Larry's Blog

The source for Larry Rodriguez's personal blog about computational biophysics, molecular simulation, artificial intelligence, chemistry, gene editing, and related research.

Ubuntu installation with Conda

From the repository root, create the blog environment and install the locked Jekyll dependencies:

conda create --yes --name blog --channel conda-forge --override-channels \
  ruby=3.2.2 make compilers pkg-config
conda activate blog
gem install bundler --version 2.5.5 --no-document

# Make conda-forge's RubyGems launchers resolve the environment's Ruby binary.
ln -sfn ../../../bin/ruby "$CONDA_PREFIX/share/rubygems/bin/ruby"

bundle _2.5.5_ install

Start the local site and open http://localhost:4000:

conda activate blog
bundle exec jekyll serve --livereload

Use conda deactivate when you are finished. On later sessions, only conda activate blog and the Jekyll command are needed.

Create a new post

The quickest path is the interactive launcher. It needs nothing but bash — no Conda or Ruby — and prompts you through every field with a numbered category menu (Artificial Intelligence, Molecular Dynamics, Biophysics, Genetic Engineering, Chemistry, Updates) plus yes/no toggles for math, table of contents, and comments:

./scripts/new-post.sh

A flag-based Ruby generator is also available for scripting:

conda activate blog
ruby scripts/new_post.rb "A clear post title" \
  --description "A concise homepage and search summary." \
  --category research \
  --tags molecular-dynamics,crispr \
  --math

Both refuse invalid dates, empty titles, and filename collisions. Posts no longer need a per-post <style> block — paragraph indentation and .container image centering live in assets/css/style.scss, and math is enabled by the use_math: true flag. See docs/POST_AUTHORING.md for all options, image fields, preview instructions, and the front-matter contract.

Repository Structure:

\____main
|
|____editing

If you're reading this you're probably at my github page:

https://github.com/lrodrz/lrodrz.github.io

The published blog is available at:

https://lrodrz.github.io

Information:

To build a local cloned repo:

Clone the repo:

$git clone https://github.com/lrodrz/lrodrz.github.io.git

You might want to use the editing branch to do edits:

$git checkout editing

check if everything is up-to-date:

$git pull origin main editing

Make sure you have jekyll installed. If not, there are guides available for your favorite operating system at: https://jekyllrb.com/docs/installation/

setup the gems:

$bundle install

Launch the blog locally:

$bundle exec jekyll serve

or

$bash blogstart.sh

If you would like to build a similar blog, here is some information about how I put together this GitHub Pages site.

The blog was built using Jekyll and the following guide: https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/creating-a-github-pages-site-with-jekyll

The standard Jekyll directory structure can be found at:

https://jekyllrb.com/docs/structure/

Features:

June 2026:

Refactored the site onto a Hux-inspired custom theme. The _layouts, _includes, and _sass/assets directories now live in the repo and are version-controlled directly (no longer hidden inside an external theme gem).

Added an interactive post scaffolder, scripts/new-post.sh. It runs in pure bash (no Conda/Ruby needed), offers a numbered category menu, and toggles math, table of contents, and comments per post.

Removed the per-post <style> block. Paragraph indentation and .container image centering are now defined once in assets/css/style.scss, so every post inherits them automatically.

Repaired MathJax. The retired cdn.mathjax.org endpoint was replaced with MathJax 3 served from jsDelivr (_includes/mathjax_support.html), so LaTeX now renders again on any post with use_math: true.

December 2025:

Comments are available on blog posts so readers can leave feedback and discuss the topics covered.

I'm planning on using the utterances repository: https://utteranc.es/

As the archive grows, I may add ways for readers to support tutorials and other useful material.

https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/displaying-a-sponsor-button-in-your-repository

Shipped a dark theme. The site first migrated to the Midnight theme and has since moved to the custom Hux-inspired theme described in the June 2026 notes above.

https://github.com/pages-themes/midnight?tab=readme-ov-file

April 2022:

Plotting:

Might add some plotting capability. atm don't have much time but here's a nice link I found by Ethan Cheong.

https://ethan-cheong.github.io/plotly-in-jekyll/

March 2022:

LaTeX:

Added Mathjax support using the following guides. This allows me to use LaTeX support so that I can write math equations in my posts.

Used Fabrizio Musacchio's Guide for the general flow:

https://www.fabriziomusacchio.com/blog/2021-08-10-How_to_use_LaTeX_in_Markdown/

My actual mathjax_support.html file uses the code I found from Ben Lansdell's How-To:

https://benlansdell.github.io/computing/mathjax/

Note (historical): This site was originally bootstrapped from jekyll new on the minima theme, where _layouts, _includes, and _sass lived inside the theme gem rather than the repo. To get LaTeX support back then, the _includes folder (including the MathJax support HTML) was vendored into the repo. As of the June 2026 refactor the site runs a fully self-contained custom Hux-inspired theme, so all of those directories are version-controlled here directly, and MathJax is loaded from MathJax 3 on jsDelivr.