Updated publication list and installation instructions

.gitignore

@@ -1,14 +1,5 @@
 _site
 .sass-cache
-.DS_Store
-Gemfile.lock
-*.sublime-project
-*.sublime-workspace
-codekit-config.json
-node_modules
-_asset_bundler_cache
-images/molecules-raw
-.bundle
+.jekyll-cache
 .jekyll-metadata
-.markdownlint.json
-ruby/
+vendor

Gemfile

@@ -1,6 +1,35 @@
-source 'https://rubygems.org'
+source "https://rubygems.org"
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+#     bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+gem "jekyll", "~> 4.3.2"
+# This is the default theme for new Jekyll sites. You may change this to anything you like.
+gem "minima", "~> 2.5"
+# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
+# uncomment the line below. To upgrade, run `bundle update github-pages`.
+# gem "github-pages", group: :jekyll_plugins
+# If you have any plugins, put them here!
+group :jekyll_plugins do
+  gem "jekyll-feed", "~> 0.12"
+end
 
-gem 'jekyll'
-gem "jekyll-sitemap"
-gem 'octopress', '~> 3.0.0.rc.12'
-gem 'github-pages'
+# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
+# and associated library.
+platforms :mingw, :x64_mingw, :mswin, :jruby do
+  gem "tzinfo", ">= 1", "< 3"
+  gem "tzinfo-data"
+end
+
+# Performance-booster for watching directories on Windows
+gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin]
+
+# Lock `http_parser.rb` gem to `v0.6.x` on JRuby builds since newer versions of the gem
+# do not have a Java counterpart.
+gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby]
+
+gem "webrick", "~> 1.8"

README.md

@@ -8,29 +8,56 @@ web page](http://mmistakes.github.io/minimal-mistakes/theme-setup/).
 
 To ensure whatever you create/change appears as faithfully as possible after pushing to the main repository, install the version of Ruby and the gems used by Github. See a list [here](https://pages.github.com/versions/).
 
-### Installation Instructions (updt. Feb. 2016)
+### Installation Instructions (updt. Nov. 2023)
+
+Following the instructions from: https://github.com/BillRaymond/install-jekyll-apple-silicon/blob/main/README.md
+
+And using homebrew
+
+
+1. Install ruby3.0
 
-1. Install [RVM](https://rvm.io) (optional, to manage your Ruby installations)
-```bash
-\curl -sSL https://get.rvm.io | bash -s stable --ruby
-rvm install ruby-2.6.3
-rvm --default use ruby-2.6.3
+```
+brew install [email protected]
 ```
 
-2. Install Bundler
-```bash
-gem install bundler
+2. Add path to ruby3.0 in .bashrc (or .bash_provile)
+
+export PATH="/opt/homebrew/opt/[email protected]/bin/:$PATH"
+
+3. Restart your terminal and make sure you are now using ruby3.0
+
+```
+ruby -v
+```
+
+4. Install Jekyll and Bundler
+
+```
+gem install --user-install bundler jekyll
 ```
 
-3. Clone the haddocking.github.io repository and install all dependency Gems with Bundler
+5. Add the path to the gems to in .bashrc (or .bash_provile)
+
+export PATH="~/.local/share/gem/ruby/3.0.0/bin:$PATH"
+
+
+6. Clone the haddocking.github.io repository and install all dependency Gems with Bundler
 
 ```bash
 git clone https://github.com/haddocking/haddocking.github.io.git haddocking-website
 cd haddocking-website
+bundle init
+bundle add jekyll --version "~>4.2"
+bundle config set --local path 'vendor/bundle'
+bundle install
+bundle exec jekyll new --force --skip-bundle .
+bundle add webrick
 bundle install
+bundle update
 ```
 
-4. Adapt the settings in _config.yml accordingly
+7. Adapt the settings in _config.yml accordingly
 In order for links to properly work, the `url` setting in must be set accordingly, otherwise you will be redirected to the live version. This sets all the `site.url` variable calls throughout _layouts/,  _includes/, etc.
 
 ```yaml
@@ -52,7 +79,7 @@ To preview changes, which you should always do before committing anything or mak
     $ python _utilities/create_new_article.py 'A Random Post'
 ```
 
-4. For updating jeckyll and bundle
+8. For updating jeckyll and bundle
 
 ```bash
     $ gem update jekyll

_config.yml

@@ -1,61 +1,55 @@
-# For general help on the options
-# # http://jekyllrb.com/docs/configuration/
-
-# Site wide configuration
-
-title:            Bonvin Lab
-locale:           en_US
-url:              https://www.bonvinlab.org
-#url:              http://127.0.0.1:4000/
-
-# RSS Feed configuration
-name: Bonvin Lab
-description: Webpage of the computational structural biology lab of Alexandre Bonvin
-rss: true
-
-# Jekyll configuration
-permalink:   /:categories/:title/
-post_dir: false
-markdown:    kramdown
-sass:
-  sass_dir: _sass
-  style: compressed
+# Welcome to Jekyll!
+#
+# This config file is meant for settings that affect your whole blog, values
+# which you are expected to set up once and rarely edit after that. If you find
+# yourself editing this file very often, consider using Jekyll's data files
+# feature for the data you need to update frequently.
+#
+# For technical reasons, this file is *NOT* reloaded automatically when you use
+# 'bundle exec jekyll serve'. If you change this file, please restart the server process.
+#
+# If you need help with YAML syntax, here are some quick references for you:
+# https://learn-the-web.algonquindesign.ca/topics/markdown-yaml-cheat-sheet/#yaml
+# https://learnxinyminutes.com/docs/yaml/
+#
+# Site settings
+# These are used to personalize your new site. If you look in the HTML files,
+# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
+# You can create any custom variable you would like, and they will be accessible
+# in the templates via {{ site.myvariable }}.
+
+title: Your awesome title
+email: [email protected]
+description: >- # this means to ignore newlines until "baseurl:"
+  Write an awesome description for your new site here. You can edit this
+  line in _config.yml. It will appear in your document head meta (for
+  Google search results) and in your feed.xml site description.
+baseurl: "" # the subpath of your site, e.g. /blog
+url: "" # the base hostname & protocol for your site, e.g. http://example.com
+twitter_username: jekyllrb
+github_username:  jekyll
+
+# Build settings
+theme: minima
 plugins:
-  - jekyll-sitemap
-  - jekyll-coffeescript
-  - jekyll-paginate
-
-kramdown:
-  auto_ids: true
-  footnote_nr: 1
-  entity_output: as_char
-  toc_levels: 1..6
-
-# Github Specific Settings that *cannot* be changed
-# To ensure proper reproducibility
-# https://help.github.com/articles/configuring-jekyll/
-gist:
-  noscript: false
-github: [metadata]
-highlighter: rouge
-incremental: false
-lsi: false
-safe: true
-
-# Site owner
-owner:
-  name: Alexandre Bonvin
-  avatar: bio-haddock.png
-  bio: "Computational Structural Biology group focusing on dissecting, understanding and predicting biomolecular interactions at the molecular level."
-  email: [email protected]
-  youtube: haddocking
-  google:
-    analytics: G-RNH61RX63Z
-    verify:
-    ad-client:
-    ad-slot:
-  github: haddocking
-
-include: [".htaccess"]
-#exclude: [vendor, ruby]
-exclude: ["lib", "config.rb", "Capfile", "config", "log", "Rakefile", "Rakefile.rb", "tmp", "less", "*.sublime-project", "*.sublime-workspace", "test", "spec", "Gruntfile.js", "package.json", "node_modules", "Gemfile", "Gemfile.lock", "LICENSE", "README.md", "_utilities"]
+  - jekyll-feed
+
+# Exclude from processing.
+# The following items will not be processed, by default.
+# Any item listed under the `exclude:` key here will be automatically added to
+# the internal "default list".
+#
+# Excluded items can be processed by explicitly listing the directories or
+# their entries' file path in the `include:` list.
+#
+# exclude:
+#   - .sass-cache/
+#   - .jekyll-cache/
+#   - gemfiles/
+#   - Gemfile
+#   - Gemfile.lock
+#   - node_modules/
+#   - vendor/bundle/
+#   - vendor/cache/
+#   - vendor/gems/
+#   - vendor/ruby/

publications/index.md

@@ -6,9 +6,11 @@ image:
 ---
 ## 2023
 
+* M. Giulini, C. Schneider, D. Cutting, N. Desai, C. Deane and **A.M.J.J. Bonvin**. [Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking](https://doi.org/10.1101/2023.11.17.567543). _BioRxiv_ 10.1101/2023.11.17.567543 (2023).
+
 * M. Giulini, R.V. Honorato, J.L. Rivera, **A.M.J.J. Bonvin**. [ARCTIC-3D: Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information](https://doi.org/10.1101/2023.07.10.548477). _BioRxiv_ 2023.07.10.548477 (2023).
 
-* X. Xu, **A.M.J.J. Bonvin**. [DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model](https://doi.org/10.1101/2023.06.22.546080). _BioRxiv_  2023.06.22.546080 (2023).
+* X. Xu, **A.M.J.J. Bonvin**. [DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model](https://doi.org/10.1101/2023.06.22.546080). _BioRxiv_  10.1101/2023.06.22.546080 (2023).
 
 * **A.M.J.J. Bonvin**. [Empowering Global Collaboration in Structural Biology and Life Sciences](https://zenodo.org/record/8135315). DOI:10.5281/zenodo.8135315 (2023).