Skip to content

Commit 3495f58

Browse files
supernordsupernord
authored
Merge pull request #26 from supernord/edits
Edits to structure and content
2 parents 1db2fef + 248795b commit 3495f58

51 files changed

Lines changed: 1044 additions & 169 deletions

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

‎.github/workflows/jekyll.yml‎

Lines changed: 7 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,7 @@ name: Jekyll site CI
22

33
on:
44
push:
5+
branches: [ main, master, edits ]
56
pull_request:
67
branches: [ main, master, edits ]
78
workflow_dispatch:
@@ -13,7 +14,7 @@ permissions:
1314

1415
jobs:
1516
build:
16-
runs-on: ubuntu-latest
17+
runs-on: ubuntu-24.04
1718
steps:
1819
- name: Checkout
1920
uses: actions/checkout@v4
@@ -23,7 +24,7 @@ jobs:
2324
- name: Setup Ruby
2425
uses: ruby/setup-ruby@v1.204.0
2526
with:
26-
ruby-version: '3.1'
27+
ruby-version: '3.3'
2728
bundler-cache: true
2829
cache-version: 0
2930

@@ -41,7 +42,7 @@ jobs:
4142
bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
4243
env:
4344
PAGES_REPO_NWO: ${{ github.repository }}
44-
JEKYLL_ENV: ${{ steps.name.outputs.jekyll_env }}
45+
JEKYLL_ENV: production
4546
JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
4647
JEKYLL_BUILD_BRANCH: ${{ github.ref_name }}
4748
JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }}
@@ -50,7 +51,7 @@ jobs:
5051
uses: actions/upload-pages-artifact@v3
5152

5253
deploy:
53-
runs-on: ubuntu-latest
54+
runs-on: ubuntu-24.04
5455
needs: build
5556

5657
if: |
@@ -63,8 +64,8 @@ jobs:
6364
environment:
6465
name: github-pages
6566
url: ${{ steps.deployment.outputs.page_url }}
66-
67+
6768
steps:
6869
- name: Deploy to GitHub Pages
6970
id: deployment
70-
uses: actions/deploy-pages@v4
71+
uses: actions/deploy-pages@v4

‎.github/workflows/update_guides.yml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ jobs:
99
update_guides:
1010
runs-on: ubuntu-latest
1111
steps:
12-
- uses: actions/checkout@v3
12+
- uses: actions/checkout@v4
1313

1414
- name: setup python
1515
uses: actions/setup-python@v2
@@ -35,4 +35,4 @@ jobs:
3535
uses: ad-m/github-push-action@v0.6.0
3636
with:
3737
github_token: ${{ secrets.GITHUB_TOKEN }}
38-
branch: main
38+
branch: main

‎README.md‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,9 @@
11
## What this repository is for
22

3-
Gathering information to get structural biologists oriented on beginninging their journey top adopt the most recent and accurate computational tools
3+
Gathering information to get structural biologists oriented on beginning their journey top adopt the most recent and accurate computational tools
44

5-
If you're seeing this you're on the coding-style backend. This provides a place to manage code versions, share data, store images, project manage etc with typical GitHub features
5+
If you're seeing this you're on the coding-style backend. This provides a place to manage code versions, share data, store images, project manage etc, with typical GitHub features.
66

7-
## Where is the *website* not just the raw source code?
7+
## Where is the *website*, not just the raw source code?
88

99
Point your browser to https://australian-structural-biology-computing.github.io/website/

‎_config.yml‎

Lines changed: 12 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
1-
title: StructBio Computing
1+
title: Australian Structural Biology Computing
22
# This appears in the html browser tab for the site title (seen mostly by search engines, not users)
33

44
topnav_title: Australian Structural Biology Computing
55
# Optional: this appears on the top navigation bar next to the main_logo.svg icon
66

7-
#description: "Example of ELIXIR toolkit theme as a remote jekyll theme"
7+
description: "A website for the Australian Structural Biology Computing community."
88
# Metadata description of the website
99

1010
# Following AusBioCommons minimal gh-pages with remote deploy - https://github.com/AustralianBioCommons/how-to-guides/blob/main/_config.yml
@@ -25,6 +25,16 @@ defaults:
2525
permalink: /:basename
2626
layout: "page"
2727
sidebar: main
28+
- scope:
29+
path: "pages"
30+
type: "pages"
31+
values:
32+
sidebar: main
33+
- scope:
34+
path: "workgroup_template_directory"
35+
type: "pages"
36+
values:
37+
sidebar: workgroup_example
2838

2939
theme_variables:
3040
# git_host: GitHub

‎_data/CONTRIBUTORS.yml‎

Lines changed: 68 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -47,9 +47,71 @@ Michael Healy:
4747
orcid: 0000-0003-2924-9179
4848
affiliation: Postdoctoral Research Fellow, University of Queensland
4949

50-
# Josh was listed as a contributor during testing - checked with him to remove -- KR
51-
#Joshua Storm Caley:
52-
#git: jscgh
53-
#email: j.caley@unsw.edu.au
54-
#orcid: 0000-0002-9374-0969
55-
#affiliation: Computational Systems Officer, Structural Biology Facility UNSW
50+
Joshua Storm Caley:
51+
git: jscgh
52+
email: j.caley@unsw.edu.au
53+
orcid: 0000-0002-9374-0969
54+
affiliation: Computational Systems Officer, Structural Biology Facility UNSW
55+
56+
Thomas Litfin:
57+
git: tlitfin-unsw
58+
email: t.litfin@unsw.edu.au
59+
orcid: 0000-0002-4863-3865
60+
affiliation: Senior Research Associate, Structural Biology Facility UNSW
61+
62+
Ziad Al-Bkhetan:
63+
git: ziadbkh
64+
orcid: 0000-0002-4032-5331
65+
affiliation: Product Manager, Australian BioCommons
66+
67+
Sarah Beecroft:
68+
git: SarahBeecroft
69+
affiliation: Bioinformatics Applications Specialist, Pawsey Supercomputing Research Centre
70+
71+
Cameron Hyde:
72+
git: neoformit
73+
orcid: 0000-0002-5913-9766
74+
affiliation: Bioinformatician, Queensland Cyber Infrastructure Foundation (QCIF)
75+
76+
Mitchell O'Brien:
77+
git: Mitchob
78+
affiliation: Senior Bioinformatics Engineer, Sydney Informatics Hub
79+
80+
Matthew Downton:
81+
git: mattdton
82+
orcid: 0000-0002-4693-1965
83+
affiliation: Associate Director - Performance Optimisation, National Computational Infrastructure (NCI)
84+
85+
Kisaru Liyanage:
86+
git: kisarur
87+
affiliation: HPC specialist (Life and Health Sciences), National Computational Infrastructure (NCI)
88+
89+
Wenjing Xue:
90+
affiliation: HPC Specialist (Life and Health Sciences), National Computational Infrastructure (NCI)
91+
92+
Gavin Knott:
93+
affiliation: Group Leader, Monash Biomedicine Discovery Institute, Monash University
94+
orcid: 0000-0002-9007-6273
95+
96+
Rhys Grinter:
97+
affiliation: Lab head, University of Melbourne
98+
git: RhysWG
99+
orcid: 0000-0002-8195-5348
100+
101+
Josh Hardy:
102+
affiliation: Senior Research Officer, Lucet Lab, WEHI
103+
git: joshhardywehi
104+
email: hardy.j@wehi.edu.au
105+
orcid: 0000-0002-8014-8552
106+
107+
#Richard Birkinshaw:
108+
# affiliation: Senior Research Scientist, Walter and Eliza Hall Institute of Medical Research
109+
# orcid: 0000-0003-1825-0182
110+
111+
Melissa Burke:
112+
affiliation: Training Manager, Australian BioCommons
113+
orcid: 0000-0002-5571-8664
114+
115+
Cyntia Taveneau:
116+
affiliation: Research Fellow, Knott Lab, Monash University
117+
orcid: 0000-0002-3395-4957

‎_data/events.yml‎

Lines changed: 14 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -8,18 +8,24 @@
88
# location: Cyberspace
99
- name: BioMolecular Horizons
1010
startDate: 2024-09-22
11-
description: Launch of the website at [BioMolecular Horizons 2024](https://www.bmh2024.com/)
11+
description: "Launch of the website at [BioMolecular Horizons 2024](https://www.bmh2024.com/)"
1212
- name: Computational Structural Biology Community Meeting
1313
startDate: 2024-10-22
14-
startTime: 13:30
1514
endDate: 2024-10-22
16-
endTime: 14:30
17-
description: Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting.
15+
description: "Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting."
1816
location: Online
1917
- name: Computational Structural Biology Community Meeting
2018
startDate: 2025-04-09
21-
startTime: 13:00
2219
endDate: 2025-04-09
23-
endTime: 14:30
24-
description: Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting.
25-
location: Online
20+
description: "Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting."
21+
location: Online
22+
- name: Computational structural biology community meeting
23+
startDate: 2025-06-18
24+
endDate: 2025-06-18
25+
description: "Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting."
26+
location: Online
27+
- name: Australian Structural Biology Computing community meeting
28+
startDate: 2025-08-27
29+
endDate: 2025-08-27
30+
description: "Visit the [rolling agenda](https://docs.google.com/document/d/1miRyOOOW7HeDsCvzJwVEOhaAzPBve8od9WUvsAsFfcw/edit#heading=h.owmugrvs22hi) for details on how to join the next meeting."
31+
location: Online

‎_data/news.yml‎

Lines changed: 4 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,6 @@
1-
- name: Script for Alphafold output validation metrics!
1+
- name: "Script for Alphafold output validation metrics!"
22
date: 2024-11-01
3-
description: Python Script and info about configuring AF2 to output pTM, ipTM and MSA depth. Many thanks to the Australian Galaxy team (special shout out to Cam!) for making this happen (https://github.com/usegalaxy-au/tools-au/tree/master/tools/alphafold#generating-additional-outputs)
4-
5-
- name: Script for updating Alphafold2 dependencies to stop 'template missing' failures (MMCIF patch)
3+
description: "Python Script and info about configuring AF2 to output pTM, ipTM and MSA depth. Many thanks to the Australian Galaxy team (special shout out to Cam!) for making this happen (<https://github.com/usegalaxy-au/tools-au/tree/master/tools/alphafold#generating-additional-outputs>)"
4+
- name: "Script for updating Alphafold2 dependencies to stop 'template missing' failures (MMCIF patch)"
65
date: 2024-11-01
7-
description: MMCIF patch python script. Many thanks to the Australian Galaxy team (Cam again!) for making this happen (https://github.com/usegalaxy-au/tools-au/tree/master/tools/alphafold/scripts/db/patch_mmcif)
6+
description: "MMCIF patch python script. Many thanks to the Australian Galaxy team (Cam again!) for making this happen (<https://github.com/usegalaxy-au/tools-au/tree/master/tools/alphafold/scripts/db/patch_mmcif>)"

‎_data/sidebars/main.yml‎

Lines changed: 25 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -1,29 +1,29 @@
11
subitems:
22
- title: Home
33
url: /index
4-
- title: Example page
5-
url: /example_page
6-
- title: Contributing
7-
subitems:
8-
- title: Provide us your document
9-
url: /provide_documentation
10-
- title: Write your own guides
11-
url: /guide_template
12-
- title: Visualisations
4+
- title: Activities
5+
url: /activities
6+
- title: How-to Guides
7+
url: /guides
8+
- title: External resources
139
subitems:
14-
- title: Pymol
15-
url: /pymol
16-
- title: Protein Structure Prediction
17-
subitems:
18-
- title: AlphaFold How To Guide
19-
url: /AlphaFold2_how_to_guide
20-
- title: Best practices AlphaFold models in a paper
21-
url: /best-practices-alphafold
22-
- title: AlphaFold Tutorial - European Bioinformatics Institute
23-
url: /EBI-alphafold-guide
24-
- title: Protein structure inference options
25-
url: /protein_struct_inference
26-
- title: Command Line Instructions
27-
subitems:
28-
- title: Basics
29-
url: /basics
10+
- title: Servers
11+
url: /external_servers
12+
- title: Databases
13+
url: /external_databases
14+
- title: Guides
15+
url: /external_guides
16+
- title: Visualization
17+
url: /external_viz
18+
- title: Videos
19+
url: /external_videos
20+
- title: Communities
21+
url: /external_communities
22+
- title: Contributing
23+
url: /contributing
24+
- title: Contributors
25+
url: /contributors
26+
- title: Events
27+
url: /events
28+
- title: News
29+
url: /news

‎_data/sidebars/workgroup_example.yml‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
subitems:
2+
- title: Home
3+
url: /index
4+
- title: Working group index
5+
url: /workgroup_index

‎_data/topnav.yml‎

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
11
##
22
## if you want to list an external url, use external_url instead of url. the theme will apply a different link base.
3-
subitems:
4-
- title: Home
5-
url: /index
6-
3+
#subitems:
4+
#- title: Home
5+
# url: /index
6+
#- title: Working group example
7+
# url: /workgroup_index

0 commit comments

Comments
 (0)