Use macros for events, add readme, add issue template for educational…

… resource

.github/ISSUE_TEMPLATE/new-educational-resource.yml

@@ -0,0 +1,59 @@
+name: Add an educational resource
+description: Propose to add a new entry to the educational resources
+labels: ["education", "education-form"]
+body:
+  - type: input
+    id: resource-name
+    attributes:
+      label: Resource name
+      description: Succinct name of the resource, for instance `Lectures on Computation Proteomics by Prof. X`
+    validations:
+      required: true
+  - type: input
+    id: resource-year
+    attributes:
+      label: Year the resource was published
+      placeholder: yyyy
+    validations:
+      required: true
+  - type: input
+    id: resource-url
+    attributes:
+      label: Resource URL
+      description: URL to the event website, for instance `https://hupo2024.org`
+      placeholder: https://example.com/
+    validations:
+      required: true
+  - type: textarea
+    id: resource-description
+    attributes:
+      label: Resource description
+      description: Very brief description of the resource.
+    validations:
+      required: false
+  - type: dropdown
+    id: resource-type
+    attributes:
+      label: Resource type
+      options:
+        - Lecture
+        - Course
+        - Workshop
+        - Tutorial
+        - Other
+    validations:
+      required: true
+  - type: checkboxes
+    id: relevance
+    attributes:
+      label: Relevance to the European proteomics community
+      options:
+        - label: I confirm that this resource is relevant to the European proteomics community
+          required: true
+  - type: checkboxes
+    id: availability
+    attributes:
+      label: Availability
+      options:
+        - label: I confirm that this resource is freely available to the public
+          required: true

.github/ISSUE_TEMPLATE/new-event.yml

@@ -1,6 +1,6 @@
 name: Add an event
 description: Propose to add a new entry to the event calendar
-labels: ["event"]
+labels: ["event", "event-form"]
 body:
   - type: input
     id: event-name
@@ -12,18 +12,34 @@ body:
   - type: input
     id: event-dates
     attributes:
-      label: Event dates
+      label: Event date range
       description: Event date range in the format dd-dd month yyyy, for instance `20-24 October 2024`
       placeholder: dd-dd month yyyy
     validations:
       required: true
+  - type: input
+    id: event-start
+    attributes:
+      label: Event start date
+      description: Event start date in the format yyyy-mm-dd, for instance `2024-10-20`
+      placeholder: yyyy-mm-dd
+    validations:
+      required: true
   - type: input
     id: event-location
     attributes:
       label: Event location
       description: City and country where the event takes place, for instance `Dresden, Germany`
     validations:
       required: true
+  - type: input
+    id: event-url
+    attributes:
+      label: Event URL
+      description: URL to the event website, for instance `https://hupo2024.org`
+      placeholder: https://example.com/
+    validations:
+      required: true
   - type: textarea
     id: event-description
     attributes:

README.md

@@ -1,2 +1,33 @@
-# proteomics-academy
-Proteomics Academy website
+# Proteomics Academy
+
+Proteomics Academy is a collection of tutorials and resources for learning about
+proteomics. We also list upcoming events and recommend Q&A forums and job boards
+for proteomics researchers.
+
+Visit the website at [proteomics-academy.org](https://proteomics-academy.org).
+
+## Contributing
+
+Anyone is welcome to contribute to Proteomics Academy. This can be done by:
+
+- Requesting the addition of a new resource or event through an [issue][issues]
+- Submitting a [pull request][pulls] to add/update content
+- Contacting us at _proteomics-academy [at] eubic-ms [dot] org_.
+
+## Local development
+
+The website is built using mkdocs. To run the website locally, first install
+Python. Then install the project with
+
+```bash
+pip install --editable .
+```
+
+Then run the website with
+
+```bash
+mkdocs serve
+```
+
+[issues]: https://github.com/eubic/proteomics-academy/issues
+[pulls]: https://github.com/eubic/proteomics-academy/pulls

docs/events/index.md

@@ -2,7 +2,7 @@
 
 This page lists conferences, workshops, and webinars that are relevant to the
 proteomics community. If you want to add an event, please [open an issue][issue]
-or [pull request][pr] on GitHub, or contact us at _info [at] eubic-ms.org_.
+or [pull request][pr] on GitHub, or contact us at _proteomics-academy [at] eubic-ms.org_.
 
 [issue]: https://github.com/eubic/proteomics-academy/issues
 [pr]: https://github.com/eubic/proteomics-academy/pulls

docs/events/posts/2024-01-eubic2024.md

@@ -1,13 +1,20 @@
 ---
 date: 2024-01-15
+date_range: 15-19 January 2024
+title: EuBIC-MS Winter School 2024
+location: Winterberg, Germany
+url: https://eubic-ms.org/events/2024-winter-school/
+description: |
+  The EuBIC-MS Winter School is organized each second year by the European
+  Bioinformatics Community for Mass Spectrometry (EuBIC-MS), an initiative of
+  the European Proteomics Association (EuPA) for user-oriented bioinformatics
+  for mass spectrometry-based omics.
 ---
 
-# EuBIC-MS Winter School 2024
+# {{ title }}
 
-:fontawesome-regular-calendar: 15-19 January 2024 <br/>
-:fontawesome-solid-location-dot: Winterberg, Germany <br />
-:material-web: [Info & registration](https://eubic-ms.org/events/2024-winter-school/)
+:fontawesome-regular-calendar: {{ date_range }} <br/>
+:fontawesome-solid-location-dot: {{ location }} <br />
+:material-web: [Info & registration]({{ url }})
 
-The EuBIC-MS Winter School is organized each second year by the European Bioinformatics Community for Mass Spectrometry (EuBIC-MS), an initiative of the European Proteomics Association (EuPA) for user-oriented bioinformatics for mass spectrometry-based omics.
-
-The Winter School starts with an educational day dedicated to workshops and training in established computation MS tools and workflows. The following days, internationally renowned invited speakers give lectures and practical workshops covering the aspects of identification, quantification, result interpretation, and integration of MS data.
+{{ description }}

docs/events/posts/2024-10-hupo.md

@@ -1,11 +1,20 @@
 ---
 date: 2024-10-20
+date_range: 20-24 October 2024
+title: HUPO 2024
+location: Dresden, Germany
+url: https://hupo2024.org/
+description: |
+  The 2024 HUPO World Congress brings together an extraordinary scientific program
+  with world renowned speakers, a variety of workshops, sessions, training courses,
+  poster sessions, networking opportunities, industry seminars, exhibits and much,
+  much more!
 ---
 
-# HUPO 2024
+# {{ title }}
 
-:fontawesome-regular-calendar: 20-24 October 2024 <br/>
-:fontawesome-solid-location-dot: Dresden, Germany <br/>
-:material-web: [Info & registration](https://hupo2024.org/)
+:fontawesome-regular-calendar: {{ date_range }} <br/>
+:fontawesome-solid-location-dot: {{ location }} <br />
+:material-web: [Info & registration]({{ url }})
 
-The 2024 HUPO World Congress brings together an extraordinary scientific program with world renowned speakers, a variety of workshops, sessions, training courses, poster sessions, networking opportunities, industry seminars, exhibits and much, much more!
+{{ description }}

docs/events/posts/2024-10-iscms.md

@@ -1,11 +1,17 @@
 ---
 date: 2024-10-26
+date_range: 26-28 October 2024
+title: iSCMS 2024
+location: Copenhagen, Denmark
+url: https://singlecellms.org
+description: |
+  Single-cell -omics, particularly RNA sequencing, has transformed our understanding of cellular heterogeneity, but traditional methods lack the ability to capture a cell’s complete molecular profile. Recent breakthroughs in single-cell mass spectrometry now allow in-depth analysis of the proteome, lipidome, and metabolome, making it a rapidly growing field. The conference will unite experts from academia and industry to discuss new technologies and applications, fostering collaboration to advance our understanding of cellular biology and drive innovations in medicine.
 ---
 
-# iSCMS 2024
+# {{ title }}
 
-:fontawesome-regular-calendar: 26-28 October 2024 <br/>
-:fontawesome-solid-location-dot: Copenhagen, Denmark <br/>
-:material-web: [Info & registration](https://singlecellms.org)
+:fontawesome-regular-calendar: {{ date_range }} <br/>
+:fontawesome-solid-location-dot: {{ location }} <br />
+:material-web: [Info & registration]({{ url }})
 
-Single-cell -omics, particularly RNA sequencing, has transformed our understanding of cellular heterogeneity, but traditional methods lack the ability to capture a cell’s complete molecular profile. Recent breakthroughs in single-cell mass spectrometry now allow in-depth analysis of the proteome, lipidome, and metabolome, making it a rapidly growing field. The conference will unite experts from academia and industry to discuss new technologies and applications, fostering collaboration to advance our understanding of cellular biology and drive innovations in medicine.
+{{ description }}

docs/events/posts/2024-11-crg-course.md

@@ -1,11 +1,17 @@
 ---
 date: 2024-11-17
+date_range: 17-22 November 2024
+title: Practical Course on Targeted Proteomics
+location: Barcelona, Spain
+url: https://courses.crg.eu/events/targetedproteomics/
+description: |
+  The Practical Course on Targeted Proteomics bridges the gap between theory and practical implementation of targeted proteomics workflows. It includes daily keynote talks, hands-on tutorials, and practical demonstrations covering experimental design and data analysis. Participants will also engage in poster sessions and networking events to discuss research and explore emerging applications.
 ---
 
-# Practical Course on Targeted Proteomics
+# {{ title }}
 
-:fontawesome-regular-calendar: 17-22 November 2024 <br/>
-:fontawesome-solid-location-dot: Barcelona, Spain <br/>
-:material-web: [Info & registration](https://courses.crg.eu/events/targetedproteomics/)
+:fontawesome-regular-calendar: {{ date_range }} <br/>
+:fontawesome-solid-location-dot: {{ location }} <br />
+:material-web: [Info & registration]({{ url }})
 
-The Practical Course on Targeted Proteomics bridges the gap between theory and practical implementation of targeted proteomics workflows. It includes daily keynote talks, hands-on tutorials, and practical demonstrations covering experimental design and data analysis. Participants will also engage in poster sessions and networking events to discuss research and explore emerging applications.
+{{ description }}

docs/events/posts/2024-12-bepac.md

@@ -1,11 +1,17 @@
 ---
 date: 2024-12-05
+date_range: 5-6 December 2024
+title: BePA Conference
+location: Ghent, Belgium
+url: https://belgianproteomics.be/events/bepac/
+description: |
+  The Belgian Proteomics Association has its yearly conference in Ghent, Belgium on December 5-6, 2024. The conference will feature a mix of invited speakers and selected talks from submitted abstracts. The conference will cover a broad range of topics in proteomics, including immunopeptidomics, single-cell proteomics, clinical proteomics, unconventional proteomics, and quality control.
 ---
 
-# BePA Conference
+# {{ title }}
 
-:fontawesome-regular-calendar: 5-6 December 2024 <br/>
-:fontawesome-solid-location-dot: Ghent, Belgium <br/>
-:material-web: [Info & registration](https://belgianproteomics.be/events/bepac/)
+:fontawesome-regular-calendar: {{ date_range }} <br/>
+:fontawesome-solid-location-dot: {{ location }} <br />
+:material-web: [Info & registration]({{ url }})
 
-The Belgian Proteomics Association has its yearly conference in Ghent, Belgium on December 5-6, 2024. The conference will feature a mix of invited speakers and selected talks from submitted abstracts. The conference will cover a broad range of topics in proteomics, including immunopeptidomics, single-cell proteomics, clinical proteomics, unconventional proteomics, and quality control.
+{{ description }}

docs/events/posts/2025-02-eubic2025.md

@@ -1,11 +1,17 @@
 ---
 date: 2025-02-07
+date_range: 7-11 February 2025
+title: EuBIC-MS Developers Meeting 2025
+location: Brixen, Italy
+url: https://eubic-ms.org/events/2025-developers-meeting/
+description: |
+  The EuBIC-MS Developers Meeting is a biennial event that brings together developers of bioinformatics tools for mass spectrometry-based proteomics. The meeting is organized by the European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) and aims to foster collaboration and exchange of knowledge between developers of computational mass spectrometry tools.
 ---
 
-# EuBIC-MS Developers Meeting 2025
+# {{ title }}
 
-:fontawesome-regular-calendar: 7-11 February 2025 <br/>
-:fontawesome-solid-location-dot: Brixen, Italy <br/>
-:material-web: [Info & registration](https://eubic-ms.org/events/2025-developers-meeting/)
+:fontawesome-regular-calendar: {{ date_range }} <br/>
+:fontawesome-solid-location-dot: {{ location }} <br />
+:material-web: [Info & registration]({{ url }})
 
-The EuBIC-MS Developers Meeting is a biennial event that brings together developers of bioinformatics tools for mass spectrometry-based proteomics. The meeting is organized by the European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) and aims to foster collaboration and exchange of knowledge between developers of computational mass spectrometry tools.
+{{ description }}

docs/events/posts/2025-06-eupa.md

@@ -1,10 +1,18 @@
 ---
 date: 2025-06-16
+date_range: 16-20 June 2025
+title: EuPA Conference 2025
+location: Saint-Malo, France
+url: https://eupa.org/events/
+description: |
+  The 2025 conference of the European Proteomics Association will be held in Saint-Malo, France.
+  Stay tuned for more information.
 ---
 
-# EuPA Conference 2025
+# {{ title }}
 
-:fontawesome-regular-calendar: 16-20 June 2025 <br/>
-:fontawesome-solid-location-dot: Saint-Malo, France <br/>
-:material-web: [Info & registration](https://eupa.org/events/)
+:fontawesome-regular-calendar: {{ date_range }} <br/>
+:fontawesome-solid-location-dot: {{ location }} <br />
+:material-web: [Info & registration]({{ url }})
 
+{{ description }}

docs/index.md

@@ -12,7 +12,7 @@ hide:
 
 Proteomics Academy is an educational resource for scientists wanting to exchange on Proteomics. It is a joint effort of the [European Proteomics Association (EuPA)][eupa] educational committee and the [European Bioinformatics Community for Mass Spectrometry (EuBIC-MS)][eubic] to foster exchange of knowledge on proteomics.
 
-The website and its different components are under constant improvement, feel free to explore, share your ideas, and contact us if you want to contribute!
+The website and its different components are under constant improvement. Feel free to explore, share your ideas, and contact us if you want to contribute!
 
 <br/>
 

mkdocs.yml

@@ -1,6 +1,7 @@
 site_name: Proteomics Academy
 site_url: http://eubic.github.io/proteomics-academy/
 repo_url: https://github.com/eubic/proteomics-academy
+repo_name: EuBIC/proteomics-academy
 copyright: This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 License.
 theme:
   name: material
@@ -28,6 +29,7 @@ extra:
       link: https://mstdn.science/@EuBIC_MS
   generator: false
 plugins:
+  - macros
   - blog:
       post_readtime: false
       archive_name: By year
@@ -45,7 +47,6 @@ nav:
   - External links:
     - EuBIC-MS: https://eubic-ms.org/
     - EuPA: https://www.eupa.org/
-
 markdown_extensions:
   - admonition
   - attr_list

pyproject.toml

@@ -1,7 +1,4 @@
 [project]
-name="proteomics_academy"
+name = "proteomics_academy"
 version = "0.0.0"
-dependencies = [
-    "mkdocs",
-    "mkdocs-material",
-]
+dependencies = ["mkdocs", "mkdocs-material", "mkdocs-macros-plugin"]