reusable tutorial sections concept

[rvhonorato]

I started working on changing the antibody-antigen tutorial to add sections for the web service and I noticed that you have ALL the information in a single 3.000 lines file.

This website uses a very powerful jekyll templating engine that I think could be utilized to help organize the tutorials.

So in this PR I re-organized it to demonstrate what is possible in terms of reusable sections

Concept

Instead of having ALL the sections into one single file, you can divide them into separate files, for example:

sections/
├── ab
│   ├── intro.md
│   ├── preparing-antibody.md
│   └── preparing-antigen.md
└── general
    ├── haddock-concepts.md
    └── intro-to-haddock3.md

Then when you are creating a given tutorial, you do not need to copy-paste anything, you simply re-use the sections.

This tutorial consists of the following sections:

{:toc}

<hr />

{% include_relative sections/ab/intro.md %}
{% include_relative sections/general/haddock-concepts.md %}
{% include_relative sections/general/intro-to-haddock3.md %}
{% include_relative sections/ab/preparing-antigen.md %}
{% include_relative sections/ab/preparing-antibody.md %}

{% etc %}

## You can still write specific stuff here

Benefits

• Re-usable sections across tutorials - no more copy-pasting
• Easier to update: fix a section once, it propagates everywhere it is included
• Consistent content across tutorials
• Smaller, focused files are easier to review in PRs and easier to maintain
• Event-specific sections (e.g. cluster setup for a workshop) can be added or removed from a tutorial without
  touching the core content
• The index.md becomes a clear table of contents which is easy to see the tutorial structure at a glance

Drawbacks

• Content across multiple files, may need to edit multiple files instead of just one
• Change in workflow, people will need to adapt to writing sections instead one single large file

---

Needless to say nothing changes from the user side and the page is rendered exactly the same.

Please have a look at the file structure and let me know if you want to move forward with this re-usable section approach.

For example, this is how the antibody-antigen tutorial index.md would look like:

{% include_relative sections/intro.md %}
{% include_relative sections/prompt-legend.md %}
{% include_relative sections/haddock-concepts.md %}
{% include_relative sections/haddock3-intro.md %}
{% include_relative sections/setup-intro.md %}
{% include_relative sections/setup-ljubljana-2026.md %}
{% include_relative sections/setup-kobe-2026.md %}
{% include_relative sections/setup-pula-2025.md %}
{% include_relative sections/setup-local.md %}
{% include_relative sections/preparing-pdb-intro.md %}
{% include_relative sections/preparing-antibody.md %}
{% include_relative sections/preparing-antigen.md %}
{% include_relative sections/restraints-intro.md %}
{% include_relative sections/restraints-paratope.md %}
{% include_relative sections/restraints-epitope.md %}
{% include_relative sections/restraints-ambiguous.md %}
{% include_relative sections/restraints-validation.md %}
{% include_relative sections/restraints-multichain.md %}
{% include_relative sections/docking-intro.md %}
{% include_relative sections/docking-workflow.md %}
{% include_relative sections/run-haddock3-intro.md %}
{% include_relative sections/run-bioexcel2025.md %}
{% include_relative sections/run-discoverer.md %}
{% include_relative sections/run-truba.md %}
{% include_relative sections/run-fugaku.md %}
{% include_relative sections/run-ljubljana-2026.md %}
{% include_relative sections/haddock3-execution-modes.md %}
{% include_relative sections/analysis-intro.md %}
{% include_relative sections/analysis-clusters.md %}
{% include_relative sections/analysis-scores.md %}
{% include_relative sections/analysis-single-structure.md %}
{% include_relative sections/analysis-contacts.md %}
{% include_relative sections/analysis-visualization.md %}
{% include_relative sections/conclusions.md %}
{% include_relative sections/bonus1-mutations.md %}
{% include_relative sections/bonus2-arctic3d.md %}
{% include_relative sections/bonus3-ai-models.md %}
{% include_relative sections/bonus4-ensemble.md %}
{% include_relative sections/bonus5-alphafold2.md %}
{% include_relative sections/bonus6-scoring.md %}
{% include_relative sections/congratulations.md %}

[VGPReys]

Great job:

• I think this will help a lot, not to have to change the same thing in multiple files.
• Indeed, having to have 30 different small files for the tutorial can be a little difficult, and overall reading while writing cannot be made unless we render it
• we also need to modify some of the haddock3 notebooks that are pointing to pictures URLs that now have a different path

[rvhonorato]

In this PR here I split the files kinda arbitrary, could probably make larger blocks and/or separate better what is specific to this ab example and what could be used in others and such.

But yeah, the advantage is that the sections are re-usable but indeed it changes the way you write them