Sandbox project coordinator, beyond being also a data scientist. She is based at the university of Copenhagen. Jennifer has a long experience in bacterial genomics and metabolomics, transcriptomics and pathway analysis.