From 3ddf37e8161b64ff5d675533f13d9b66fb2077a5 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 17 Dec 2024 15:12:05 +0100 Subject: [PATCH 01/23] move this to production only --- _plugins/api.rb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/_plugins/api.rb b/_plugins/api.rb index 9b1d41d3c5ed3d..597b5a066c2372 100644 --- a/_plugins/api.rb +++ b/_plugins/api.rb @@ -279,7 +279,9 @@ def generate(site) Jekyll::Hooks.register :site, :post_read do |site| - Gtn::Hooks.by_tool(site) + if Jekyll.env == 'production' + Gtn::Hooks.by_tool(site) + end end # Basically like `PageWithoutAFile`, we just write out the ones we'd created earlier. From 948f4c2ef3a83e5ff316590713100382f4098a47 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 18 Dec 2024 15:19:02 +0100 Subject: [PATCH 02/23] move objectify to util --- _plugins/feeds.rb | 24 ------------------------ _plugins/util.rb | 28 ++++++++++++++++++++++++++++ 2 files changed, 28 insertions(+), 24 deletions(-) diff --git a/_plugins/feeds.rb b/_plugins/feeds.rb index 718b6e62dc207b..312c1c631012d3 100644 --- a/_plugins/feeds.rb +++ b/_plugins/feeds.rb @@ -43,30 +43,6 @@ def track(url) end end -def objectify(attrs, url, path) - obj = attrs.clone - obj['__path'] = path - obj['__url'] = url - - def obj.data - self - end - - def obj.path - self['__path'] - end - - def obj.url - self['__url'] - end - - def obj.content - self.fetch('content', 'NO CONTENT AVAILABLE') - end - - obj -end - FEED_WIDGET_XSLT = Nokogiri::XSLT(File.read('feed-widget.xslt.xml')) def serialise(site, feed_path, builder) diff --git a/_plugins/util.rb b/_plugins/util.rb index 7130ec765edc14..5732a200cdb72b 100644 --- a/_plugins/util.rb +++ b/_plugins/util.rb @@ -154,6 +154,34 @@ def tool_id_extractor(wf, path: []) res end +def objectify(attrs, url, path) + obj = attrs.clone + obj['__path'] = path + obj['__url'] = url + + def obj.data + self + end + + def obj.path + self['__path'] + end + + def obj.url + self['__url'] + end + + def obj.content + self.fetch('content', 'NO CONTENT AVAILABLE') + end + + def obj.title + self['title'] + end + + obj +end + if __FILE__ == $PROGRAM_NAME require 'test/unit' # Testing for the class From 90583f6c3adad8ac1241d42d7bc85ee478f63f8e Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 18 Dec 2024 15:19:20 +0100 Subject: [PATCH 03/23] move resource list to topic filter --- _plugins/feeds.rb | 131 +---------------------------- _plugins/jekyll-topic-filter.rb | 144 ++++++++++++++++++++++++++++++++ 2 files changed, 145 insertions(+), 130 deletions(-) diff --git a/_plugins/feeds.rb b/_plugins/feeds.rb index 312c1c631012d3..d934634795cbc9 100644 --- a/_plugins/feeds.rb +++ b/_plugins/feeds.rb @@ -197,135 +197,6 @@ def generate_tag_topic_feeds(_site) '' end -def all_date_sorted_materials(site) - events = site.pages.select { |x| x['layout'] == 'event' || x['layout'] == 'event-external' } - materials = Gtn::TopicFilter.list_all_materials(site).reject { |k, _v| k['draft'] } - news = site.posts.select { |x| x['layout'] == 'news' } - faqs = site.pages.select { |x| x['layout'] == 'faq' } - pathways = site.pages.select { |x| x['layout'] == 'learning-pathway' } - workflows = Dir.glob('topics/**/*.ga') - - bucket = events.map do |e| - [Gtn::PublicationTimes.obtain_time(e.path).to_datetime, 'events', e, ['event'] + e.data.fetch('tags', [])] - end - - materials.each do |m| - tags = [m['topic_name']] + (m['tags'] || []) - m.fetch('ref_tutorials', []).map do |t| - bucket << [Gtn::PublicationTimes.obtain_time(t.path).to_datetime, 'tutorials', t, tags] - - (t['recordings'] || []).map do |r| - url = '/' + t.path.gsub(/tutorial(_[A_Z_]*)?.(html|md)$/, 'recordings/') - url += "#tutorial-recording-#{Date.parse(r['date']).strftime('%-d-%B-%Y').downcase}" - attr = {'title' => "Recording of " + t['title'], - 'contributors' => r['speakers'] + (r['captions'] || []), - 'content' => "A #{r['length']} long recording is now available."} - - obj = objectify(attr, url, t.path) - bucket << [DateTime.parse(r['date'].to_s), 'recordings', obj, tags] - end - end - - - - m.fetch('ref_slides', []).reject { |s| s.url =~ /-plain.html/ }.map do |s| - bucket << [Gtn::PublicationTimes.obtain_time(s.path).to_datetime, 'slides', s, tags] - - (s['recordings'] || []).map do |r| - url = '/' + s.path.gsub(/slides(_[A_Z_]*)?.(html|md)$/, 'recordings/') - url += "#tutorial-recording-#{Date.parse(r['date']).strftime('%-d-%B-%Y').downcase}" - attr = {'title' => "Recording of " + s['title'], - 'contributors' => r['speakers'] + (r['captions'] || []), - 'content' => "A #{r['length']} long recording is now available."} - obj = objectify(attr, url, s.path) - bucket << [DateTime.parse(r['date'].to_s), 'recordings', obj, tags] - end - end - end - - bucket += news.map do |n| - [n.date.to_datetime, 'news', n, ['news'] + n.data.fetch('tags', [])] - end - - bucket += faqs.map do |n| - tag = Gtn::PublicationTimes.clean_path(n.path).split('/')[1] - [Gtn::PublicationTimes.obtain_time(n.path).to_datetime, 'faqs', n, ['faqs', tag]] - end - - bucket += pathways.map do |n| - tags = ['learning-pathway'] + (n['tags'] || []) - [Gtn::PublicationTimes.obtain_time(n.path).to_datetime, 'learning-pathways', n, tags] - end - - bucket += workflows.map do |n| - tag = Gtn::PublicationTimes.clean_path(n).split('/')[1] - wf_data = JSON.parse(File.read(n)) - - attrs = { - 'title' => wf_data['name'], - 'description' => wf_data['annotation'], - 'tags' => wf_data['tags'], - 'contributors' => wf_data.fetch('creator', []).map do |c| - matched = site.data['contributors'].select{|k, v| - v.fetch('orcid', "does-not-exist") == c.fetch('identifier', "").gsub('https://orcid.org/', '') - }.first - if matched - matched[0] - else - c['name'] - end - end - } - - # These aren't truly stable. I'm not sure what to do about that. - obj = objectify(attrs, '/' + n.gsub(/\.ga$/, '.html'), n) - # obj = objectify(attrs, '/' + n.path[0..n.path.rindex('/')], n) - - - [Gtn::PublicationTimes.obtain_time(n).to_datetime, 'workflows', obj, ['workflows', tag] + obj['tags']] - end - - # Remove symlinks from bucket. - bucket = bucket.reject { |date, type, page, tags| - File.symlink?(page.path) || File.symlink?(File.dirname(page.path)) || File.symlink?(File.dirname(File.dirname(page.path))) - } - - bucket += site.data['contributors'].map do |k, v| - a = {'title' => "@#{k}", - 'content' => "GTN Contributions from #{k}"} - obj = objectify(a, "/hall-of-fame/#{k}/", k) - - [DateTime.parse("#{v['joined']}-01T12:00:00", 'content' => "GTN Contributions from #{k}"), 'contributors', obj, ['contributor']] - end - - bucket += site.data['grants'].map do |k, v| - a = {'title' => "@#{k}", - 'content' => "GTN Contributions from #{k}"} - obj = objectify(a, "/hall-of-fame/#{k}/", k) - - # TODO: backdate grants, organisations - if v['joined'] - [DateTime.parse("#{v['joined']}-01T12:00:00"), 'grants', obj, ['grant']] - end - end.compact - - bucket += site.data['organisations'].map do |k, v| - a = {'title' => "@#{k}", - 'content' => "GTN Contributions from #{k}"} - obj = objectify(a, "/hall-of-fame/#{k}/", k) - - if v['joined'] - [DateTime.parse("#{v['joined']}-01T12:00:00"), 'organisations', obj, ['organisation']] - end - end.compact - - bucket - .reject{|x| x[0] > DateTime.now } # Remove future-dated materials - .reject{|x| x[2]['draft'] == true } # Remove drafts - .sort_by {|x| x[0] } # Date-sorted, not strictly necessary since will be grouped. - .reverse -end - def group_bucket_by(bucket, group_by: 'day') case group_by when 'day' @@ -718,7 +589,7 @@ def generate_event_feeds(site) {title: 'Events', url: "#{site.config['url']}#{site.baseurl}/events/feed.xml"} ] - bucket = all_date_sorted_materials(site) + bucket = Gtn::TopicFilter.all_date_sorted_resources(site) bucket.freeze opml['GTN Topics'] = [] diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index 8e096b899452c8..517d25e9a18513 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -3,6 +3,7 @@ require 'json' require 'yaml' require './_plugins/gtn' +require './_plugins/util' require 'securerandom' module Gtn @@ -1235,6 +1236,149 @@ def self.list_materials_by_tool(site) # Order by most popular tool t.sort_by { |_k, v| v['tutorials'].length }.reverse.to_h end + + + ## + # Not materials but resources (including e.g. recordings, slides separate from tutorials, etc.) + # + # The structure is a large array of arrays, with [date, category, page-like object, tags] + # + # [#, + # "tutorials", + # #, + # ["single-cell"]], + # [#, + # "tutorials", + # #, + # ["single-cell"]], + # [#, + # "slides", + # #, + # ["single-cell"]]] + + def self.all_date_sorted_resources(site) + events = site.pages.select { |x| x['layout'] == 'event' || x['layout'] == 'event-external' } + materials = list_all_materials(site).reject { |k, _v| k['draft'] } + news = site.posts.select { |x| x['layout'] == 'news' } + faqs = site.pages.select { |x| x['layout'] == 'faq' } + pathways = site.pages.select { |x| x['layout'] == 'learning-pathway' } + workflows = Dir.glob('topics/**/*.ga') + + bucket = events.map do |e| + [Gtn::PublicationTimes.obtain_time(e.path).to_datetime, 'events', e, ['event'] + e.data.fetch('tags', [])] + end + + materials.each do |m| + tags = [m['topic_name']] + (m['tags'] || []) + m.fetch('ref_tutorials', []).map do |t| + bucket << [Gtn::PublicationTimes.obtain_time(t.path).to_datetime, 'tutorials', t, tags] + + (t['recordings'] || []).map do |r| + url = '/' + t.path.gsub(/tutorial(_[A_Z_]*)?.(html|md)$/, 'recordings/') + url += "#tutorial-recording-#{Date.parse(r['date']).strftime('%-d-%B-%Y').downcase}" + attr = {'title' => "Recording of " + t['title'], + 'contributors' => r['speakers'] + (r['captions'] || []), + 'content' => "A #{r['length']} long recording is now available."} + + obj = objectify(attr, url, t.path) + bucket << [DateTime.parse(r['date'].to_s), 'recordings', obj, tags] + end + end + + m.fetch('ref_slides', []).reject { |s| s.url =~ /-plain.html/ }.map do |s| + bucket << [Gtn::PublicationTimes.obtain_time(s.path).to_datetime, 'slides', s, tags] + + (s['recordings'] || []).map do |r| + url = '/' + s.path.gsub(/slides(_[A_Z_]*)?.(html|md)$/, 'recordings/') + url += "#tutorial-recording-#{Date.parse(r['date']).strftime('%-d-%B-%Y').downcase}" + attr = {'title' => "Recording of " + s['title'], + 'contributors' => r['speakers'] + (r['captions'] || []), + 'content' => "A #{r['length']} long recording is now available."} + obj = objectify(attr, url, s.path) + bucket << [DateTime.parse(r['date'].to_s), 'recordings', obj, tags] + end + end + end + + bucket += news.map do |n| + [n.date.to_datetime, 'news', n, ['news'] + n.data.fetch('tags', [])] + end + + bucket += faqs.map do |n| + tag = Gtn::PublicationTimes.clean_path(n.path).split('/')[1] + [Gtn::PublicationTimes.obtain_time(n.path).to_datetime, 'faqs', n, ['faqs', tag]] + end + + bucket += pathways.map do |n| + tags = ['learning-pathway'] + (n['tags'] || []) + [Gtn::PublicationTimes.obtain_time(n.path).to_datetime, 'learning-pathways', n, tags] + end + + bucket += workflows.map do |n| + tag = Gtn::PublicationTimes.clean_path(n).split('/')[1] + wf_data = JSON.parse(File.read(n)) + + attrs = { + 'title' => wf_data['name'], + 'description' => wf_data['annotation'], + 'tags' => wf_data['tags'], + 'contributors' => wf_data.fetch('creator', []).map do |c| + matched = site.data['contributors'].select{|k, v| + v.fetch('orcid', "does-not-exist") == c.fetch('identifier', "").gsub('https://orcid.org/', '') + }.first + if matched + matched[0] + else + c['name'] + end + end + } + # These aren't truly stable. I'm not sure what to do about that. + obj = objectify(attrs, '/' + n.gsub(/\.ga$/, '.html'), n) + # obj = objectify(attrs, '/' + n.path[0..n.path.rindex('/')], n) + [Gtn::PublicationTimes.obtain_time(n).to_datetime, 'workflows', obj, ['workflows', tag] + obj['tags']] + end + + # Remove symlinks from bucket. + bucket = bucket.reject { |date, type, page, tags| + File.symlink?(page.path) || File.symlink?(File.dirname(page.path)) || File.symlink?(File.dirname(File.dirname(page.path))) + } + + bucket += site.data['contributors'].map do |k, v| + a = {'title' => "@#{k}", + 'content' => "GTN Contributions from #{k}"} + obj = objectify(a, "/hall-of-fame/#{k}/", k) + + [DateTime.parse("#{v['joined']}-01T12:00:00", 'content' => "GTN Contributions from #{k}"), 'contributors', obj, ['contributor']] + end + + bucket += site.data['grants'].map do |k, v| + a = {'title' => "@#{k}", + 'content' => "GTN Contributions from #{k}"} + obj = objectify(a, "/hall-of-fame/#{k}/", k) + + # TODO: backdate grants, organisations + if v['joined'] + [DateTime.parse("#{v['joined']}-01T12:00:00"), 'grants', obj, ['grant']] + end + end.compact + + bucket += site.data['organisations'].map do |k, v| + a = {'title' => "@#{k}", + 'content' => "GTN Contributions from #{k}"} + obj = objectify(a, "/hall-of-fame/#{k}/", k) + + if v['joined'] + [DateTime.parse("#{v['joined']}-01T12:00:00"), 'organisations', obj, ['organisation']] + end + end.compact + + bucket + .reject{|x| x[0] > DateTime.now } # Remove future-dated materials + .reject{|x| x[2]['draft'] == true } # Remove drafts + .sort_by {|x| x[0] } # Date-sorted, not strictly necessary since will be grouped. + .reverse + end end end From bd2f7eddeb029cdcbf95f94305e11232920b14ba Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 18 Dec 2024 15:19:29 +0100 Subject: [PATCH 04/23] add functions for a new community template --- _plugins/jekyll-topic-filter.rb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index 517d25e9a18513..2c4b3f0036a491 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -1537,6 +1537,19 @@ def list_materials_flat(site, topic_name) .uniq { |x| x['id'] } end + def list_topic_materials_yearly(site, topic_name) + flat_mats = list_materials_flat(site, topic_name) + years = flat_mats.map{|x| x['pub_date'].year} + flat_mats.map{|x| x['mod_date'].year} + topic_contribs = identify_contributors({'topic' => {'materials' => flat_mats}}, site) + + # Should cache this really. + Gtn::TopicFilter.all_date_sorted_resources(site) + .select{|x| (x[3].include? 'single-cell') || (x[1] == 'contributors' && topic_contribs.include?(x[2].title[1..]))} + .group_by{|x| x[0].year} + .map{|k, v| [k, v.group_by{|z| z[1]}]} + .to_h + end + def list_all_tags(site) Gtn::TopicFilter.list_all_tags(site) end @@ -1605,6 +1618,10 @@ def tool_version_support(site, tool) def edamify(term, site) site.data['EDAM'].select{|row| row['Class ID'] == "http://edamontology.org/#{term}"}.first.to_h end + + def titlecase(term) + term.split(' ').map(&:capitalize).join(' ') + end end end end From 947e0358af351d84bd61dff59d6adeb1a5db7a1c Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 18 Dec 2024 15:19:40 +0100 Subject: [PATCH 05/23] add sc community page --- _layouts/community.html | 82 +++++++++++++++++++++++++++++++++ topics/single-cell/community.md | 5 ++ 2 files changed, 87 insertions(+) create mode 100644 _layouts/community.html create mode 100644 topics/single-cell/community.md diff --git a/_layouts/community.html b/_layouts/community.html new file mode 100644 index 00000000000000..2d5360fbb1cf74 --- /dev/null +++ b/_layouts/community.html @@ -0,0 +1,82 @@ +--- +layout: base +--- + +{% assign topic = site.data[page.topic_name] | default: page.topic %} +{% assign topic_material = site | list_materials_structured:topic.name %} +{% assign topic_material_flat = site | list_materials_flat:topic.name %} + +

{{ topic.title }} Community Home

+ +This is a new, experimental "Community Home" for a given topic. It is intended to highlight community contributions over the years to a topic! + +{% assign prio = "news events learning-pathways tutorials slides recordings faqs workflows grants organisations" | split:" " %} + +{% assign topic_material_by_years = site | list_topic_materials_yearly:topic.name %} + +{% for year in topic_material_by_years %} +
+
+

{{ year[0] }}

+

New community members!

+ {% for c in year[1]['contributors'] %} + {% assign cid = c[2].title | regex_replace_once: '@', '' %} + {% include _includes/contributor-badge-inline.html id=cid %} + {% endfor %} + +
+
+
+ {% for p in prio %} + {% if year[1][p] %} + {% assign group = year[1][p] %} +
+
+ {% assign group_len = group | size %} +
+ {{ group_len }} +
+
+ {{ p | regex_replace: '-', ' ' | titlecase }} +
+
+
+ {% endif %} + {% endfor %} +
+ +
+
+ + {% for p in prio %} + {% if year[1][p] %} + {% assign group = year[1][p] %} + +

{{ p | titlecase }}

+ + {% endif %} + {% endfor %} +
+
+ +
+ +
+ +{% endfor %} + + diff --git a/topics/single-cell/community.md b/topics/single-cell/community.md new file mode 100644 index 00000000000000..703a3dc48657ef --- /dev/null +++ b/topics/single-cell/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: single-cell +--- + From e8824791f3ff7b0935cb59fa6e40398601ba33f3 Mon Sep 17 00:00:00 2001 From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com> Date: Thu, 19 Dec 2024 00:55:17 +0000 Subject: [PATCH 06/23] Update governance_gcb_join.md --- topics/community/faqs/governance_gcb_join.md | 1 + 1 file changed, 1 insertion(+) diff --git a/topics/community/faqs/governance_gcb_join.md b/topics/community/faqs/governance_gcb_join.md index 68bfb929207ba7..a2524bea1bbf5c 100644 --- a/topics/community/faqs/governance_gcb_join.md +++ b/topics/community/faqs/governance_gcb_join.md @@ -9,6 +9,7 @@ contributors: [nomadscientist] - 📪 [Mailing list](https://lists.galaxyproject.org/lists/sig-chairs.lists.galaxyproject.org/) - 📝 [Rolling meeting notes](https://docs.google.com/document/d/19zv4rata-uVhFW43S8v_Fw83RVYq6jDGXy-1T8Aju4s/edit?usp=sharing) + - 🕶️[Add yourself to our members list](https://docs.google.com/document/d/19zv4rata-uVhFW43S8v_Fw83RVYq6jDGXy-1T8Aju4s/edit?tab=t.5cgfntg608gj) - ☕ [Chatroom](https://matrix.to/usegalaxy_commreps:matrix.org#/!JHcKrPhyfJoqHESrdD:matrix.org) - 🗓️[Community Board Google-Calendar](https://calendar.google.com/calendar/embed?height=600&wkst=1&ctz=Europe%2FLondon&bgcolor=%23ffffff&mode=AGENDA&showPrint=0&title=Galaxy%20Community%20Board&src=MDQwNDY2MDRhNGYxODE2NDk0MjBkYTQzMzUzMTBkN2E1MmQxMGJmNDkxNDgwMGEyZjNhYjEzZWE0ZWY3MzEyY0Bncm91cC5jYWxlbmRhci5nb29nbGUuY29t&color=%23F6BF26%22%20style=%22border:solid%201px%20#777%22%20width=%22800%22%20height=%22600%22%20frameborder=%220%22%20scrolling=%22no%22) - 🗓️[Community Board iCalendar](https://calendar.google.com/calendar/ical/04046604a4f181649420da4335310d7a52d10bf4914800a2f3ab13ea4ef7312c%40group.calendar.google.com/public/basic.ics) From 3e1626ffa605dae8f09ae16cfc34941573aeed91 Mon Sep 17 00:00:00 2001 From: Mirela Minkova <121402109+mirelaminkova@users.noreply.github.com> Date: Thu, 19 Dec 2024 13:06:45 +0100 Subject: [PATCH 07/23] Update 2025-01-28-src.md fixed scheduling and added registration details in description --- events/2025-01-28-src.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/events/2025-01-28-src.md b/events/2025-01-28-src.md index 60eb9037465329..6dba232a4c20f2 100644 --- a/events/2025-01-28-src.md +++ b/events/2025-01-28-src.md @@ -2,13 +2,13 @@ layout: event # Status of this page, remove these lines when ready -draft: true -status: wip +#draft: true +#status: wip # Description of your event title: Galaxy at SURF Research Cloud workshop description: | - Half-day workshop demonstrating the local Galaxy instance built for users of SURF Research Cloud. + Half-day workshop demonstrating the local Galaxy instance built for users of SURF Research Cloud. To sign up for the event, please send an email to mirela.minkova@surf.nl @@ -79,11 +79,11 @@ program: - name: surf-research-cloud-pulsar topic: admin - time: "14:10 - 14:40" + time: "14:10 - 14:30" - type: custom name: Coffee Break - time: "14:40" + time: "14:30" - name: mapping topic: sequence-analysis time: "14:40 - 15:40" From 4f4f71942a3bde1413837055cd34980a5a1e9086 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 19 Dec 2024 14:07:05 +0100 Subject: [PATCH 08/23] yea this is good, ship it --- _layouts/community.html | 246 +++++++++++++++++++++++++++++--- _plugins/jekyll-topic-filter.rb | 37 ++++- 2 files changed, 260 insertions(+), 23 deletions(-) diff --git a/_layouts/community.html b/_layouts/community.html index 2d5360fbb1cf74..41656c5b43b704 100644 --- a/_layouts/community.html +++ b/_layouts/community.html @@ -10,32 +10,62 @@

{{ topic.title }} Community Home

This is a new, experimental "Community Home" for a given topic. It is intended to highlight community contributions over the years to a topic! -{% assign prio = "news events learning-pathways tutorials slides recordings faqs workflows grants organisations" | split:" " %} +{% assign prio = "news events learning-pathways tutorials slides recordings faqs workflows grants organisations contributors" | split:" " %} + {% assign topic_material_by_years = site | list_topic_materials_yearly:topic.name %} +{% assign cumulative_counts_by_years = site | count_topic_materials_yearly:topic.name %} -{% for year in topic_material_by_years %}
-
-

{{ year[0] }}

-

New community members!

- {% for c in year[1]['contributors'] %} - {% assign cid = c[2].title | regex_replace_once: '@', '' %} - {% include _includes/contributor-badge-inline.html id=cid %} - {% endfor %} +
+
+ +
Materials Over Time
+
+
+
+
+ +
Contributors Over Time
+
+
+
+
+ +
workflows Over Time
+
+
+
+
+ +
Other Contributions Over Time
+
+
+
+{% for year in topic_material_by_years %} +
+
+
+

{{ year[0] }} Year in Review

+

So many new additions to our community!

+
-
+
{% for p in prio %} {% if year[1][p] %} {% assign group = year[1][p] %} -
-
+
+
{% assign group_len = group | size %} -
- {{ group_len }} -
+
{{ group_len }}
{{ p | regex_replace: '-', ' ' | titlecase }}
@@ -44,14 +74,15 @@

{{ year[0] }}

{% endif %} {% endfor %}
- +
+
{% for p in prio %} {% if year[1][p] %} {% assign group = year[1][p] %} - +

{{ p | titlecase }}

    {% for resource in group %} @@ -62,21 +93,196 @@

    {{ p | titlecase }}

    {% endfor %}
- +
+{% endfor %} +

Cumulative Data as CSV

+
+year,{% for point in cumulative_counts_by_years['tutorials'] %}{{ point.x | regex_replace:'-.*', '' }}{%unless forloop.last%},{%endunless%}{% endfor %}
+{% for p in prio %}{{ p }},{% for point in cumulative_counts_by_years[p] %}{{ point.y }}{%unless forloop.last%},{%endunless%}{% endfor %}
 {% endfor %}
 
+
+ + + + + + + + + diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index 2c4b3f0036a491..b588d4d2cdd54e 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -6,6 +6,13 @@ require './_plugins/util' require 'securerandom' +class Array + def cumulative_sum + sum = 0 + self.map{|x| sum += x} + end +end + module Gtn # The main GTN module to parse tutorial.md and slides.html and topics into useful lists of things that can be shown on topic pages, i.e. "materials" (a possible combination of tutorial + slides) # @@ -1255,8 +1262,13 @@ def self.list_materials_by_tool(site) # "slides", # #, # ["single-cell"]]] - def self.all_date_sorted_resources(site) + cache.getset('all_date_sorted_resources') do + self._all_date_sorted_resources(site) + end + end + + def self._all_date_sorted_resources(site) events = site.pages.select { |x| x['layout'] == 'event' || x['layout'] == 'event-external' } materials = list_all_materials(site).reject { |k, _v| k['draft'] } news = site.posts.select { |x| x['layout'] == 'news' } @@ -1542,14 +1554,33 @@ def list_topic_materials_yearly(site, topic_name) years = flat_mats.map{|x| x['pub_date'].year} + flat_mats.map{|x| x['mod_date'].year} topic_contribs = identify_contributors({'topic' => {'materials' => flat_mats}}, site) - # Should cache this really. Gtn::TopicFilter.all_date_sorted_resources(site) - .select{|x| (x[3].include? 'single-cell') || (x[1] == 'contributors' && topic_contribs.include?(x[2].title[1..]))} + .select{|x| (x[3].include? topic_name) || (x[1] == 'contributors' && topic_contribs.include?(x[2].title[1..]))} .group_by{|x| x[0].year} .map{|k, v| [k, v.group_by{|z| z[1]}]} .to_h end + def count_topic_materials_yearly(site, topic_name) + flat_mats = list_materials_flat(site, topic_name) + years = flat_mats.map{|x| x['pub_date'].year} + flat_mats.map{|x| x['mod_date'].year} + topic_contribs = identify_contributors({'topic' => {'materials' => flat_mats}}, site) + + r = Gtn::TopicFilter.all_date_sorted_resources(site) + .select{|x| (x[3].include? topic_name) || (x[1] == 'contributors' && topic_contribs.include?(x[2].title[1..]))} + .map{|x| [x[0].year, x[1]]} # Only need year + type + .group_by{|x| x[1]} # Group by type. + .map{|k, v| [k, v.map{|vv| vv[0]}.tally]} + .to_h + + years = (2015..Date.today.year).to_a + # Fill in zeros for missing years + r.map{|k, v| [k, years.map{|y| v[y] || 0} + .cumulative_sum + .map.with_index{|value, i| {"y" => value, "x" => "#{years[i]}-01-01"}}] + }.to_h + end + def list_all_tags(site) Gtn::TopicFilter.list_all_tags(site) end From abc1488f7aada45243644b1443af6a93f3334268 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 19 Dec 2024 14:10:05 +0100 Subject: [PATCH 09/23] add community pages for everyone --- topics/admin/community.md | 5 +++++ topics/ai4life/community.md | 5 +++++ topics/assembly/community.md | 5 +++++ topics/climate/community.md | 5 +++++ topics/community/community.md | 5 +++++ topics/computational-chemistry/community.md | 5 +++++ topics/contributing/community.md | 5 +++++ topics/data-science/community.md | 5 +++++ topics/dev/community.md | 5 +++++ topics/ecology/community.md | 5 +++++ topics/epigenetics/community.md | 5 +++++ topics/evolution/community.md | 5 +++++ topics/fair/community.md | 5 +++++ topics/galaxy-interface/community.md | 5 +++++ topics/genome-annotation/community.md | 5 +++++ topics/imaging/community.md | 5 +++++ topics/introduction/community.md | 5 +++++ topics/materials-science/community.md | 5 +++++ topics/metabolomics/community.md | 5 +++++ topics/microbiome/community.md | 5 +++++ topics/proteomics/community.md | 5 +++++ topics/sequence-analysis/community.md | 5 +++++ topics/statistics/community.md | 5 +++++ topics/synthetic-biology/community.md | 5 +++++ topics/teaching/community.md | 5 +++++ topics/transcriptomics/community.md | 5 +++++ topics/variant-analysis/community.md | 5 +++++ topics/visualisation/community.md | 5 +++++ 28 files changed, 140 insertions(+) create mode 100644 topics/admin/community.md create mode 100644 topics/ai4life/community.md create mode 100644 topics/assembly/community.md create mode 100644 topics/climate/community.md create mode 100644 topics/community/community.md create mode 100644 topics/computational-chemistry/community.md create mode 100644 topics/contributing/community.md create mode 100644 topics/data-science/community.md create mode 100644 topics/dev/community.md create mode 100644 topics/ecology/community.md create mode 100644 topics/epigenetics/community.md create mode 100644 topics/evolution/community.md create mode 100644 topics/fair/community.md create mode 100644 topics/galaxy-interface/community.md create mode 100644 topics/genome-annotation/community.md create mode 100644 topics/imaging/community.md create mode 100644 topics/introduction/community.md create mode 100644 topics/materials-science/community.md create mode 100644 topics/metabolomics/community.md create mode 100644 topics/microbiome/community.md create mode 100644 topics/proteomics/community.md create mode 100644 topics/sequence-analysis/community.md create mode 100644 topics/statistics/community.md create mode 100644 topics/synthetic-biology/community.md create mode 100644 topics/teaching/community.md create mode 100644 topics/transcriptomics/community.md create mode 100644 topics/variant-analysis/community.md create mode 100644 topics/visualisation/community.md diff --git a/topics/admin/community.md b/topics/admin/community.md new file mode 100644 index 00000000000000..5207147d9d70ef --- /dev/null +++ b/topics/admin/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: admin +--- + diff --git a/topics/ai4life/community.md b/topics/ai4life/community.md new file mode 100644 index 00000000000000..bf7530f4d410ce --- /dev/null +++ b/topics/ai4life/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: ai4life +--- + diff --git a/topics/assembly/community.md b/topics/assembly/community.md new file mode 100644 index 00000000000000..670e760819fb51 --- /dev/null +++ b/topics/assembly/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: assembly +--- + diff --git a/topics/climate/community.md b/topics/climate/community.md new file mode 100644 index 00000000000000..da17a1331a6e48 --- /dev/null +++ b/topics/climate/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: climate +--- + diff --git a/topics/community/community.md b/topics/community/community.md new file mode 100644 index 00000000000000..83f390ebb1402b --- /dev/null +++ b/topics/community/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: community +--- + diff --git a/topics/computational-chemistry/community.md b/topics/computational-chemistry/community.md new file mode 100644 index 00000000000000..9fc252f2ba2428 --- /dev/null +++ b/topics/computational-chemistry/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: computational-chemistry +--- + diff --git a/topics/contributing/community.md b/topics/contributing/community.md new file mode 100644 index 00000000000000..2d37741b21f355 --- /dev/null +++ b/topics/contributing/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: contributing +--- + diff --git a/topics/data-science/community.md b/topics/data-science/community.md new file mode 100644 index 00000000000000..af5100825835fb --- /dev/null +++ b/topics/data-science/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: data-science +--- + diff --git a/topics/dev/community.md b/topics/dev/community.md new file mode 100644 index 00000000000000..a49584e07f2d7f --- /dev/null +++ b/topics/dev/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: dev +--- + diff --git a/topics/ecology/community.md b/topics/ecology/community.md new file mode 100644 index 00000000000000..e54073c5871ba0 --- /dev/null +++ b/topics/ecology/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: ecology +--- + diff --git a/topics/epigenetics/community.md b/topics/epigenetics/community.md new file mode 100644 index 00000000000000..7099b392eb62a4 --- /dev/null +++ b/topics/epigenetics/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: epigenetics +--- + diff --git a/topics/evolution/community.md b/topics/evolution/community.md new file mode 100644 index 00000000000000..05b816279e487c --- /dev/null +++ b/topics/evolution/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: evolution +--- + diff --git a/topics/fair/community.md b/topics/fair/community.md new file mode 100644 index 00000000000000..eb773b706a357f --- /dev/null +++ b/topics/fair/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: fair +--- + diff --git a/topics/galaxy-interface/community.md b/topics/galaxy-interface/community.md new file mode 100644 index 00000000000000..e727024606770d --- /dev/null +++ b/topics/galaxy-interface/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: galaxy-interface +--- + diff --git a/topics/genome-annotation/community.md b/topics/genome-annotation/community.md new file mode 100644 index 00000000000000..661e13731f1823 --- /dev/null +++ b/topics/genome-annotation/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: genome-annotation +--- + diff --git a/topics/imaging/community.md b/topics/imaging/community.md new file mode 100644 index 00000000000000..11f520302f2b93 --- /dev/null +++ b/topics/imaging/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: imaging +--- + diff --git a/topics/introduction/community.md b/topics/introduction/community.md new file mode 100644 index 00000000000000..e66e3fe8aa27a3 --- /dev/null +++ b/topics/introduction/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: introduction +--- + diff --git a/topics/materials-science/community.md b/topics/materials-science/community.md new file mode 100644 index 00000000000000..5657f43aa62078 --- /dev/null +++ b/topics/materials-science/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: materials-science +--- + diff --git a/topics/metabolomics/community.md b/topics/metabolomics/community.md new file mode 100644 index 00000000000000..18428fde1d3a57 --- /dev/null +++ b/topics/metabolomics/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: metabolomics +--- + diff --git a/topics/microbiome/community.md b/topics/microbiome/community.md new file mode 100644 index 00000000000000..7c4769123f1ffd --- /dev/null +++ b/topics/microbiome/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: microbiome +--- + diff --git a/topics/proteomics/community.md b/topics/proteomics/community.md new file mode 100644 index 00000000000000..bcb0ff72e28650 --- /dev/null +++ b/topics/proteomics/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: proteomics +--- + diff --git a/topics/sequence-analysis/community.md b/topics/sequence-analysis/community.md new file mode 100644 index 00000000000000..0d4a2c80ea7d9f --- /dev/null +++ b/topics/sequence-analysis/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: sequence-analysis +--- + diff --git a/topics/statistics/community.md b/topics/statistics/community.md new file mode 100644 index 00000000000000..41f24c6fa2788e --- /dev/null +++ b/topics/statistics/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: statistics +--- + diff --git a/topics/synthetic-biology/community.md b/topics/synthetic-biology/community.md new file mode 100644 index 00000000000000..80a2a43217b351 --- /dev/null +++ b/topics/synthetic-biology/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: synthetic-biology +--- + diff --git a/topics/teaching/community.md b/topics/teaching/community.md new file mode 100644 index 00000000000000..986d4393e0325f --- /dev/null +++ b/topics/teaching/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: teaching +--- + diff --git a/topics/transcriptomics/community.md b/topics/transcriptomics/community.md new file mode 100644 index 00000000000000..a39ff33b94c99d --- /dev/null +++ b/topics/transcriptomics/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: transcriptomics +--- + diff --git a/topics/variant-analysis/community.md b/topics/variant-analysis/community.md new file mode 100644 index 00000000000000..987a88c819ae87 --- /dev/null +++ b/topics/variant-analysis/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: variant-analysis +--- + diff --git a/topics/visualisation/community.md b/topics/visualisation/community.md new file mode 100644 index 00000000000000..3793720e320799 --- /dev/null +++ b/topics/visualisation/community.md @@ -0,0 +1,5 @@ +--- +layout: community +topic_name: visualisation +--- + From ef3bbf44e0444713829dd8800bb1802c0efc850d Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 19 Dec 2024 14:11:26 +0100 Subject: [PATCH 10/23] also LPs --- _layouts/community.html | 2 +- topics/community/maintainer.md | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/_layouts/community.html b/_layouts/community.html index 41656c5b43b704..9cf8bc54519868 100644 --- a/_layouts/community.html +++ b/_layouts/community.html @@ -83,7 +83,7 @@

{{ year[0] }} Year in Review

{% if year[1][p] %} {% assign group = year[1][p] %} -

{{ p | titlecase }}

+

{{ p | regex_replace: '-', ' ' | titlecase }}

    {% for resource in group %}
  • {{ resource[2].title }}
    • diff --git a/topics/community/maintainer.md b/topics/community/maintainer.md index 4677c062c73f0f..bd1db466dab9ac 100644 --- a/topics/community/maintainer.md +++ b/topics/community/maintainer.md @@ -2,3 +2,4 @@ layout: topic-maintainer topic_name: community --- + From b63abad645589554fbeb15a6e4aa57d223c311d4 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 19 Dec 2024 14:15:02 +0100 Subject: [PATCH 11/23] sync up titles --- _layouts/community.html | 2 +- _layouts/topic-maintainer.html | 2 +- _layouts/topic.html | 4 ++++ 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/_layouts/community.html b/_layouts/community.html index 9cf8bc54519868..e1d03b301be6e6 100644 --- a/_layouts/community.html +++ b/_layouts/community.html @@ -6,7 +6,7 @@ {% assign topic_material = site | list_materials_structured:topic.name %} {% assign topic_material_flat = site | list_materials_flat:topic.name %} -

    {{ topic.title }} Community Home

    +

    {{ topic.title }} — Community Home

    This is a new, experimental "Community Home" for a given topic. It is intended to highlight community contributions over the years to a topic! diff --git a/_layouts/topic-maintainer.html b/_layouts/topic-maintainer.html index 19bb848e8a6110..fa6eb3811c2b1e 100644 --- a/_layouts/topic-maintainer.html +++ b/_layouts/topic-maintainer.html @@ -6,7 +6,7 @@ {% assign topic_material = site | list_materials_structured:topic.name %} {% assign topic_material_flat = site | list_materials_flat:topic.name %} -

    {{ topic.title }} Editorial Board Home

    +

    {{ topic.title }} — Editorial Board Home

    This is a new, experimental "Editorial Board Home" for a given topic. It is intended to provide a single place for maintainers and editorial board members to find out key information about their topic and identify action items. diff --git a/_layouts/topic.html b/_layouts/topic.html index 9a03a9894abf6c..9cc7fecdbd744b 100644 --- a/_layouts/topic.html +++ b/_layouts/topic.html @@ -112,6 +112,10 @@

    Frequently Asked Questions

    {% endif %} {% endunless %} +

    Community Resources

    + Community Home + Maintainer Home + {% if topic.editorial_board %}

    Editorial Board

    This material is reviewed by our Editorial Board:

    From 9e6f1f1349d9a8e516391c67aafa6c4de2197a6f Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 19 Dec 2024 14:32:01 +0100 Subject: [PATCH 12/23] fix missing f/o --- _layouts/community.html | 15 +++++++++------ _plugins/jekyll-topic-filter.rb | 12 ++++++++---- 2 files changed, 17 insertions(+), 10 deletions(-) diff --git a/_layouts/community.html b/_layouts/community.html index e1d03b301be6e6..b79108c6014435 100644 --- a/_layouts/community.html +++ b/_layouts/community.html @@ -38,7 +38,7 @@

    {{ topic.title }} — Community Home

    -
    workflows Over Time
    +
    Workflows Over Time
    @@ -118,6 +118,9 @@

    Cumulative Data as CSV

    padding: 0.5em; background: var(--stat-box-color); } +.col-md-8 .row .col-md-12 h3:first-child { + margin-top: 0; +} body[data-brightness="dark"] .stat-box { background: none; @@ -250,32 +253,32 @@

    Cumulative Data as CSV

    datasets: [ { data: totals.news, - label: 'news', + label: 'News', borderColor: getStyleDarker("news", true, true), backgroundColor: getStyleDarker("news", true, false), backgroundColor: getStyleDarker("news", false), }, { data: totals.events, - label: 'events', + label: 'Events', borderColor: getStyleDarker("events", true), backgroundColor: getStyleDarker("events", false), }, { data: totals['learning-pathways'], - label: 'learning-pathways', + label: 'Learning Pathways', borderColor: getStyleDarker("learning-pathways", true), backgroundColor: getStyleDarker("learning-pathways", false), }, { data: totals.recordings, - label: 'recordings', + label: 'Recordings', borderColor: getStyleDarker("recordings", true), backgroundColor: getStyleDarker("recordings", false), }, { data: totals.faqs, - label: 'faqs', + label: 'Faqs', borderColor: getStyleDarker("faqs", true), backgroundColor: getStyleDarker("faqs", false), }, diff --git a/_plugins/jekyll-topic-filter.rb b/_plugins/jekyll-topic-filter.rb index b588d4d2cdd54e..04565bdb70bcc1 100644 --- a/_plugins/jekyll-topic-filter.rb +++ b/_plugins/jekyll-topic-filter.rb @@ -1552,10 +1552,12 @@ def list_materials_flat(site, topic_name) def list_topic_materials_yearly(site, topic_name) flat_mats = list_materials_flat(site, topic_name) years = flat_mats.map{|x| x['pub_date'].year} + flat_mats.map{|x| x['mod_date'].year} - topic_contribs = identify_contributors({'topic' => {'materials' => flat_mats}}, site) + # doesn't use identify_contributors because that excludes grants/orgs. + topic_contribs = flat_mats.map{|x| x['contributions'] || {"all" => x['contributors']}}.map{|x| x.values.flatten}.flatten.uniq.sort + pfo = ['contributors', 'grants', 'organisations'] Gtn::TopicFilter.all_date_sorted_resources(site) - .select{|x| (x[3].include? topic_name) || (x[1] == 'contributors' && topic_contribs.include?(x[2].title[1..]))} + .select{|x| (x[3].include? topic_name) || (pfo.include?(x[1]) && topic_contribs.include?(x[2].title[1..]))} .group_by{|x| x[0].year} .map{|k, v| [k, v.group_by{|z| z[1]}]} .to_h @@ -1564,10 +1566,12 @@ def list_topic_materials_yearly(site, topic_name) def count_topic_materials_yearly(site, topic_name) flat_mats = list_materials_flat(site, topic_name) years = flat_mats.map{|x| x['pub_date'].year} + flat_mats.map{|x| x['mod_date'].year} - topic_contribs = identify_contributors({'topic' => {'materials' => flat_mats}}, site) + # doesn't use identify_contributors because that excludes grants/orgs. + topic_contribs = flat_mats.map{|x| x['contributions'] || {"all" => x['contributors']}}.map{|x| x.values.flatten}.flatten.uniq.sort + pfo = ['contributors', 'grants', 'organisations'] r = Gtn::TopicFilter.all_date_sorted_resources(site) - .select{|x| (x[3].include? topic_name) || (x[1] == 'contributors' && topic_contribs.include?(x[2].title[1..]))} + .select{|x| (x[3].include? topic_name) || (pfo.include?(x[1]) && topic_contribs.include?(x[2].title[1..]))} .map{|x| [x[0].year, x[1]]} # Only need year + type .group_by{|x| x[1]} # Group by type. .map{|k, v| [k, v.map{|vv| vv[0]}.tally]} From ea3e6f1f49b561b47943da9a68605e2ef40b99a9 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 19 Dec 2024 14:47:49 +0100 Subject: [PATCH 13/23] improve priorities across cloud topic --- .../admin/tutorials/cloudbursting/slides.html | 18 ++++++++-- .../tutorials/k8s-managing-galaxy/tutorial.md | 2 +- .../surf-research-cloud-galaxy/tutorial.md | 2 ++ .../surf-research-cloud-pulsar/tutorial.md | 33 +++++++++++++++++-- topics/admin/tutorials/terraform/slides.html | 2 ++ topics/admin/tutorials/terraform/tutorial.md | 2 ++ .../tutorials/wireguard-headscale/tutorial.md | 4 +++ topics/admin/tutorials/wireguard/tutorial.md | 1 + 8 files changed, 57 insertions(+), 7 deletions(-) diff --git a/topics/admin/tutorials/cloudbursting/slides.html b/topics/admin/tutorials/cloudbursting/slides.html index 91fc1a718f7959..f5e06ea4a4df7d 100644 --- a/topics/admin/tutorials/cloudbursting/slides.html +++ b/topics/admin/tutorials/cloudbursting/slides.html @@ -3,9 +3,14 @@ logo: assets/images/gat.png title: "Galaxy on the Cloud" -contributors: +contributions: + authorship: - slugger70 + editing: + - hexylena subtopic: cloud + +priority: 0 --- # All these Clouds @@ -84,7 +89,7 @@ * Education grants * Academic: * OpenStack: open source community project - * NeCTAR in Australia, Jetstream in USA, CLIMB in UK, lots of others + * NeCTAR in Australia, Jetstream in USA, CLIMB in UK, SURF in Netherlands, lots of others * Some free for researchers (NeCTAR, CLIMB), some with project grants (Jetstream) ] @@ -129,7 +134,7 @@ * with Galaxy pre-installed * with different sets of tools installed * with access to reference data - * for different clouds (AWS globally, Jetstream, NeCTAR, CLIMB etc.) + * for different clouds (AWS globally, Jetstream, NeCTAR, CLIMB, SURF etc.) * You just need credentials for the cloud you want to "launch" on. * Credentials are generally strings * An access key and a secret key or username and password with project details @@ -282,6 +287,13 @@ ... ``` + +--- + +# CloudMan Galaxy + +* Configured for Slurm out of the box + ``` ini # COMPUTE NODES NodeName=master NodeAddr=45.113.232.91 CPUs=15 RealMemory=64431 Weight=10 State=UNKNOWN diff --git a/topics/admin/tutorials/k8s-managing-galaxy/tutorial.md b/topics/admin/tutorials/k8s-managing-galaxy/tutorial.md index 600af2747835ea..8a42c3155212d9 100644 --- a/topics/admin/tutorials/k8s-managing-galaxy/tutorial.md +++ b/topics/admin/tutorials/k8s-managing-galaxy/tutorial.md @@ -32,7 +32,7 @@ requirements: topic_name: admin tutorials: - k8s-deploying-galaxy -priority: 1 +priority: 3 --- # Managing Galaxy on Kubernetes diff --git a/topics/admin/tutorials/surf-research-cloud-galaxy/tutorial.md b/topics/admin/tutorials/surf-research-cloud-galaxy/tutorial.md index 9c6ac5eb14ac36..9ea5b1e4582a6f 100644 --- a/topics/admin/tutorials/surf-research-cloud-galaxy/tutorial.md +++ b/topics/admin/tutorials/surf-research-cloud-galaxy/tutorial.md @@ -31,6 +31,8 @@ contributions: funding: - surf +priority: 10 + edam_ontology: - topic_0605 # Informatics - topic_3071 # Data Management diff --git a/topics/admin/tutorials/surf-research-cloud-pulsar/tutorial.md b/topics/admin/tutorials/surf-research-cloud-pulsar/tutorial.md index 0d7c083a56c40f..f276dd70a3d317 100644 --- a/topics/admin/tutorials/surf-research-cloud-pulsar/tutorial.md +++ b/topics/admin/tutorials/surf-research-cloud-pulsar/tutorial.md @@ -7,7 +7,12 @@ questions: - How do I start a Pulsar instance on SURF Research Cloud? - How do I connect to Pulsar? objectives: - - Be able to attach a Pulsar node to Galaxy and use interactive tools + - Be able to attach a Pulsar node to Galaxy + - Send jobs to Pulsar +key_points: + - With SRC you can start your own Pulsar on-demand instance in a secure environment. + - The Pulsar node is publicly accessible for a Galaxy with the credentials to use. + - You can send jobs to a Pulsar node from either a Galaxy instance running on SRC, or even inside your own network. requirements: - type: "none" title: Access to the SURF Research Cloud @@ -26,6 +31,8 @@ contributions: funding: - surf +priority: 11 + edam_ontology: - topic_0605 # Informatics - topic_3071 # Data Management @@ -49,9 +56,14 @@ tags: Using Pulsar via the {SRC} allows researchers to start Pulsar instances on-demand to expand their computational resources and even access GPUs to help and analyze their data in a secure environment following the {GDPR}. -The instance provides secure authentication, where users must have a SURF Research account prior to this tutorial, have set the {SRAM} authentication method, and connect an SSH key to their accounts. In case you are not familiar with {SRC} and need help in setting up your accounts, please follow the instructions on the [SURF Knowledge Base](https://servicedesk.surf.nl/wiki/display/WIKI/SURF+Research+Cloud) +There are two main use cases we envision this role being useful for: + +Saving costs on SRC +: Maybe you're already running Galaxy in SRC, but you don't want to run a GPU node because it is very expensive. By using the SRC Pulsar Catalog Item, you can launch a node to do computations and then shut it down when you're done, saving money. Pulsar instances can be started and stopped on demand, depending on personal cases and requirements, giving you a lot of freedom! + +Accessing a GPU from a local (in UMC/hospital Galaxy) +: If you do not have a GPU easily available within your institute, it may be attractive to send jobs securely to SRC, by launching a Pulsar node in SRC and attaching it to your institute's Galaxy instance. -Pulsar instances can be started and stopped on demand, depending on personal cases and requirements. Inside the SRC members should have access to all publicly available catalog items. If you are not able to create a catalog item, please [contact SURF servicedesk](mailto:servicedesk@surf.nl). > > @@ -62,6 +74,10 @@ Pulsar instances can be started and stopped on demand, depending on personal cas # Prerequisites +The instance provides secure authentication, where users must have a SURF Research account prior to this tutorial, have set the {SRAM} authentication method, and connect an SSH key to their accounts. In case you are not familiar with {SRC} and need help in setting up your accounts, please follow the instructions on the [SURF Knowledge Base](https://servicedesk.surf.nl/wiki/display/WIKI/SURF+Research+Cloud) + +Inside the SRC members should have access to all publicly available catalog items. If you are not able to create a catalog item, please [contact SURF servicedesk](mailto:servicedesk@surf.nl). + This tutorial assumes you are member of a {CO} in {SRAM} that has access to {SRC} and a wallet with budget in SRC with enough sources to create Galaxy and Pulsar catalog items. (For more information please refer to the [SURF Knowledge Base](https://servicedesk.surf.nl/wiki/display/WIKI/Budgets%2C+wallets%2C+contracts). You should have previous experience working with data inside Galaxy. @@ -229,4 +245,15 @@ You can find the tool ID from the dropdown at the top right, just to the left of With that, you're done, and for the length of time your node is running, your chosen tools (or everything) will be executed on that Pulsar node with more memory and CPU than the Galaxy host, and maybe a GPU as well! +> Launch a Job on Pulsar +> 1. Login to your Galaxy +> 2. Run one of the tools you have decided to send to Pulsar +> 3. On the pulsar machine, you can check that it runs by following the logs: +> +> ```bash +> sudo journalctl -fu pulsar +> ``` +> +{: .hands_on} + Congratulations on launching Pulsar in SRC! 🌌 diff --git a/topics/admin/tutorials/terraform/slides.html b/topics/admin/tutorials/terraform/slides.html index 31238267ad5cce..387062a5b41328 100644 --- a/topics/admin/tutorials/terraform/slides.html +++ b/topics/admin/tutorials/terraform/slides.html @@ -17,6 +17,8 @@ subtopic: cloud contributors: - hexylena + +priority: 30 --- ### Why Terraform diff --git a/topics/admin/tutorials/terraform/tutorial.md b/topics/admin/tutorials/terraform/tutorial.md index 5e0340fce1e5ba..36e6e04318db18 100644 --- a/topics/admin/tutorials/terraform/tutorial.md +++ b/topics/admin/tutorials/terraform/tutorial.md @@ -23,6 +23,8 @@ tags: - deploying - cloud priority: 3 + +priority: 30 --- # Overview diff --git a/topics/admin/tutorials/wireguard-headscale/tutorial.md b/topics/admin/tutorials/wireguard-headscale/tutorial.md index c94c99bab6a688..0400a169419e0b 100644 --- a/topics/admin/tutorials/wireguard-headscale/tutorial.md +++ b/topics/admin/tutorials/wireguard-headscale/tutorial.md @@ -31,6 +31,10 @@ subtopic: cloud tags: - wireguard - networking +edam_ontology: +- topic_3263 # data security +- topic_3372 # software engineering +priority: 20 --- [Tailscale](https://tailscale.com/) makes secure networking easy, it really is like magic. If you've used wireguard before, you know it takes a bit to setup and some configuration if you need to do anything fancy. diff --git a/topics/admin/tutorials/wireguard/tutorial.md b/topics/admin/tutorials/wireguard/tutorial.md index 1d78e2b492e771..6d8ef996855035 100644 --- a/topics/admin/tutorials/wireguard/tutorial.md +++ b/topics/admin/tutorials/wireguard/tutorial.md @@ -26,6 +26,7 @@ subtopic: cloud tags: - wireguard - networking +priority: 20 --- In this tutorial we will briefly cover what [Wireguard](https://www.wireguard.com/) is and how you can leverage it for your needs. This will not make you an expert on Wireguard but will give you the tools you need in order to setup a local Wireguard network. From dcd16606e5d66eb2e2919f39c7dd531ed917f4f5 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 19 Dec 2024 14:49:11 +0100 Subject: [PATCH 14/23] tag SRC event --- events/2025-01-28-src.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/events/2025-01-28-src.md b/events/2025-01-28-src.md index 6dba232a4c20f2..d00b2ac116f253 100644 --- a/events/2025-01-28-src.md +++ b/events/2025-01-28-src.md @@ -99,7 +99,10 @@ program: - type: custom name: Borreltje time: "16:30 - 17:00" - +tags: +- admin +- surf +- netherlands --- During the workshop, you will see a short demo and get a chance to test the catalog item yourself. This will be followed by a discussion about your needs as Galaxy researchers, helping us work toward a better future for the Dutch research community. We will conclude the day with drinks and networking with fellow Galaxy NL users. From 7f2091f72b200a18e3f74405fe38a4a4f67bf4d8 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 19 Dec 2024 14:50:25 +0100 Subject: [PATCH 15/23] make the reg link clearer --- events/2025-01-28-src.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/events/2025-01-28-src.md b/events/2025-01-28-src.md index d00b2ac116f253..ce4b27e4838dc6 100644 --- a/events/2025-01-28-src.md +++ b/events/2025-01-28-src.md @@ -8,7 +8,9 @@ layout: event # Description of your event title: Galaxy at SURF Research Cloud workshop description: | - Half-day workshop demonstrating the local Galaxy instance built for users of SURF Research Cloud. To sign up for the event, please send an email to mirela.minkova@surf.nl + Half-day workshop demonstrating the local Galaxy instance built for users of SURF Research Cloud. + + **Registration**: To sign up for the event, please send an email to [Mirela Minkova](mailto:mirela.minkova@surf.nl) From 60497df7032b785198e3887b8c4f99fca91ba4a5 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 19 Dec 2024 14:52:27 +0100 Subject: [PATCH 16/23] make it a subject link --- events/2025-01-28-src.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/events/2025-01-28-src.md b/events/2025-01-28-src.md index ce4b27e4838dc6..c5115075340a89 100644 --- a/events/2025-01-28-src.md +++ b/events/2025-01-28-src.md @@ -10,7 +10,7 @@ title: Galaxy at SURF Research Cloud workshop description: | Half-day workshop demonstrating the local Galaxy instance built for users of SURF Research Cloud. - **Registration**: To sign up for the event, please send an email to [Mirela Minkova](mailto:mirela.minkova@surf.nl) + **Registration**: To sign up for the event, please send an email to [Mirela Minkova](mailto:mirela.minkova@surf.nl?subject=Registering%20SRC%20Galaxy%20Workshop) From 42a5f7208a65099d97dc2fa2a2221eb1846eedfd Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 19 Dec 2024 14:57:45 +0100 Subject: [PATCH 17/23] baseurl --- _layouts/community.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_layouts/community.html b/_layouts/community.html index b79108c6014435..9f6de7ab65a61c 100644 --- a/_layouts/community.html +++ b/_layouts/community.html @@ -86,7 +86,7 @@

    {{ year[0] }} Year in Review

    {{ p | regex_replace: '-', ' ' | titlecase }}

    {% endif %} From c392642124e4b5ef24c35afc64154bbdbc87fbb3 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 19 Dec 2024 15:02:53 +0100 Subject: [PATCH 18/23] some missing maintainer pages --- topics/admin/maintainer.md | 5 +++++ topics/ai4life/maintainer.md | 5 +++++ topics/contributing/maintainer.md | 5 +++++ topics/data-science/maintainer.md | 5 +++++ topics/dev/maintainer.md | 5 +++++ topics/fair/maintainer.md | 5 +++++ topics/teaching/maintainer.md | 5 +++++ 7 files changed, 35 insertions(+) create mode 100644 topics/admin/maintainer.md create mode 100644 topics/ai4life/maintainer.md create mode 100644 topics/contributing/maintainer.md create mode 100644 topics/data-science/maintainer.md create mode 100644 topics/dev/maintainer.md create mode 100644 topics/fair/maintainer.md create mode 100644 topics/teaching/maintainer.md diff --git a/topics/admin/maintainer.md b/topics/admin/maintainer.md new file mode 100644 index 00000000000000..5fb86125978c65 --- /dev/null +++ b/topics/admin/maintainer.md @@ -0,0 +1,5 @@ +--- +layout: topic-maintainer +topic_name: admin +--- + diff --git a/topics/ai4life/maintainer.md b/topics/ai4life/maintainer.md new file mode 100644 index 00000000000000..42f8446ff927ff --- /dev/null +++ b/topics/ai4life/maintainer.md @@ -0,0 +1,5 @@ +--- +layout: topic-maintainer +topic_name: ai4life +--- + diff --git a/topics/contributing/maintainer.md b/topics/contributing/maintainer.md new file mode 100644 index 00000000000000..80d834fbcdd3a6 --- /dev/null +++ b/topics/contributing/maintainer.md @@ -0,0 +1,5 @@ +--- +layout: topic-maintainer +topic_name: contributing +--- + diff --git a/topics/data-science/maintainer.md b/topics/data-science/maintainer.md new file mode 100644 index 00000000000000..ca7840b555178d --- /dev/null +++ b/topics/data-science/maintainer.md @@ -0,0 +1,5 @@ +--- +layout: topic-maintainer +topic_name: data-science +--- + diff --git a/topics/dev/maintainer.md b/topics/dev/maintainer.md new file mode 100644 index 00000000000000..b02cc701c06a66 --- /dev/null +++ b/topics/dev/maintainer.md @@ -0,0 +1,5 @@ +--- +layout: topic-maintainer +topic_name: dev +--- + diff --git a/topics/fair/maintainer.md b/topics/fair/maintainer.md new file mode 100644 index 00000000000000..9c5e2419c71765 --- /dev/null +++ b/topics/fair/maintainer.md @@ -0,0 +1,5 @@ +--- +layout: topic-maintainer +topic_name: fair +--- + diff --git a/topics/teaching/maintainer.md b/topics/teaching/maintainer.md new file mode 100644 index 00000000000000..09bcf3c04af112 --- /dev/null +++ b/topics/teaching/maintainer.md @@ -0,0 +1,5 @@ +--- +layout: topic-maintainer +topic_name: teaching +--- + From 347a25b3cbd45a451b58eebbdfc9817ae2888192 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 19 Dec 2024 15:03:15 +0100 Subject: [PATCH 19/23] hide community links on tag based topics as they do not exist, they would need to be added to the generation process. Something for someone else to do, it's an easy fix! enjoy. --- _layouts/topic.html | 2 ++ 1 file changed, 2 insertions(+) diff --git a/_layouts/topic.html b/_layouts/topic.html index 9cc7fecdbd744b..5d81bdf93e66b1 100644 --- a/_layouts/topic.html +++ b/_layouts/topic.html @@ -112,9 +112,11 @@

    Frequently Asked Questions

    {% endif %} {% endunless %} + {% unless topic.tag_based %}

    Community Resources

    Community Home Maintainer Home + {% endunless %} {% if topic.editorial_board %}

    Editorial Board

    From 72c4f33bf6f217567e62820e64f4c365dc33f7bc Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 19 Dec 2024 15:16:02 +0100 Subject: [PATCH 20/23] Move smaller values to back --- _layouts/community.html | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/_layouts/community.html b/_layouts/community.html index 9f6de7ab65a61c..00f3b42322fc4b 100644 --- a/_layouts/community.html +++ b/_layouts/community.html @@ -209,12 +209,6 @@

    Cumulative Data as CSV

    type: 'line', data: { datasets: [ - { - data: totals.contributors, - label: 'Contributors', - borderColor: getStyleDarker("contributors", true), - backgroundColor: getStyleDarker("contributors", false), - }, { data: totals.grants, label: 'Grants', @@ -227,6 +221,12 @@

    Cumulative Data as CSV

    borderColor: getStyleDarker("organisations", true), backgroundColor: getStyleDarker("organisations", false), }, + { + data: totals.contributors, + label: 'Contributors', + borderColor: getStyleDarker("contributors", true), + backgroundColor: getStyleDarker("contributors", false), + }, ] }, options: options From ac2cdc3672a82ea48ba8a1e17fadcad54d1371e8 Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Thu, 19 Dec 2024 15:19:07 +0100 Subject: [PATCH 21/23] add topic tags to news and events optimize new community home pages --- events/2022-07-08-gat.md | 3 +++ events/2023-04-17-gat-gent.md | 3 +++ events/2023-10-02-mtb-ngs.md | 3 +++ events/2024-04-01-example-event-external.md | 5 +++++ events/2024-04-01-example-event.md | 3 +++ events/2024-06-10-mtb-ngs.md | 2 +- events/2024-06-18-FAIR-data-management.md | 5 ++++- ...nalysis-and-interpretation-of-bulk-rna-seq-data.md | 2 ++ events/2024-07-22-freiburg-july.md | 8 ++++++++ events/2024-09-10-biont-rnaseq.md | 6 +++++- events/2025-03-10-hts-workshop-freiburg.md | 8 ++++++++ events/galaxy-academy-2024.md | 11 +++++++++++ news/_posts/2021-03-16-slides_to_videos.md | 2 +- news/_posts/2021-03-17-smorgasbord_report.md | 2 +- news/_posts/2021-03-18-gtn_cofest_may.md | 2 +- news/_posts/2021-03-24-faqs.md | 2 +- news/_posts/2021-04-06-new-video-player.md | 2 +- news/_posts/2021-05-20-spanish_project_begins.md | 2 +- news/_posts/2021-05-25-abbreviations-tag.md | 2 +- news/_posts/2021-05-25-new-dev-tutorial.md | 2 +- news/_posts/2021-06-01-archive-menu.md | 2 +- news/_posts/2021-06-25-gitpod.md | 2 +- news/_posts/2021-06-26-tutorial-volcanoplot-r.md | 4 ++-- ...021-06-30-tutorial-sars-cov-2-variant-discovery.md | 2 +- news/_posts/2021-07-27-a11y.md | 2 +- news/_posts/2021-07-28-feedback.md | 2 +- news/_posts/2021-09-24-jupyter.md | 2 +- news/_posts/2021-09-29-survey.md | 2 +- news/_posts/2021-10-12-data-science.md | 2 +- news/_posts/2021-10-12-speed.md | 2 +- news/_posts/2021-11-10-api.md | 2 +- news/_posts/2021-11-23-video-library.md | 2 +- news/_posts/2021-12-01-FAIR.md | 2 +- news/_posts/2021-12-14-funding.md | 2 +- news/_posts/2021-12-14-smorgasbord.md | 2 +- news/_posts/2022-01-28-rmarkdown.md | 2 +- news/_posts/2022-04-12-cyot.md | 2 +- news/_posts/2022-05-20-schema.md | 2 +- news/_posts/2022-06-02-workflow-reports-tutorial.md | 2 +- news/_posts/2022-09-11-data-manipulation-tutorial.md | 2 +- news/_posts/2023-01-10-gtn-paper.md | 2 +- news/_posts/2023-01-23-new-covid19-topic.md | 2 +- news/_posts/2023-01-24-prometheus.md | 2 +- news/_posts/2023-01-26-pathogen-detection-tutorial.md | 2 +- news/_posts/2023-02-02-black-history-month.md | 2 +- news/_posts/2023-02-08-top-tools.md | 2 +- news/_posts/2023-03-21-galaxy-trainer-directory.md | 2 +- news/_posts/2023-04-13-learning-pathways.md | 2 +- news/_posts/2023-04-19-click-to-run.md | 2 +- news/_posts/2023-04-19-gtn-rdoc.md | 2 +- news/_posts/2023-04-19-shortlinks.md | 2 +- news/_posts/2023-04-20-my-galaxy-training.md | 2 +- news/_posts/2023-05-11-ro-crate.md | 4 ++-- news/_posts/2023-05-15-isoform-usage-training.md | 2 +- news/_posts/2023-06-01-hart.md | 2 +- news/_posts/2023-06-07-pan-galactic-search.md | 2 +- news/_posts/2023-06-21-fair.md | 2 +- news/_posts/2023-06-27-ai4life.md | 2 +- news/_posts/2023-07-20-prefs.md | 2 +- news/_posts/2023-10-05-wendi.md | 2 +- news/_posts/2023-10-12-sc_subdomain.md | 2 +- news/_posts/2023-11-20-workflow-search.md | 2 +- news/_posts/2023-11-21-mastodon.md | 2 +- news/_posts/2023-11-21-video.md | 2 +- news/_posts/2023-12-12-tutorial-run-wfh-ds.md | 2 +- news/_posts/2023-12-18-medchem-user.md | 8 ++++---- news/_posts/2023-12-20-matrix-bots.md | 6 +++--- news/_posts/2024-01-17-sc-fair-data.md | 4 ++-- ...-simplified-gtn-news-submission-via-google-form.md | 2 ++ news/_posts/2024-01-30-oembed-testing.md | 2 ++ news/_posts/2024-01-31-postmarketos.md | 2 +- news/_posts/2024-02-29-new-gmod-topic.md | 4 ++-- news/_posts/2024-03-18-url-persistence.md | 1 + news/_posts/2024-03-28-by-covid-pathways.md | 3 +++ news/_posts/2024-05-13-fair.md | 2 ++ news/_posts/2024-05-22-introducing-gtn-event-pages.md | 2 ++ news/_posts/2024-06-03-onedata.md | 4 ++-- news/_posts/2024-06-04-gtn-standards-rss.md | 1 + news/_posts/2024-06-04-tool-form-integration.md | 1 + news/_posts/2024-06-06-400-tutorials-milestone.md | 4 +++- news/_posts/2024-06-06-dada2-tutorial.md | 5 +++-- ...4-06-11-GalaxyTrainingAcademy-Call-Contribution.md | 2 ++ ...n-intern-to-tutorial-author-to-bioinformatician.md | 1 + ...etics-tutorial-takes-researchers-back-to-basics.md | 1 + news/_posts/2024-06-14-gtn-video-library.md | 3 +++ ...ycobacterium-tuberculosis-complex-ngs-made-easy.md | 2 ++ news/_posts/2024-07-09-gcc-updates.md | 1 + news/_posts/2024-07-17-google-forms.md | 1 + ...-Administrator-Time-Burden-and-Technology-Usage.md | 5 +++-- ...cking-of-mitochondria-and-capturing-mitoflashes.md | 1 + news/_posts/2024-12-02-reviewing.md | 4 +++- news/_posts/2024-12-17-gta-feedback.md | 2 +- 92 files changed, 164 insertions(+), 79 deletions(-) diff --git a/events/2022-07-08-gat.md b/events/2022-07-08-gat.md index b986234f4c5cca..498274e5d1d324 100644 --- a/events/2022-07-08-gat.md +++ b/events/2022-07-08-gat.md @@ -13,6 +13,9 @@ date_start: 2022-07-08 cover-image: /assets/images/gat-small.png cover-image-alt: GTN logo on a spiral galaxy background with text galaxy admin training +tags: +- admin + registration: link: "https://galaxyproject.org/events/gcc2022/" deadline: 2022-06-01 diff --git a/events/2023-04-17-gat-gent.md b/events/2023-04-17-gat-gent.md index bea47e80fb06e3..e1425b1031e656 100644 --- a/events/2023-04-17-gat-gent.md +++ b/events/2023-04-17-gat-gent.md @@ -18,6 +18,9 @@ date_end: 2023-04-21 cover-image: /assets/images/gat-small.png cover-image-alt: GTN logo on a spiral galaxy background with text galaxy admin training +tags: +- admin + registration: link: "https://docs.google.com/forms/d/e/1FAIpQLSc3zgDTfcLZ2-92EdgJvfR4j0KxQeOv0tiFMzGXZ6hdW7JlwQ/viewform" deadline: 2022-03-01 diff --git a/events/2023-10-02-mtb-ngs.md b/events/2023-10-02-mtb-ngs.md index fd66eba63da949..a0d3689412c604 100644 --- a/events/2023-10-02-mtb-ngs.md +++ b/events/2023-10-02-mtb-ngs.md @@ -13,6 +13,9 @@ cover-image-alt: banner for the course date_start: 2023-10-02 date_end: 2023-10-06 # optional, if event is more than one day +tags: +- microbiome + contributions: organisers: # GTN contributors or funders, must be defined in CONTRIBUTORS.yaml - dbrites diff --git a/events/2024-04-01-example-event-external.md b/events/2024-04-01-example-event-external.md index a0689937b40000..aeebf6c39d2c59 100644 --- a/events/2024-04-01-example-event-external.md +++ b/events/2024-04-01-example-event-external.md @@ -15,6 +15,11 @@ description: | date_start: 1970-04-01 date_end: # if multi-day event +# add tags to help users find your event +# tag with a topic to have it show op on the topic community page +tags: +- single-cell + contributions: organisers: # organisers must be defined in CONTRIBUTORS.yaml - shiltemann diff --git a/events/2024-04-01-example-event.md b/events/2024-04-01-example-event.md index a772fdabed49a1..24929b4a7a11d7 100644 --- a/events/2024-04-01-example-event.md +++ b/events/2024-04-01-example-event.md @@ -14,6 +14,9 @@ description: | cover-image: # image for your corse, put in 'events/images' folder cover-image-alt: # supply alt text describing your image +# Tags to help users find your event. Tag with a topic id to have it show op on the topic community page +tags: +- single-cell # Practical Information date_start: 1970-04-01 diff --git a/events/2024-06-10-mtb-ngs.md b/events/2024-06-10-mtb-ngs.md index f9b135a9860da7..19f2a4e8ff6b1b 100644 --- a/events/2024-06-10-mtb-ngs.md +++ b/events/2024-06-10-mtb-ngs.md @@ -12,7 +12,7 @@ cover-image-alt: banner for the course date_start: 2024-06-10 date_end: 2024-06-14 # optional, if event is more than one day -tags: [one-health, tuberculosis, NGS, Galaxy, training] +tags: [one-health, tuberculosis, NGS, Galaxy, training, microbiome] contributions: organisers: # GTN contributors or funders, must be defined in CONTRIBUTORS.yaml diff --git a/events/2024-06-18-FAIR-data-management.md b/events/2024-06-18-FAIR-data-management.md index d1daba43d1aac4..812b2d714a4c91 100644 --- a/events/2024-06-18-FAIR-data-management.md +++ b/events/2024-06-18-FAIR-data-management.md @@ -19,4 +19,7 @@ contributions: location: name: Online ---- \ No newline at end of file +tags: +- fair +- single-cell +--- diff --git a/events/2024-07-22-bioconductor-carpentries-workshop-analysis-and-interpretation-of-bulk-rna-seq-data.md b/events/2024-07-22-bioconductor-carpentries-workshop-analysis-and-interpretation-of-bulk-rna-seq-data.md index b2b066795406d4..4620f91f3f0230 100644 --- a/events/2024-07-22-bioconductor-carpentries-workshop-analysis-and-interpretation-of-bulk-rna-seq-data.md +++ b/events/2024-07-22-bioconductor-carpentries-workshop-analysis-and-interpretation-of-bulk-rna-seq-data.md @@ -17,4 +17,6 @@ location: country: USA date_start: 2024-07-22 date_end: 2024-07-23 +tags: +- transcriptomics --- diff --git a/events/2024-07-22-freiburg-july.md b/events/2024-07-22-freiburg-july.md index 16efe9e26ef43b..6f6479b87fd831 100644 --- a/events/2024-07-22-freiburg-july.md +++ b/events/2024-07-22-freiburg-july.md @@ -42,6 +42,14 @@ infrastructure: - server: https://usegalaxy.eu name: Galaxy EU +tags: +- microbiome +- transcriptomics +- sequence-analysis +- introduction +- epigenetics +- variant-analysis + # Program of your course # Add GTN tutorials by supplying the topic and tutorial name program: diff --git a/events/2024-09-10-biont-rnaseq.md b/events/2024-09-10-biont-rnaseq.md index 41d4b4d8c243e6..6f13edcd93da16 100644 --- a/events/2024-09-10-biont-rnaseq.md +++ b/events/2024-09-10-biont-rnaseq.md @@ -2,7 +2,7 @@ layout: event-external title: A practical introduction to bioinformatics and RNA-seq using Galaxy external: "https://www.cecam.org/workshop-details/a-practical-introduction-to-bioinformatics-and-rna-seq-using-galaxy-1359" -description: | +description: | Join us for an engaging 4-half day online workshop and dive into the captivating world of RNA-seq data analysis using Galaxy! This hands-on workshop will equip you with the skills to effectively analyze RNA-seq data from start to finish. You will learn about: Galaxy, Quality Control, Mapping and Quantification and Downstream Analysis. Don't miss this opportunity to enhance your bioinformatics skills. date_start: 2024-09-10 date_end: 2024-09-13 @@ -16,4 +16,8 @@ contributions: - biont location: name: Online +tags: +- transcriptomics +- sequence-analysis +- introduction --- diff --git a/events/2025-03-10-hts-workshop-freiburg.md b/events/2025-03-10-hts-workshop-freiburg.md index db851d23763371..1d0323bc3ae492 100644 --- a/events/2025-03-10-hts-workshop-freiburg.md +++ b/events/2025-03-10-hts-workshop-freiburg.md @@ -42,6 +42,14 @@ infrastructure: - server: https://usegalaxy.eu name: Galaxy EU +tags: +- introduction +- sequence-analysis +- epigenetics +- transcriptomics +- variant-analysis +- microbiome + # Program of your course # Add GTN tutorials by supplying the topic and tutorial name program: diff --git a/events/galaxy-academy-2024.md b/events/galaxy-academy-2024.md index a238aae31fc972..edc70bd6ea76ad 100644 --- a/events/galaxy-academy-2024.md +++ b/events/galaxy-academy-2024.md @@ -25,6 +25,17 @@ contact_email: academy@galaxyproject.org async: true mode: online +tags: +- microbiome +- single-cell +- proteomics +- introduction +- galaxy-interface +- ecology +- assembly +- one-health +- statistics + contributions: organisers: - teresa-m diff --git a/news/_posts/2021-03-16-slides_to_videos.md b/news/_posts/2021-03-16-slides_to_videos.md index 527e183acc2433..faf478fd94c223 100644 --- a/news/_posts/2021-03-16-slides_to_videos.md +++ b/news/_posts/2021-03-16-slides_to_videos.md @@ -2,7 +2,7 @@ title: "New Feature: Automatic Slides-to-video conversion" contributions: authorship: [hexylena,delphine-l] -tags: [new feature, videos, gtn, pandemic, remote-teaching] +tags: [new feature, videos, gtn, pandemic, remote-teaching, contributing] layout: news --- diff --git a/news/_posts/2021-03-17-smorgasbord_report.md b/news/_posts/2021-03-17-smorgasbord_report.md index afc12cab3b2f9f..e3e5e40f491c5c 100644 --- a/news/_posts/2021-03-17-smorgasbord_report.md +++ b/news/_posts/2021-03-17-smorgasbord_report.md @@ -1,6 +1,6 @@ --- title: Report on the GTN Smörgåsbord event -tags: [event, pandemic, remote-teaching] +tags: [event, pandemic, remote-teaching, teaching] contributions: authorship: [shiltemann,hexylena] cover: "https://gallantries.github.io/assets/images/smorgasbord/emoji-cloud.jpeg" diff --git a/news/_posts/2021-03-18-gtn_cofest_may.md b/news/_posts/2021-03-18-gtn_cofest_may.md index b4b912e48a7b3a..bafa0adab62d1c 100644 --- a/news/_posts/2021-03-18-gtn_cofest_may.md +++ b/news/_posts/2021-03-18-gtn_cofest_may.md @@ -1,6 +1,6 @@ --- title: "Next GTN CoFest May 20, 2021" -tags: [cofest] +tags: [cofest, contributing] contributions: authorship: [shiltemann, hexylena, bebatut, jennaj, delphine-l, annasyme, mblue9] layout: news diff --git a/news/_posts/2021-03-24-faqs.md b/news/_posts/2021-03-24-faqs.md index 0fca47edcf2b6f..c2795b60436c9d 100644 --- a/news/_posts/2021-03-24-faqs.md +++ b/news/_posts/2021-03-24-faqs.md @@ -2,7 +2,7 @@ title: "New Feature: FAQs" contributions: authorship: [shiltemann, hexylena, bebatut] -tags: [gtn infrastructure, contributors, instructors, new feature] +tags: [gtn infrastructure, contributors, instructors, new feature, contributing] layout: news tutorial: "topics/contributing/tutorials/create-new-tutorial-content/tutorial.html#faqs-snippets" --- diff --git a/news/_posts/2021-04-06-new-video-player.md b/news/_posts/2021-04-06-new-video-player.md index a3a745af71696a..75737170427fd1 100644 --- a/news/_posts/2021-04-06-new-video-player.md +++ b/news/_posts/2021-04-06-new-video-player.md @@ -2,7 +2,7 @@ title: "New Feature: Video Player" contributions: authorship: [hexylena] -tags: [gtn infrastructure, video, new feature] +tags: [gtn infrastructure, video, new feature, contributing] cover: topics/contributing/images/slides-to-video.png coveralt: Example of video player mimicking youtube's interface with a video at the top, a transcript at the bottom left, and suggested videos at the bottom right. layout: news diff --git a/news/_posts/2021-05-20-spanish_project_begins.md b/news/_posts/2021-05-20-spanish_project_begins.md index e03aa10c92b078..a237acdcfcdc77 100644 --- a/news/_posts/2021-05-20-spanish_project_begins.md +++ b/news/_posts/2021-05-20-spanish_project_begins.md @@ -1,6 +1,6 @@ --- title: "¿Hablas español?: The first curated tutorial in Spanish!" -tags: [new tutorial, español] +tags: [new tutorial, español, introduction] contributions: authorship: [nomadscientist, beatrizserrano, pclo, ales-ibt, shiltemann, hexylena] cover: "topics/introduction/images/hello-languages.png" diff --git a/news/_posts/2021-05-25-abbreviations-tag.md b/news/_posts/2021-05-25-abbreviations-tag.md index c09ad47e6771c8..fabf706dcff63c 100644 --- a/news/_posts/2021-05-25-abbreviations-tag.md +++ b/news/_posts/2021-05-25-abbreviations-tag.md @@ -1,6 +1,6 @@ --- title: "New Feature: Easy Abbreviation" -tags: [new feature] +tags: [new feature, contributing] contributions: authorship: [hexylena, rikeshi, simonbray] tutorial: "topics/dev/tutorials/bioblend-dev/tutorial.html" diff --git a/news/_posts/2021-05-25-new-dev-tutorial.md b/news/_posts/2021-05-25-new-dev-tutorial.md index 60fd8e8a258202..1ec192530a2884 100644 --- a/news/_posts/2021-05-25-new-dev-tutorial.md +++ b/news/_posts/2021-05-25-new-dev-tutorial.md @@ -1,6 +1,6 @@ --- title: "Contributing to BioBlend as a developer" -tags: [new tutorial] +tags: [new tutorial, dev] contributions: authorship: [rikeshi, simonbray] tutorial: "topics/dev/tutorials/bioblend-dev/tutorial.html" diff --git a/news/_posts/2021-06-01-archive-menu.md b/news/_posts/2021-06-01-archive-menu.md index b8b19e708330c2..8d7aa2a8d21fa2 100644 --- a/news/_posts/2021-06-01-archive-menu.md +++ b/news/_posts/2021-06-01-archive-menu.md @@ -1,6 +1,6 @@ --- title: "Oh no, it changed! Quick, to the archive menu." -tags: [new feature] +tags: [new feature, contributing] contributions: authorship: [hexylena, shiltemann] layout: news diff --git a/news/_posts/2021-06-25-gitpod.md b/news/_posts/2021-06-25-gitpod.md index 77a14ad6bee1f2..7ad16e81660947 100644 --- a/news/_posts/2021-06-25-gitpod.md +++ b/news/_posts/2021-06-25-gitpod.md @@ -1,6 +1,6 @@ --- title: "New Tutorial: GitPod for contributing to the GTN" -tags: [new tutorial, contributors] +tags: [new tutorial, contributing] contributions: authorship: [shiltemann, hexylena] tutorial: "topics/contributing/tutorials/gitpod/tutorial.html" diff --git a/news/_posts/2021-06-26-tutorial-volcanoplot-r.md b/news/_posts/2021-06-26-tutorial-volcanoplot-r.md index cc57359e594e6c..5567427d59fd57 100644 --- a/news/_posts/2021-06-26-tutorial-volcanoplot-r.md +++ b/news/_posts/2021-06-26-tutorial-volcanoplot-r.md @@ -1,6 +1,6 @@ --- title: "New Tutorial: Visualization of RNA-Seq results with Volcano Plot in R" -tags: [new tutorial, visualization] +tags: [new tutorial, visualisation, transcriptomics ] contributions: authorship: [mblue9] tutorial: "topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot-r/tutorial.html" @@ -9,7 +9,7 @@ coveralt: "Screenshot of Volcano Plot customised in R. Significant genes had the layout: news --- -The [Volcano plot]({% link topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.md %}) tutorial introduced volcano plots and showed how they can be easily generated with the Galaxy Volcano plot tool. This new tutorial shows how you can customise a plot using the R script output from the tool and RStudio in Galaxy. A [short video](https://www.youtube.com/embed/4dspgiwkuxk) for the tutorial is also available on YouTube, created for the [GCC2021 Training week](https://galaxyproject.org/events/gcc2021/training/). +The [Volcano plot]({% link topics/transcriptomics/tutorials/rna-seq-viz-with-volcanoplot/tutorial.md %}) tutorial introduced volcano plots and showed how they can be easily generated with the Galaxy Volcano plot tool. This new tutorial shows how you can customise a plot using the R script output from the tool and RStudio in Galaxy. A [short video](https://www.youtube.com/embed/4dspgiwkuxk) for the tutorial is also available on YouTube, created for the [GCC2021 Training week](https://galaxyproject.org/events/gcc2021/training/). Happy plotting! {% include _includes/youtube.html id="4dspgiwkuxk" title="GTN Tutorial: Volcano Plots in R" %} diff --git a/news/_posts/2021-06-30-tutorial-sars-cov-2-variant-discovery.md b/news/_posts/2021-06-30-tutorial-sars-cov-2-variant-discovery.md index e2151d0e6c5bd9..93c116b91fa951 100644 --- a/news/_posts/2021-06-30-tutorial-sars-cov-2-variant-discovery.md +++ b/news/_posts/2021-06-30-tutorial-sars-cov-2-variant-discovery.md @@ -1,6 +1,6 @@ --- title: "New Tutorial: Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data" -tags: [new tutorial, variant-analysis, covid-19] +tags: [new tutorial, variant-analysis, covid-19, one-health] contributions: authorship: [bebatut, wm75] tutorial: "topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html" diff --git a/news/_posts/2021-07-27-a11y.md b/news/_posts/2021-07-27-a11y.md index c4c9770d3402c4..33775858501b80 100644 --- a/news/_posts/2021-07-27-a11y.md +++ b/news/_posts/2021-07-27-a11y.md @@ -2,7 +2,7 @@ title: "Accessibility Improvements" contributions: authorship: [hexylena] -tags: [new feature] +tags: [new feature, contributing] layout: news --- diff --git a/news/_posts/2021-07-28-feedback.md b/news/_posts/2021-07-28-feedback.md index 90e3ca6f439e00..a5e752566d2062 100644 --- a/news/_posts/2021-07-28-feedback.md +++ b/news/_posts/2021-07-28-feedback.md @@ -2,7 +2,7 @@ title: "New Feature: a feedback page to aggregate and display feedback answers" contributions: authorship: [bebatut] -tags: [new feature, contributors] +tags: [new feature, contributing] cover: "news/images/2021-07-28-feedback.png" coveralt: "Screenshot of the top of the feedback page with the titles and 2 graphs: the cumulative number of feedback answers over month for all topics, and a barplot with number of answers for different scores" layout: news diff --git a/news/_posts/2021-09-24-jupyter.md b/news/_posts/2021-09-24-jupyter.md index 85dc0eb3f172e5..9dce74253a6b1d 100644 --- a/news/_posts/2021-09-24-jupyter.md +++ b/news/_posts/2021-09-24-jupyter.md @@ -2,7 +2,7 @@ title: "New Feature: Automatic Jupyter Notebooks" contributions: authorship: [hexylena] -tags: [gtn infrastructure, new feature] +tags: [gtn infrastructure, new feature, contributing] cover: topics/contributing/images/jupyter-notebook.png coveralt: Image comparing Markdown, GTN materials, and new Jupyter Notebook output layout: news diff --git a/news/_posts/2021-09-29-survey.md b/news/_posts/2021-09-29-survey.md index 0d6c80341ddd31..17594bcc255f9b 100644 --- a/news/_posts/2021-09-29-survey.md +++ b/news/_posts/2021-09-29-survey.md @@ -2,7 +2,7 @@ title: "Got a minute? Take our survey about Galaxy for training and have your say!" contributions: authorship: [bebatut] -tags: [feedback] +tags: [feedback, contributing] cover: "news/images/2021-09-29-survey.png" coveralt: "Adversitement for the survey. Written: Got a minute? Did you use Galaxy for training / teaching? Have your say... Take our survey. We appreciate your feedback. Logos: Galaxy Project and Galaxy Training Network" layout: news diff --git a/news/_posts/2021-10-12-data-science.md b/news/_posts/2021-10-12-data-science.md index 06ef58db9e6bb6..85417c75a1724d 100644 --- a/news/_posts/2021-10-12-data-science.md +++ b/news/_posts/2021-10-12-data-science.md @@ -3,7 +3,7 @@ title: "New Topic: Data Science Survival Kit" contributions: authorship: [shiltemann, hexylena, bebatut, abretaud, yvanlebras, fpsom, carpentries] funding: [gallantries] -tags: [gtn infrastructure, new topic] +tags: [gtn infrastructure, new topic, data-science] layout: news --- diff --git a/news/_posts/2021-10-12-speed.md b/news/_posts/2021-10-12-speed.md index db7d178d6fc6c5..592a4f19c96c23 100644 --- a/news/_posts/2021-10-12-speed.md +++ b/news/_posts/2021-10-12-speed.md @@ -1,6 +1,6 @@ --- title: "Attention Contributors: GTN Performance Enhancements" -tags: [authors, developers, performance] +tags: [authors, developers, performance, contributing] contributions: authorship: [hexylena] layout: news diff --git a/news/_posts/2021-11-10-api.md b/news/_posts/2021-11-10-api.md index 21c1be34670109..d058a4452a1cab 100644 --- a/news/_posts/2021-11-10-api.md +++ b/news/_posts/2021-11-10-api.md @@ -2,7 +2,7 @@ title: "New Feature: GTN API with OpenAPI 3 specification" contributions: authorship: [hexylena] -tags: [gtn infrastructure, new feature] +tags: [gtn infrastructure, new feature, contributing] cover: assets/images/swagger.png coveralt: Image showing an OpenAPI / Swagger UI to the training material API featuring several APIs like topics, tutorials, contributors, and a couple internal APIs. At the bottom are a couple of data models. layout: news diff --git a/news/_posts/2021-11-23-video-library.md b/news/_posts/2021-11-23-video-library.md index 518e81f575fd28..20ebb10dda1a97 100644 --- a/news/_posts/2021-11-23-video-library.md +++ b/news/_posts/2021-11-23-video-library.md @@ -3,7 +3,7 @@ title: "New Feature: GTN Video Library" contributions: authorship: [shiltemann, hexylena] infrastructure: [shiltemann, hexylena] -tags: [gtn infrastructure, new feature] +tags: [gtn infrastructure, new feature, contributing] cover: news/images/gtn-videolib-stats.png coveralt: Screenshot of the GTN Video Library Home page layout: news diff --git a/news/_posts/2021-12-01-FAIR.md b/news/_posts/2021-12-01-FAIR.md index 3baa34d5db4bd8..10f81328a03119 100644 --- a/news/_posts/2021-12-01-FAIR.md +++ b/news/_posts/2021-12-01-FAIR.md @@ -2,7 +2,7 @@ title: "New FAQs: How does the GTN stay FAIR and Collaborative" contributions: authorship: [hexylena] -tags: [faq] +tags: [faq, fair, contributing] layout: news --- diff --git a/news/_posts/2021-12-14-funding.md b/news/_posts/2021-12-14-funding.md index ebb0ab6e3d7048..f6210f0b449686 100644 --- a/news/_posts/2021-12-14-funding.md +++ b/news/_posts/2021-12-14-funding.md @@ -1,6 +1,6 @@ --- title: Support for annotating Funding Agencies -tags: [new-feature] +tags: [new-feature, contributing] contributions: authorship: - hexylena diff --git a/news/_posts/2021-12-14-smorgasbord.md b/news/_posts/2021-12-14-smorgasbord.md index 32605622ad33ff..07a11b6ec9d351 100644 --- a/news/_posts/2021-12-14-smorgasbord.md +++ b/news/_posts/2021-12-14-smorgasbord.md @@ -1,7 +1,7 @@ --- layout: news title: "GTN Smörgåsbord 2: Tapas Edition" -tags: [event] +tags: [event, contributing, teaching] link: "https://gallantries.github.io/posts/2021/12/14/smorgasbord2-tapas/?utm_source=gtn&utm_medium=news&utm_campaign=smorgasbord2" external: true cover: "https://gallantries.github.io/assets/images/smorgasbord2/banner-500.png" diff --git a/news/_posts/2022-01-28-rmarkdown.md b/news/_posts/2022-01-28-rmarkdown.md index c3d582ae3965f8..6d8ee9187f80b2 100644 --- a/news/_posts/2022-01-28-rmarkdown.md +++ b/news/_posts/2022-01-28-rmarkdown.md @@ -3,7 +3,7 @@ title: "New Feature: Automatic RMarkdown" contributions: authorship: [hexylena] funding: [gallantries, avans-atgm] -tags: [gtn infrastructure, new feature] +tags: [gtn infrastructure, new feature, contributing] cover: topics/data-science/images/rstudio/r-preview-output.png coveralt: Image showing content from a tutorial, rendered as an rmarkdown html via knitting. A table of contents appears on the left, and code and outputs on the right. layout: news diff --git a/news/_posts/2022-04-12-cyot.md b/news/_posts/2022-04-12-cyot.md index bd1ed6a5d708c5..ad0d823bad8529 100644 --- a/news/_posts/2022-04-12-cyot.md +++ b/news/_posts/2022-04-12-cyot.md @@ -3,7 +3,7 @@ title: "New Tutorial Feature: Choose Your Own Tutorial" contributions: authorship: [hexylena] funding: [gallantries] -tags: [gtn infrastructure, new feature, tutorial authors] +tags: [gtn infrastructure, new feature, tutorial authors, contributing] cover: assets/images/cyot.gif coveralt: Gif showing a user switching between two branches of a tutorial layout: news diff --git a/news/_posts/2022-05-20-schema.md b/news/_posts/2022-05-20-schema.md index baa2d6605a38cc..69a8740877c731 100644 --- a/news/_posts/2022-05-20-schema.md +++ b/news/_posts/2022-05-20-schema.md @@ -1,6 +1,6 @@ --- title: GTN Metadata Schemas -tags: [new feature] +tags: [new feature, contributing] contributions: authorship: [hexylena] layout: news diff --git a/news/_posts/2022-06-02-workflow-reports-tutorial.md b/news/_posts/2022-06-02-workflow-reports-tutorial.md index ea8d084b868d8b..05545febb2b26e 100644 --- a/news/_posts/2022-06-02-workflow-reports-tutorial.md +++ b/news/_posts/2022-06-02-workflow-reports-tutorial.md @@ -1,6 +1,6 @@ --- title: "New Tutorial: Workflow Reports" -tags: [new tutorial, Galaxy Tips & Tricks] +tags: [new tutorial, Galaxy Tips & Tricks, galaxy-interface] contributions: authorship: [shiltemann] cover: "topics/galaxy-interface/tutorials/workflow-reports/images/invocations-list.png" diff --git a/news/_posts/2022-09-11-data-manipulation-tutorial.md b/news/_posts/2022-09-11-data-manipulation-tutorial.md index 89494886ff6d03..963876bf8c5b5d 100644 --- a/news/_posts/2022-09-11-data-manipulation-tutorial.md +++ b/news/_posts/2022-09-11-data-manipulation-tutorial.md @@ -1,6 +1,6 @@ --- title: "New Tutorial: Data Manipulation" -tags: [new tutorial] +tags: [new tutorial, introduction] contributions: authorship: [shiltemann] cover: "topics/introduction/tutorials/data-manipulation-olympics/images/cover.jpg" diff --git a/news/_posts/2023-01-10-gtn-paper.md b/news/_posts/2023-01-10-gtn-paper.md index f06dae69098ae9..792ecf159001f3 100644 --- a/news/_posts/2023-01-10-gtn-paper.md +++ b/news/_posts/2023-01-10-gtn-paper.md @@ -1,6 +1,6 @@ --- title: 'New GTN paper: "Galaxy Training: A powerful framework for teaching!"' -tags: [paper] +tags: [paper, contributing] contributions: authorship: [bebatut,shiltemann,hexylena] cover: "news/images/2023-01-10-gtn-paper-fig2.png" diff --git a/news/_posts/2023-01-23-new-covid19-topic.md b/news/_posts/2023-01-23-new-covid19-topic.md index 023e96cad6f5da..5efe816dec31a9 100644 --- a/news/_posts/2023-01-23-new-covid19-topic.md +++ b/news/_posts/2023-01-23-new-covid19-topic.md @@ -1,6 +1,6 @@ --- title: "New GTN Feature Tag-based Topics enables new SARS-CoV-2 topic" -tags: [new topic,new feature] +tags: [new topic,new feature, one-health] contributions: authorship: [hexylena,wm75] layout: news diff --git a/news/_posts/2023-01-24-prometheus.md b/news/_posts/2023-01-24-prometheus.md index f851e4f1968edf..d80714663c540f 100644 --- a/news/_posts/2023-01-24-prometheus.md +++ b/news/_posts/2023-01-24-prometheus.md @@ -2,7 +2,7 @@ title: "New Feature: Prometheus Metrics endpoint" contributions: authorship: [hexylena] -tags: [new feature, gtn] +tags: [new feature, gtn, contributing] layout: news --- diff --git a/news/_posts/2023-01-26-pathogen-detection-tutorial.md b/news/_posts/2023-01-26-pathogen-detection-tutorial.md index b2b984873dba13..49d76e95a78b81 100644 --- a/news/_posts/2023-01-26-pathogen-detection-tutorial.md +++ b/news/_posts/2023-01-26-pathogen-detection-tutorial.md @@ -1,6 +1,6 @@ --- title: "New Tutorial: Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition" -tags: [new tutorial] +tags: [new tutorial, microbiome] contributions: authorship: [bebatut, EngyNasr] cover: "topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/images/FoodBorne-Workflow-updated.png" diff --git a/news/_posts/2023-02-02-black-history-month.md b/news/_posts/2023-02-02-black-history-month.md index 1e83cc681d3355..87425ea5313e06 100644 --- a/news/_posts/2023-02-02-black-history-month.md +++ b/news/_posts/2023-02-02-black-history-month.md @@ -1,6 +1,6 @@ --- title: "GTN Celebrates Black History Month" -tags: [] +tags: [contributing] contributions: authorship: [hexylena] layout: news diff --git a/news/_posts/2023-02-08-top-tools.md b/news/_posts/2023-02-08-top-tools.md index 89e3c988eb7fac..75f4be4190a248 100644 --- a/news/_posts/2023-02-08-top-tools.md +++ b/news/_posts/2023-02-08-top-tools.md @@ -1,6 +1,6 @@ --- title: What are the most used tools in the GTN? -tags: [new feature, gtn] +tags: [new feature, gtn, contributing, community] contributions: authorship: - hexylena diff --git a/news/_posts/2023-03-21-galaxy-trainer-directory.md b/news/_posts/2023-03-21-galaxy-trainer-directory.md index c322f1f82225e0..8072fb3bf6c419 100644 --- a/news/_posts/2023-03-21-galaxy-trainer-directory.md +++ b/news/_posts/2023-03-21-galaxy-trainer-directory.md @@ -1,6 +1,6 @@ --- title: "New Feature: Trainer Directory! (Add yourself today!)" -tags: [new feature, community building, capacity building] +tags: [new feature, community building, capacity building, contributing] contributions: authorship: [hexylena, lldelisle] funding: [gallantries] diff --git a/news/_posts/2023-04-13-learning-pathways.md b/news/_posts/2023-04-13-learning-pathways.md index c2f0417e1fdb41..6973ff2c080c5f 100644 --- a/news/_posts/2023-04-13-learning-pathways.md +++ b/news/_posts/2023-04-13-learning-pathways.md @@ -1,6 +1,6 @@ --- title: "New Feature: Learning Pathways!" -tags: [new feature] +tags: [new feature, contributing] contributions: authorship: [shiltemann, hexylena] funding: [gallantries] diff --git a/news/_posts/2023-04-19-click-to-run.md b/news/_posts/2023-04-19-click-to-run.md index 80fae0cfb2f031..0220a93e650278 100644 --- a/news/_posts/2023-04-19-click-to-run.md +++ b/news/_posts/2023-04-19-click-to-run.md @@ -2,7 +2,7 @@ title: "New Feature: Click-to-run Workflows" contributions: authorship: [hexylena] -tags: [new feature, gtn] +tags: [new feature, gtn, contributing] layout: news tutorial: topics/microbiome/tutorials/mothur-miseq-sop-short/workflows/ --- diff --git a/news/_posts/2023-04-19-gtn-rdoc.md b/news/_posts/2023-04-19-gtn-rdoc.md index c1c70266db4e5e..c26128ad0380d8 100644 --- a/news/_posts/2023-04-19-gtn-rdoc.md +++ b/news/_posts/2023-04-19-gtn-rdoc.md @@ -2,7 +2,7 @@ title: "New Feature: GTN Rdoc" contributions: authorship: [hexylena] -tags: [new feature, gtn] +tags: [new feature, gtn, contributing] layout: news --- diff --git a/news/_posts/2023-04-19-shortlinks.md b/news/_posts/2023-04-19-shortlinks.md index a7ae099c7a96b5..30bd6e8a1b8ef3 100644 --- a/news/_posts/2023-04-19-shortlinks.md +++ b/news/_posts/2023-04-19-shortlinks.md @@ -2,7 +2,7 @@ title: "New Feature: Persistent URLs (PURLs) / Shortlinks" contributions: authorship: [hexylena] -tags: [new feature, gtn] +tags: [new feature, gtn, contributing] layout: news cover: "assets/images/purl.png" coveralt: the bottom left corner of an overview box from a training material is shown, a label short link clearly has a short link as described in the tutorial diff --git a/news/_posts/2023-04-20-my-galaxy-training.md b/news/_posts/2023-04-20-my-galaxy-training.md index 30eb49dcb66e89..35f0470dd33b08 100644 --- a/news/_posts/2023-04-20-my-galaxy-training.md +++ b/news/_posts/2023-04-20-my-galaxy-training.md @@ -2,7 +2,7 @@ title: "New Feature: my.galaxy.training" contributions: authorship: [hexylena] -tags: [new feature, gtn] +tags: [new feature, gtn, contributing] layout: news --- diff --git a/news/_posts/2023-05-11-ro-crate.md b/news/_posts/2023-05-11-ro-crate.md index 7e9cc98f2515ea..4a4214b8704604 100644 --- a/news/_posts/2023-05-11-ro-crate.md +++ b/news/_posts/2023-05-11-ro-crate.md @@ -1,6 +1,6 @@ --- title: "BY-COVID and RO-Crate collaboration brings new topic: FAIR Data, Workflows & More" -tags: [new topic,new feature] +tags: [new topic,new feature, fair] contributions: authorship: [simleo, pauldg, stain, ilveroluca, kikkomep] editing: [hexylena] @@ -38,7 +38,7 @@ These tutorials are meant to help you learn how to use and create RO-Crates in y ## Where can I learn more? -These tutorials will be taught at [Smörgåsbord 3](https://gallantries.github.io/video-library/events/smorgasbord3/) so +These tutorials will be taught at [Smörgåsbord 3](https://gallantries.github.io/video-library/events/smorgasbord3/) so if you want to learn more, [go sign up now!](https://gxy.io/smorgasbord3-register) ## I want more FAIR Training! diff --git a/news/_posts/2023-05-15-isoform-usage-training.md b/news/_posts/2023-05-15-isoform-usage-training.md index 1b3ab4e0f53160..9024524d10e1a8 100644 --- a/news/_posts/2023-05-15-isoform-usage-training.md +++ b/news/_posts/2023-05-15-isoform-usage-training.md @@ -6,7 +6,7 @@ contributions: cover: news/images/isoform_usage_post.jpg coveralt: "Schematic of an isoform switch and detection pipeline. Data is annotated and a prediction is made for isoform switch consequences" -tags: [new tutorial] +tags: [new tutorial, transcriptomics] tutorial: topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html --- diff --git a/news/_posts/2023-06-01-hart.md b/news/_posts/2023-06-01-hart.md index 81084d2140b7e6..9d4916fe617505 100644 --- a/news/_posts/2023-06-01-hart.md +++ b/news/_posts/2023-06-01-hart.md @@ -1,6 +1,6 @@ --- title: "GTN Celebrates Pride Month: Alan Hart & M. Tuberculosis" -tags: [] +tags: [contributing] contributions: authorship: [hexylena] layout: news diff --git a/news/_posts/2023-06-07-pan-galactic-search.md b/news/_posts/2023-06-07-pan-galactic-search.md index 117933346388a9..4d5298f02d3b84 100644 --- a/news/_posts/2023-06-07-pan-galactic-search.md +++ b/news/_posts/2023-06-07-pan-galactic-search.md @@ -2,7 +2,7 @@ title: "New Feature: Pan-Galactic Tool Search" contributions: authorship: [hexylena] -tags: [new feature, gtn] +tags: [new feature, gtn, contributing] layout: news abbreviations: SEO: Search Engine Optimisation diff --git a/news/_posts/2023-06-21-fair.md b/news/_posts/2023-06-21-fair.md index 865415774abcf1..97795122c0c325 100644 --- a/news/_posts/2023-06-21-fair.md +++ b/news/_posts/2023-06-21-fair.md @@ -1,6 +1,6 @@ --- title: "ELIXIR-UK Fellow Launches New FAIR Data Management Training" -tags: [new topic,new tutorial] +tags: [new topic,new tutorial, fair] contributions: authorship: [kkamieniecka, poterlowicz-lab] funding: [elixir-fair-data] diff --git a/news/_posts/2023-06-27-ai4life.md b/news/_posts/2023-06-27-ai4life.md index dd08d2f43a286a..4b8f520ea501be 100644 --- a/news/_posts/2023-06-27-ai4life.md +++ b/news/_posts/2023-06-27-ai4life.md @@ -1,7 +1,7 @@ --- layout: news title: AI4Life teams up with GTN to enhance training resources -tags: [new topic,new community] +tags: [new topic,new community, imaging] link: "https://ai4life.eurobioimaging.eu/ai4life-teams-up-with-galaxy-training-network-gtn-to-enhance-training-resources/" external: true contributions: diff --git a/news/_posts/2023-07-20-prefs.md b/news/_posts/2023-07-20-prefs.md index f9955c209c6f7d..63aab2234fc0d9 100644 --- a/news/_posts/2023-07-20-prefs.md +++ b/news/_posts/2023-07-20-prefs.md @@ -3,7 +3,7 @@ title: "New Feature: GTN User Preferences" contributions: authorship: [hexylena] infrastructure: [hexylena] -tags: [new feature, gtn] +tags: [new feature, gtn, contributing] layout: news --- diff --git a/news/_posts/2023-10-05-wendi.md b/news/_posts/2023-10-05-wendi.md index c8c7bab44cec22..14dce305b2bafa 100644 --- a/news/_posts/2023-10-05-wendi.md +++ b/news/_posts/2023-10-05-wendi.md @@ -3,7 +3,7 @@ title: "New Feature: Embeddable GTN Tutorial Lists and UseGalaxy Workflow List W contributions: authorship: [hexylena] testing: [nomadscientist] -tags: [new feature, gtn] +tags: [new feature, gtn, contrributing, community] layout: news --- diff --git a/news/_posts/2023-10-12-sc_subdomain.md b/news/_posts/2023-10-12-sc_subdomain.md index cf17e9f2aa2d58..b8485b3db7ea5d 100644 --- a/news/_posts/2023-10-12-sc_subdomain.md +++ b/news/_posts/2023-10-12-sc_subdomain.md @@ -3,7 +3,7 @@ title: "Single cell subdomain re-launch: Unified and feedback-driven" contributions: authorship: [nomadscientist, pavanvidem] infrastructure: [kysrpex] -tags: [gtn, singlecell] +tags: [gtn, single-cell] cover: "news/images/2023-10-12-singlecell_subdomain.png" coveralt: "screenshot of the Single Cell Omics subdomain page, with purple mastheader, Single Cell Tools categories along the side, and an updated logo combining the Single Cell Omics connected cells image with the Human Cell Atlas blue embyro logo" layout: news diff --git a/news/_posts/2023-11-20-workflow-search.md b/news/_posts/2023-11-20-workflow-search.md index 6236678c1cb977..436dbc0bd4a54d 100644 --- a/news/_posts/2023-11-20-workflow-search.md +++ b/news/_posts/2023-11-20-workflow-search.md @@ -3,7 +3,7 @@ title: "Update: Workflow List now searches WorkflowHub.eu, advanced query syntax contributions: authorship: [hexylena] testing: [paulzierep, wm75] -tags: [feature update, gtn] +tags: [feature update, gtn, contributing] layout: news --- diff --git a/news/_posts/2023-11-21-mastodon.md b/news/_posts/2023-11-21-mastodon.md index a3f6edf743eac0..8927834951cf42 100644 --- a/news/_posts/2023-11-21-mastodon.md +++ b/news/_posts/2023-11-21-mastodon.md @@ -2,7 +2,7 @@ title: "GTN has left Twitter/X as of October" contributions: authorship: [hexylena] -tags: [gtn, communications] +tags: [gtn, communications, contributing] layout: news --- diff --git a/news/_posts/2023-11-21-video.md b/news/_posts/2023-11-21-video.md index b33f8fde1bf61c..fdb52921e809f1 100644 --- a/news/_posts/2023-11-21-video.md +++ b/news/_posts/2023-11-21-video.md @@ -2,7 +2,7 @@ title: "Feedback: Easy slide recordings" contributions: authorship: [hexylena] -tags: [feedback, testimonial, gtn] +tags: [feedback, testimonial, gtn, contributing] layout: news --- diff --git a/news/_posts/2023-12-12-tutorial-run-wfh-ds.md b/news/_posts/2023-12-12-tutorial-run-wfh-ds.md index 7aae22ed6765b3..3849a50e2dda84 100644 --- a/news/_posts/2023-12-12-tutorial-run-wfh-ds.md +++ b/news/_posts/2023-12-12-tutorial-run-wfh-ds.md @@ -3,7 +3,7 @@ title: "Tutorial Feature: Easier launching of WorkflowHub & Dockstore Workflows" contributions: authorship: [hexylena] funding: [by-covid] -tags: [feature update, gtn, tutorials] +tags: [feature update, gtn, tutorials, contributing] layout: news --- diff --git a/news/_posts/2023-12-18-medchem-user.md b/news/_posts/2023-12-18-medchem-user.md index d1e41290764114..84a95a88fddca0 100644 --- a/news/_posts/2023-12-18-medchem-user.md +++ b/news/_posts/2023-12-18-medchem-user.md @@ -1,16 +1,16 @@ --- title: "User story: Where Galaxy meets medicinal chemistry" -tags: [computational chemistry,user story,gtn] +tags: [computational-chemistry,user story,gtn] contributions: authorship: [wee-snufkin] layout: news --- -As a medicinal chemistry student, I undertook a semester project on natural products isolation and derivatisation. One of the compounds my group was working on was piperine, extracted from black pepper. Inspired by literature findings, we found out that the derivatives of piperine can inhibit monoamine oxidase-B and thus can be possibly used in Parkinson’s disease. As a novelty element in our project, we came up with new structures of derivatives that could act as inhibitors. +As a medicinal chemistry student, I undertook a semester project on natural products isolation and derivatisation. One of the compounds my group was working on was piperine, extracted from black pepper. Inspired by literature findings, we found out that the derivatives of piperine can inhibit monoamine oxidase-B and thus can be possibly used in Parkinson’s disease. As a novelty element in our project, we came up with new structures of derivatives that could act as inhibitors. -Before synthesising any new molecules, it would make sense to check if they correctly dock into the active site. As an enthusiastic user and developer of Galaxy, the idea of using GTN came straight to my mind. Even though molecular docking was beyond the scope of our project, I knew that Galaxy and GTN give such an amazing opportunity to do it in the blink of an eye that I wouldn't be myself if I hadn't tried! Therefore, by using the [tutorial on molecular docking]({% link topics/computational-chemistry/tutorials/cheminformatics/tutorial.md %}), I identified the pocket, then I studied the binding of the approved drugs such as Safinamide and Zonisamide and finally I checked how our proposed molecule fits within the pocket. After that, we were ready to synthesise the derivative we came up with! +Before synthesising any new molecules, it would make sense to check if they correctly dock into the active site. As an enthusiastic user and developer of Galaxy, the idea of using GTN came straight to my mind. Even though molecular docking was beyond the scope of our project, I knew that Galaxy and GTN give such an amazing opportunity to do it in the blink of an eye that I wouldn't be myself if I hadn't tried! Therefore, by using the [tutorial on molecular docking]({% link topics/computational-chemistry/tutorials/cheminformatics/tutorial.md %}), I identified the pocket, then I studied the binding of the approved drugs such as Safinamide and Zonisamide and finally I checked how our proposed molecule fits within the pocket. After that, we were ready to synthesise the derivative we came up with! ![Picture of piperine derivative docking into MAO-B pocket.]({% link news/images/2023-12-18-medchem-user.jpg %} "Piperine derivative as a potential inhibitor of MAO-B") -This example shows how GTN and Galaxy can facilitate and accelerate the work of medicinal chemists before starting the synthesis. It is easy to follow the GTN tutorials, the results are reproducible, the datasets are stored in the history and can be easily shared with anyone on the team. +This example shows how GTN and Galaxy can facilitate and accelerate the work of medicinal chemists before starting the synthesis. It is easy to follow the GTN tutorials, the results are reproducible, the datasets are stored in the history and can be easily shared with anyone on the team. diff --git a/news/_posts/2023-12-20-matrix-bots.md b/news/_posts/2023-12-20-matrix-bots.md index 775f72cd3be01f..5c8227ac222b65 100644 --- a/news/_posts/2023-12-20-matrix-bots.md +++ b/news/_posts/2023-12-20-matrix-bots.md @@ -4,7 +4,7 @@ contributions: authorship: [mtekman] editing: [hexylena] infrastructure: [mtekman, hexylena] -tags: [gtn, communications] +tags: [gtn, communications, contributing] layout: news --- @@ -15,14 +15,14 @@ the non-Matrix side of the Galaxy-verse. ## Galaxy Help Posts The newest bot we've added looks through the [Galaxy Help](https://help.galaxyproject.org/) forum for topics in need of -answering, and forwards those to the humans in Matrix channels related to those topics! +answering, and forwards those to the humans in Matrix channels related to those topics! We are currently trialing this new integration to provide high quality human help with the Single Cell CoP. If it's successful, our first expansion will be to the admin channel. ## GTN Contributions Our existing GTN bot summarizes the contributions to the GTN each day and delivers the great news to the -[GTN Matrix Lobby](https://app.element.io/#/room/#Galaxy-Training-Network_Lobby:gitter.im), as well as single-cell specific updates just to the [Single Cell User Community](https://app.element.io/#/room/#!yuLoaCWKpFHkWPmVEO:gitter.im). +[GTN Matrix Lobby](https://app.element.io/#/room/#Galaxy-Training-Network_Lobby:gitter.im), as well as single-cell specific updates just to the [Single Cell User Community](https://app.element.io/#/room/#!yuLoaCWKpFHkWPmVEO:gitter.im). Would your community like to receive these daily GTN updates for your community? Reach out to us on [Matrix](https://app.element.io/#/room/#Galaxy-Training-Network_Lobby:gitter.im) or [GitHub](https://github.com/galaxyproject/training-material/issues/). Currently this integration is only available for Matrix but if it would be useful as an RSS feed please let us know. diff --git a/news/_posts/2024-01-17-sc-fair-data.md b/news/_posts/2024-01-17-sc-fair-data.md index 271ec9577d99bc..ecd617947dd020 100644 --- a/news/_posts/2024-01-17-sc-fair-data.md +++ b/news/_posts/2024-01-17-sc-fair-data.md @@ -1,6 +1,6 @@ --- title: "FAIR Data management in single cell analysis" -tags: [single cell,data management,data import,fair] +tags: [single-cell,data management,data import,fair] contributions: authorship: [wee-snufkin, hexhowells, nomadscientist] funding: [elixir-fair-data] @@ -9,7 +9,7 @@ layout: news # New single cell section: Changing data formats & preparing objects -Now a nightmare of switching between single cell datatypes or importing the data is gone! With the new section on Changing data formats & preparing objects, the users can now confidently jump into the analysis. Some of those tutorials were created in the framework of ELIXIR-UK: FAIR Data Stewardship training, which aims to improve Findable Accessible Interoperable Reusable (FAIR) data management in the life sciences. +Now a nightmare of switching between single cell datatypes or importing the data is gone! With the new section on Changing data formats & preparing objects, the users can now confidently jump into the analysis. Some of those tutorials were created in the framework of ELIXIR-UK: FAIR Data Stewardship training, which aims to improve Findable Accessible Interoperable Reusable (FAIR) data management in the life sciences. We have developed the following tutorials: - [Converting between common single cell data formats]({% link topics/single-cell/tutorials/scrna-data-ingest/tutorial.md %}) diff --git a/news/_posts/2024-01-29-simplified-gtn-news-submission-via-google-form.md b/news/_posts/2024-01-29-simplified-gtn-news-submission-via-google-form.md index 8e2165b3f028b5..4f4082dd1c797a 100644 --- a/news/_posts/2024-01-29-simplified-gtn-news-submission-via-google-form.md +++ b/news/_posts/2024-01-29-simplified-gtn-news-submission-via-google-form.md @@ -14,6 +14,8 @@ contributions: infrastructure: - hexylena link: https://forms.gle/TqGTr6y46wrJDri7A +tags: [contributing, community] + --- Based on user feedback of the difficulties of the GTN news submission process we have significantly simplified and removed the need for manually editing a YAML file by providing a quick and easy [Google Form](https://forms.gle/TqGTr6y46wrJDri7A) diff --git a/news/_posts/2024-01-30-oembed-testing.md b/news/_posts/2024-01-30-oembed-testing.md index f15c7b8b0b77e8..00143c70545398 100644 --- a/news/_posts/2024-01-30-oembed-testing.md +++ b/news/_posts/2024-01-30-oembed-testing.md @@ -15,6 +15,8 @@ contributions: - jennaj infrastructure: - hexylena + +tags: [contributing, community] --- Howdy teachers and support staff! We are exploring displaying GTN content directly in the Galaxy Help site, furthering the integration between the GTN and the Galaxy community infrastructure. diff --git a/news/_posts/2024-01-31-postmarketos.md b/news/_posts/2024-01-31-postmarketos.md index 17b47b97e50bad..04626eef318a1c 100644 --- a/news/_posts/2024-01-31-postmarketos.md +++ b/news/_posts/2024-01-31-postmarketos.md @@ -1,6 +1,6 @@ --- title: "🪐📲 Hosting Galaxy at the Edge: Directly in Your Pocket!" -tags: [fun, system administrators, developers, humour] +tags: [fun, system administrators, developers, humour, admin] contributions: authorship: [mtekman] editing: [hexylena] diff --git a/news/_posts/2024-02-29-new-gmod-topic.md b/news/_posts/2024-02-29-new-gmod-topic.md index 9bf7e3d6d3d6c6..bb3e05afe3c3da 100644 --- a/news/_posts/2024-02-29-new-gmod-topic.md +++ b/news/_posts/2024-02-29-new-gmod-topic.md @@ -1,6 +1,6 @@ --- title: "GTN ❤️ GMOD" -tags: [new topic, new feature, genome annotation] +tags: [new topic, new feature, genome-annotation, GMOD] contributions: authorship: [hexylena, abretaud] infrastructure: [hexylena] @@ -8,7 +8,7 @@ layout: news tutorial: topics/gmod/index.html --- -Building upon the work previously done for the [SARS-Cov-2 Topic](/training-material/news/2023/01/23/new-covid19-topic.html) we have further expanded the 'tag based topics' to support a new GMOD topic. +Building upon the work previously done for the [SARS-Cov-2 Topic](/training-material/news/2023/01/23/new-covid19-topic.html) we have further expanded the 'tag based topics' to support a new GMOD topic. # Generic Model Organism Database diff --git a/news/_posts/2024-03-18-url-persistence.md b/news/_posts/2024-03-18-url-persistence.md index b4546f5075104b..cc3c6657f567e0 100644 --- a/news/_posts/2024-03-18-url-persistence.md +++ b/news/_posts/2024-03-18-url-persistence.md @@ -4,6 +4,7 @@ layout: news tags: - gtn infrastructure - new feature +- contributing contributions: authorship: - hexylena diff --git a/news/_posts/2024-03-28-by-covid-pathways.md b/news/_posts/2024-03-28-by-covid-pathways.md index b9948715b921d6..5741bc09844c60 100644 --- a/news/_posts/2024-03-28-by-covid-pathways.md +++ b/news/_posts/2024-03-28-by-covid-pathways.md @@ -7,6 +7,9 @@ tags: - minerva - gtn infrastructure - new feature +- one-health +- transcriptomics + contributions: authorship: - hexylena diff --git a/news/_posts/2024-05-13-fair.md b/news/_posts/2024-05-13-fair.md index 21f2b5036e4da0..808733aa852ab5 100644 --- a/news/_posts/2024-05-13-fair.md +++ b/news/_posts/2024-05-13-fair.md @@ -3,6 +3,8 @@ title: Perfectly FAIR Training! layout: news tags: - gtn infrastructure +- fair +- contributing contributions: authorship: - hexylena diff --git a/news/_posts/2024-05-22-introducing-gtn-event-pages.md b/news/_posts/2024-05-22-introducing-gtn-event-pages.md index a86b13efdfa7c3..6f979ea9bbab76 100644 --- a/news/_posts/2024-05-22-introducing-gtn-event-pages.md +++ b/news/_posts/2024-05-22-introducing-gtn-event-pages.md @@ -6,6 +6,8 @@ tags: - gtn infrastructure - new feature - events +- contributing +- community contributions: authorship: - shiltemann diff --git a/news/_posts/2024-06-03-onedata.md b/news/_posts/2024-06-03-onedata.md index 6afca018129714..dbb31141009e99 100644 --- a/news/_posts/2024-06-03-onedata.md +++ b/news/_posts/2024-06-03-onedata.md @@ -6,7 +6,7 @@ contributions: funding: - eurosciencegateway - egi -tags: [esg-wp4, esg] +tags: [esg-wp4, esg, contributing] cover: news/images/galaxy-data-upload.png coveralt: screenshot of galaxy data upload interface showing a folder named GTN Training Data layout: news @@ -54,7 +54,7 @@ You can access all GTN training data using several methods: 4. **Onedata clients** — access the data using the public read-only access token and [Oneclient](https://www.onedata.org/#/home/documentation/21.02/user-guide/oneclient.html) (local POSIX mount) - or [OnedataFS](https://onedata.org/#/home/documentation/21.02/user-guide/onedatafs.html) + or [OnedataFS](https://onedata.org/#/home/documentation/21.02/user-guide/onedatafs.html) ([PyFilesystem](https://www.pyfilesystem.org/) interface), e.g.: ```bash diff --git a/news/_posts/2024-06-04-gtn-standards-rss.md b/news/_posts/2024-06-04-gtn-standards-rss.md index b12ce98489dc6f..d4cff6a45dd64c 100644 --- a/news/_posts/2024-06-04-gtn-standards-rss.md +++ b/news/_posts/2024-06-04-gtn-standards-rss.md @@ -4,6 +4,7 @@ layout: news tags: - gtn infrastructure +- contributing contributions: authorship: - hexylena diff --git a/news/_posts/2024-06-04-tool-form-integration.md b/news/_posts/2024-06-04-tool-form-integration.md index e7032f2956b137..6c04a3acc7d685 100644 --- a/news/_posts/2024-06-04-tool-form-integration.md +++ b/news/_posts/2024-06-04-tool-form-integration.md @@ -12,6 +12,7 @@ tags: - gtn - new feature - already-on-hub + - contributing abbreviations: GTN: Galaxy Training Network cover: news/images/2024-06-04-tool-form-integration.png diff --git a/news/_posts/2024-06-06-400-tutorials-milestone.md b/news/_posts/2024-06-06-400-tutorials-milestone.md index 1033bd7625e75a..11ffa9ee47d064 100644 --- a/news/_posts/2024-06-06-400-tutorials-milestone.md +++ b/news/_posts/2024-06-06-400-tutorials-milestone.md @@ -8,13 +8,15 @@ contributions: - shiltemann tags: - gtn + - contributing + - community abbreviations: GTN: Galaxy Training Network cover: news/images/2024-06-06-400-tutorials.png coveralt: 400 tutorials --- -The Galaxy Training Network (GTN) has reached an exciting milestone: **our 400th tutorial**! This achievement is a testament to the dedication and hard work of our community of educators, researchers, and developers over the last 9 years. +The Galaxy Training Network (GTN) has reached an exciting milestone: **our 400th tutorial**! This achievement is a testament to the dedication and hard work of our community of educators, researchers, and developers over the last 9 years. The GTN was established to provide comprehensive and accessible training materials for users of the [Galaxy](https://galaxyproject.org/), a widely-used, open-source platform that empowers researchers worldwide to conduct data analysis. Over the years, the network has massively grown, both in content and community engagement, reflecting the dynamic nature of scientific research and the continuous need for up-to-date training resources. diff --git a/news/_posts/2024-06-06-dada2-tutorial.md b/news/_posts/2024-06-06-dada2-tutorial.md index 583e44087d0d82..6b502f9ca2c02f 100644 --- a/news/_posts/2024-06-06-dada2-tutorial.md +++ b/news/_posts/2024-06-06-dada2-tutorial.md @@ -2,10 +2,11 @@ layout: news title: "New Galaxy training: Building an amplicon sequence variant (ASV) table from 16S data using DADA2" contributions: - authorship: + authorship: - bebatut -tags: +tags: - new tutorial +- microbiome tutorial: topics/microbiome/tutorials/dada-16S/tutorial.html --- diff --git a/news/_posts/2024-06-11-GalaxyTrainingAcademy-Call-Contribution.md b/news/_posts/2024-06-11-GalaxyTrainingAcademy-Call-Contribution.md index 67adb876662993..630aa58bd34359 100644 --- a/news/_posts/2024-06-11-GalaxyTrainingAcademy-Call-Contribution.md +++ b/news/_posts/2024-06-11-GalaxyTrainingAcademy-Call-Contribution.md @@ -3,6 +3,8 @@ title: "Open Call for Trainers for the Galaxy Training Academy" layout: news tags: - gtn + - teaching + - contributing contributions: authorship: - teresa-m diff --git a/news/_posts/2024-06-13-from-gtn-intern-to-tutorial-author-to-bioinformatician.md b/news/_posts/2024-06-13-from-gtn-intern-to-tutorial-author-to-bioinformatician.md index 73a6c7e752eafd..1f303fe5fc82b7 100644 --- a/news/_posts/2024-06-13-from-gtn-intern-to-tutorial-author-to-bioinformatician.md +++ b/news/_posts/2024-06-13-from-gtn-intern-to-tutorial-author-to-bioinformatician.md @@ -8,6 +8,7 @@ tags: - trajectory - user - contributor +- contributing from_google_form: true contributions: authorship: diff --git a/news/_posts/2024-06-13-phylogenetics-tutorial-takes-researchers-back-to-basics.md b/news/_posts/2024-06-13-phylogenetics-tutorial-takes-researchers-back-to-basics.md index 0b5f4e0d26286c..1b4860f80973cb 100644 --- a/news/_posts/2024-06-13-phylogenetics-tutorial-takes-researchers-back-to-basics.md +++ b/news/_posts/2024-06-13-phylogenetics-tutorial-takes-researchers-back-to-basics.md @@ -6,6 +6,7 @@ tags: - Tutorial - GTN - Australian BioCommons +- evolution from_google_form: true contributions: authorship: diff --git a/news/_posts/2024-06-14-gtn-video-library.md b/news/_posts/2024-06-14-gtn-video-library.md index 5b61af26f21c89..305b7b32ad17c0 100644 --- a/news/_posts/2024-06-14-gtn-video-library.md +++ b/news/_posts/2024-06-14-gtn-video-library.md @@ -3,6 +3,9 @@ title: "GTN Video Library 2.0: 107 hours of learning across 154 videos" layout: news tags: - gtn + - contributing + - teaching + - community cover: "assets/images/video-library.png" coveralt: Screenshot of the GTN Video Library showing a tutorial recording with a large youtube player and extensive metadata about who created the video (Natalie Kucher) and when, how long, etc. diff --git a/news/_posts/2024-07-08-4th-mycobamycobacterium-tuberculosis-complex-ngs-made-easy.md b/news/_posts/2024-07-08-4th-mycobamycobacterium-tuberculosis-complex-ngs-made-easy.md index a643895392fe4d..85f252067bbcb4 100644 --- a/news/_posts/2024-07-08-4th-mycobamycobacterium-tuberculosis-complex-ngs-made-easy.md +++ b/news/_posts/2024-07-08-4th-mycobamycobacterium-tuberculosis-complex-ngs-made-easy.md @@ -8,6 +8,8 @@ tags: - transmission - evolution - one-health +- microbiome + from_google_form: true contributions: authorship: diff --git a/news/_posts/2024-07-09-gcc-updates.md b/news/_posts/2024-07-09-gcc-updates.md index deab8fb1191f8a..25fb0e608dafa9 100644 --- a/news/_posts/2024-07-09-gcc-updates.md +++ b/news/_posts/2024-07-09-gcc-updates.md @@ -4,6 +4,7 @@ layout: news tags: - gcc - gtn infrastructure +- contributing contributions: authorship: - shiltemann diff --git a/news/_posts/2024-07-17-google-forms.md b/news/_posts/2024-07-17-google-forms.md index 80a35fb7b30214..f9073fdf0eade9 100644 --- a/news/_posts/2024-07-17-google-forms.md +++ b/news/_posts/2024-07-17-google-forms.md @@ -5,6 +5,7 @@ tags: - gtn infrastructure - new feature - automation +- contributing contributions: authorship: - hexylena diff --git a/news/_posts/2024-07-22-Galaxy-Administrator-Time-Burden-and-Technology-Usage.md b/news/_posts/2024-07-22-Galaxy-Administrator-Time-Burden-and-Technology-Usage.md index 68431340655106..5d2728b0c0c8ad 100644 --- a/news/_posts/2024-07-22-Galaxy-Administrator-Time-Burden-and-Technology-Usage.md +++ b/news/_posts/2024-07-22-Galaxy-Administrator-Time-Burden-and-Technology-Usage.md @@ -5,6 +5,7 @@ tags: - deploying - maintenance - survey +- admin contributions: authorship: - vladvisan @@ -21,5 +22,5 @@ tutorial: topics/admin/tutorials/poll-ssa/slides.html Have you wondered how difficult Galaxy is to run? How much time people must spend to run Galaxy? - In February 2024, we collected 9 responses from the [Galaxy Small Scale Admin group](https://galaxyproject.org/community/sig/small-scale-admins/). -- The questions cover various time burdens and technological choices. -- The report provides answers to prospective future admins' most common questions. \ No newline at end of file +- The questions cover various time burdens and technological choices. +- The report provides answers to prospective future admins' most common questions. diff --git a/news/_posts/2024-11-29-tracking-of-mitochondria-and-capturing-mitoflashes.md b/news/_posts/2024-11-29-tracking-of-mitochondria-and-capturing-mitoflashes.md index db83948cfc0b2e..6bdf2f45ffeeba 100644 --- a/news/_posts/2024-11-29-tracking-of-mitochondria-and-capturing-mitoflashes.md +++ b/news/_posts/2024-11-29-tracking-of-mitochondria-and-capturing-mitoflashes.md @@ -5,6 +5,7 @@ tags: - bioimaging - mitoflash - mitochondria +- imaging contributions: authorship: - dianichj diff --git a/news/_posts/2024-12-02-reviewing.md b/news/_posts/2024-12-02-reviewing.md index 2b7e67b5141a47..802a2094de10b6 100644 --- a/news/_posts/2024-12-02-reviewing.md +++ b/news/_posts/2024-12-02-reviewing.md @@ -5,6 +5,8 @@ tags: - gtn infrastructure - new feature - automation +- contributing +- community contributions: authorship: - hexylena @@ -21,4 +23,4 @@ We would like to recognise and thank all of the reviewers who have contributed t However given our extensive automation, the we took that one step further! The GTN has recently implemented a new automation that collects metadata about every pull request that is merged into the GTN. This metadata includes the reviewers of learning materials, so of course we can automatically annotate this on every single material within our codebase, leading to our updated headers including up to dozens of previously uncredited reviewers per tutorial. -Thank you all for your hard work and dedication to the GTN community! +Thank you all for your hard work and dedication to the GTN community! diff --git a/news/_posts/2024-12-17-gta-feedback.md b/news/_posts/2024-12-17-gta-feedback.md index b22bc4a3be3efb..c1b0524b17fec4 100644 --- a/news/_posts/2024-12-17-gta-feedback.md +++ b/news/_posts/2024-12-17-gta-feedback.md @@ -2,7 +2,7 @@ title: "Organizing GTA2025: Give us feedback and your availability!" contributions: authorship: [teresa-m] -tags: [gtn, event] +tags: [gtn, event, teaching, contributing, community] layout: news cover: "events/images/galaxy-academy-logo.png" coveralt: "A laptop displaying shapes resembling a statistical plot with a program from Galaxy Training Academy. Surrounding the laptop, there are DNA strands as well as a pen displayed." From 50e9511d873fa9cf3e5ea11d30d37ff15fbc96ac Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Thu, 19 Dec 2024 15:31:01 +0100 Subject: [PATCH 22/23] add topic tags to LPs --- learning-pathways/admin-training.md | 2 +- learning-pathways/amr-gene-detection.md | 2 +- learning-pathways/building_tutorials.md | 2 ++ learning-pathways/climate-learning.md | 2 ++ learning-pathways/clinical-metaproteomics.md | 2 +- learning-pathways/data-driven-biology.md | 2 +- learning-pathways/dev_tools_training.md | 2 +- learning-pathways/genome-annotation-eukaryote.md | 2 +- learning-pathways/genome-annotation-prokaryote.md | 2 +- learning-pathways/intro-to-galaxy-and-ecology.md | 2 +- learning-pathways/intro-to-galaxy-and-genomics.md | 2 +- learning-pathways/intro-to-r-and-ml.md | 2 +- learning-pathways/pathway-example.md | 2 +- learning-pathways/proteogenomics.md | 2 +- learning-pathways/python.md | 2 +- learning-pathways/reloaded_single_cell.md | 2 +- learning-pathways/sql.md | 2 +- learning-pathways/train-the-trainers.md | 2 +- 18 files changed, 20 insertions(+), 16 deletions(-) diff --git a/learning-pathways/admin-training.md b/learning-pathways/admin-training.md index 436cc5c9110f3e..8094009054e4f9 100644 --- a/learning-pathways/admin-training.md +++ b/learning-pathways/admin-training.md @@ -14,7 +14,7 @@ editorial_board: - natefoo - slugger70 -tags: [Galaxy administrators, 5-day course] +tags: [Galaxy administrators, 5-day course, admin] pathway: - section: "Monday: Setting up Galaxy with Ansible" diff --git a/learning-pathways/amr-gene-detection.md b/learning-pathways/amr-gene-detection.md index 0fedc63a5ddb76..781be3b5d638cd 100644 --- a/learning-pathways/amr-gene-detection.md +++ b/learning-pathways/amr-gene-detection.md @@ -4,7 +4,7 @@ title: Detection of AMR genes in bacterial genomes description: | This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy. type: use -tags: [amr, bacteria, microgalaxy, one-health] +tags: [amr, bacteria, microgalaxy, one-health, microbiome] editorial_board: - bebatut diff --git a/learning-pathways/building_tutorials.md b/learning-pathways/building_tutorials.md index a9fb1f2bf6818b..2dd6441fb879ca 100644 --- a/learning-pathways/building_tutorials.md +++ b/learning-pathways/building_tutorials.md @@ -6,6 +6,8 @@ type: instructors editorial_board: - nomadscientist +tags: [contributing] + priority: 1 title: Building training material in Galaxy diff --git a/learning-pathways/climate-learning.md b/learning-pathways/climate-learning.md index 83f910e283c18f..99092ec634a02a 100644 --- a/learning-pathways/climate-learning.md +++ b/learning-pathways/climate-learning.md @@ -11,6 +11,8 @@ tags: [Climate, Overview] editorial_board: - Marie59 +tags: [climate] + type: use pathway: diff --git a/learning-pathways/clinical-metaproteomics.md b/learning-pathways/clinical-metaproteomics.md index ad9b78175211f7..89d9c47fb9b811 100644 --- a/learning-pathways/clinical-metaproteomics.md +++ b/learning-pathways/clinical-metaproteomics.md @@ -1,6 +1,6 @@ --- layout: learning-pathway -tags: [beginner] +tags: [beginner, proteomics] type: use diff --git a/learning-pathways/data-driven-biology.md b/learning-pathways/data-driven-biology.md index 5728045f7919e4..ab5a112117315e 100644 --- a/learning-pathways/data-driven-biology.md +++ b/learning-pathways/data-driven-biology.md @@ -2,7 +2,7 @@ layout: learning-pathway cover-image: /assets/images/genomics_intro.png cover-image-alt: "Genomics intro" -tags: [introduction, real-course] +tags: [introduction, real-course, data-science] type: use editorial_board: - nekrut diff --git a/learning-pathways/dev_tools_training.md b/learning-pathways/dev_tools_training.md index be2c159d933192..93fe43dd116f95 100644 --- a/learning-pathways/dev_tools_training.md +++ b/learning-pathways/dev_tools_training.md @@ -10,7 +10,7 @@ cover-image-alt: Image of a researcher or developer on a computer thinking of bu editorial_board: - Marie59 -tags: [subdomain, community, tool development, 3-day course] +tags: [subdomain, community, tool development, 3-day course, dev] pathway: diff --git a/learning-pathways/genome-annotation-eukaryote.md b/learning-pathways/genome-annotation-eukaryote.md index 31ca3b5a68f338..ffef6dfeff5d4f 100644 --- a/learning-pathways/genome-annotation-eukaryote.md +++ b/learning-pathways/genome-annotation-eukaryote.md @@ -4,7 +4,7 @@ title: Genome annotation for eukaryotes description: | Learn how to annotate an eukaryotic genome sequence: identify repeated regions, find the position and function of genes, and even set up a manual curation environment with Apollo. type: use -tags: [genome annotation, eukaryote] +tags: [genome-annotation, eukaryote] cover-image: assets/images/gga.png cover-image-alt: "Galaxy Genome Annotation logo" diff --git a/learning-pathways/genome-annotation-prokaryote.md b/learning-pathways/genome-annotation-prokaryote.md index d814c752fe8020..a44f8c735980bf 100644 --- a/learning-pathways/genome-annotation-prokaryote.md +++ b/learning-pathways/genome-annotation-prokaryote.md @@ -4,7 +4,7 @@ title: Genome annotation for prokaryotes description: | Learn how to annotate a prokaryotic genome sequence: find the position and function of genes, and even set up a manual curation environment with Apollo. type: use -tags: [genome annotation, prokaryote] +tags: [genome-annotation, prokaryote] cover-image: assets/images/gga.png cover-image-alt: "Galaxy Genome Annotation logo" diff --git a/learning-pathways/intro-to-galaxy-and-ecology.md b/learning-pathways/intro-to-galaxy-and-ecology.md index 6a36a12ec4a981..0393f7200730bd 100644 --- a/learning-pathways/intro-to-galaxy-and-ecology.md +++ b/learning-pathways/intro-to-galaxy-and-ecology.md @@ -9,7 +9,7 @@ description: | steps of biodiversity data analysis: download, check, filter and explore biodiversity data and analyze abundance data through modeling. -tags: [beginner] +tags: [beginner, ecology] cover-image: assets/images/galaxy-e-logo.png cover-image-alt: "Drawing of an Ecological System" diff --git a/learning-pathways/intro-to-galaxy-and-genomics.md b/learning-pathways/intro-to-galaxy-and-genomics.md index dadc6f297c5dd1..fa3e5cbd5f9065 100644 --- a/learning-pathways/intro-to-galaxy-and-genomics.md +++ b/learning-pathways/intro-to-galaxy-and-genomics.md @@ -1,6 +1,6 @@ --- layout: learning-pathway -tags: [beginner] +tags: [beginner, introcuction, sequence-analysis, assembly] type: use editorial_board: diff --git a/learning-pathways/intro-to-r-and-ml.md b/learning-pathways/intro-to-r-and-ml.md index 26efdfa7dea5f2..07307be14052eb 100644 --- a/learning-pathways/intro-to-r-and-ml.md +++ b/learning-pathways/intro-to-r-and-ml.md @@ -1,6 +1,6 @@ --- layout: learning-pathway -tags: [beginner] +tags: [beginner, statistics, data-science] type: use editorial_board: diff --git a/learning-pathways/pathway-example.md b/learning-pathways/pathway-example.md index 3a6962741f4b9d..57c60277bc4f45 100644 --- a/learning-pathways/pathway-example.md +++ b/learning-pathways/pathway-example.md @@ -8,7 +8,7 @@ description: | lists all the learning paths, and at the top of the pathway page type: use # 'use' for science topics, or admin-dev or instructors -tags: [some, keywords, here ] +tags: [some, keywords, here, gtn-topic-id ] editorial_board: - shiltemann diff --git a/learning-pathways/proteogenomics.md b/learning-pathways/proteogenomics.md index b63b6156332b94..694de181dbe73a 100644 --- a/learning-pathways/proteogenomics.md +++ b/learning-pathways/proteogenomics.md @@ -1,6 +1,6 @@ --- layout: learning-pathway -tags: [beginner] +tags: [beginner, proteomics] type: use diff --git a/learning-pathways/python.md b/learning-pathways/python.md index 1e7491e8a46961..4dd5a766ad2cc9 100644 --- a/learning-pathways/python.md +++ b/learning-pathways/python.md @@ -12,7 +12,7 @@ funding: - gallantries - avans-atgm -tags: [python, real-course] +tags: [python, real-course, data-science] pathway: - section: "Week 1: Python is a Calculator" diff --git a/learning-pathways/reloaded_single_cell.md b/learning-pathways/reloaded_single_cell.md index fe9b3f65721cbd..5c4773b65a42f8 100644 --- a/learning-pathways/reloaded_single_cell.md +++ b/learning-pathways/reloaded_single_cell.md @@ -1,6 +1,6 @@ --- layout: learning-pathway -tags: [advanced] +tags: [advanced, single-cell] cover-image: assets/images/wab-annotatedcells-2.png cover-image-alt: "Image of cells in different coloured clusters" type: use diff --git a/learning-pathways/sql.md b/learning-pathways/sql.md index cc021b06fd1d00..6f58a6117cf07a 100644 --- a/learning-pathways/sql.md +++ b/learning-pathways/sql.md @@ -12,7 +12,7 @@ funding: - gallantries - avans-atgm -tags: [python, real-course] +tags: [python, real-course, data-science] pathway: - section: "Week 1: SQL Basics" diff --git a/learning-pathways/train-the-trainers.md b/learning-pathways/train-the-trainers.md index a580352c23f247..dbda99ad6ee88f 100644 --- a/learning-pathways/train-the-trainers.md +++ b/learning-pathways/train-the-trainers.md @@ -5,7 +5,7 @@ type: instructors title: Train the Trainers description: | This pathway introduces trainers to learning principles, training techniques, lesson, session, course, and material design as well as assessment and feedback. This is has been developed for by trainers in the bioinformatics but is suitable for all trainers and educators in higher education. -tags: [training, trainers] +tags: [training, trainers, teaching, community] editorial_board: - bebatut From 5e096dab2b6dfc60daf24d8c1ab72270c505b52d Mon Sep 17 00:00:00 2001 From: Saskia Hiltemann Date: Thu, 19 Dec 2024 15:33:40 +0100 Subject: [PATCH 23/23] add topic tags to LPs --- learning-pathways/io1.md | 2 +- learning-pathways/io2.md | 2 +- learning-pathways/io3.md | 2 +- learning-pathways/io4.md | 2 +- learning-pathways/io5.md | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/learning-pathways/io1.md b/learning-pathways/io1.md index aa54d6bf3c8073..f136ea2ffc72fc 100644 --- a/learning-pathways/io1.md +++ b/learning-pathways/io1.md @@ -1,6 +1,6 @@ --- layout: learning-pathway -tags: [beginner] +tags: [beginner, data-science, contributing, sequence-analysis, transcriptomics] type: use editorial_board: diff --git a/learning-pathways/io2.md b/learning-pathways/io2.md index 3585a1a00288cd..9eee6c43a82671 100644 --- a/learning-pathways/io2.md +++ b/learning-pathways/io2.md @@ -1,6 +1,6 @@ --- layout: learning-pathway -tags: [beginner] +tags: [beginner, galaxy-interface, microbiome, visualisation, data-science, variant-analysis ] type: use editorial_board: diff --git a/learning-pathways/io3.md b/learning-pathways/io3.md index 4ddea1067d401c..0be496b2d7b93f 100644 --- a/learning-pathways/io3.md +++ b/learning-pathways/io3.md @@ -1,6 +1,6 @@ --- layout: learning-pathway -tags: [beginner] +tags: [beginner, genome-annotation] type: use editorial_board: diff --git a/learning-pathways/io4.md b/learning-pathways/io4.md index 59bcf47a8fa718..f6f8101e38529a 100644 --- a/learning-pathways/io4.md +++ b/learning-pathways/io4.md @@ -1,6 +1,6 @@ --- layout: learning-pathway -tags: [beginner] +tags: [beginner, ecology] type: use editorial_board: diff --git a/learning-pathways/io5.md b/learning-pathways/io5.md index 11a317f24573f7..6c978c2a2cc0ed 100644 --- a/learning-pathways/io5.md +++ b/learning-pathways/io5.md @@ -1,6 +1,6 @@ --- layout: learning-pathway -tags: [beginner] +tags: [beginner, contributing, teaching] type: use editorial_board: