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186 changes: 186 additions & 0 deletions _data/learning-materials.yml
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# Learning materials shown on /learning-materials.html
#
# text: Title of the material (required)
# url: Link to the repository or guide (required)
# icon: Either a Bootstrap Icons class ("bi bi-github") or a path/URL to
# an image to use as the icon ("/images/logos/rstudio.png")
# description: Short summary, rendered as markdown
# tags: List of tags; these populate the sidebar tag selector
# last updated: YYYY-MM-DD, used by the default "Recently updated" sort
# featured: true to highlight the material and pin it to the top of the
# default listing (the pin is dropped once a visitor sorts)

- text: Build a Conda-based Container for Bioinformatics
url: https://github.com/CHTC/biocafe-containers
icon: "bi bi-github"
description: |
This tutorial covers the basics of how to use containers to deploy software.
While this example is bioinformatics-flavored, the concepts can be applied
to any software stack.
tags:
- conda
- HTC
- bioinformatics
- CHTC-created
- container
last updated: 2026-05-11

- text: Learn How to Deploy R Calculations
url: https://github.com/chtc/tutorial-rstudio-to-chtc
icon: "bi bi-github"
description: |
A step-by-step example of transitioning from running R calculations
on your computer using RStudio, to running many such calculations
on a HTC system.
tags:
- R
- CHTC-created
- beginner-friendly
- HTC
last updated: 2026-04-02

- text: Predict Protein Structures with Alphafold3
url: https://github.com/CHTC/tutorial-CHTC-AF3
icon: "bi bi-github"
description: |
AlphaFold3 (AF3) predicts atomic-resolution biomolecular structures
for proteins, nucleic acids, and complexes.
tags:
- bioinformatics
- CHTC-created
- HTC
- GPU
last updated: 2026-06-24

- text: Machine Learning on GPUs with PyTorch
url: https://github.com/CHTC/tutorial-pytorch-gpu
icon: "bi bi-github"
description: |
Train and evaluate a PyTorch model on GPU capacity, including how to
request GPUs, check for CUDA availability, and checkpoint long-running
training jobs.
tags:
- machine-learning
- GPU
- python
- CHTC-created
- HTC
last updated: 2026-07-15

- text: Package Python Environments for Distributed Jobs
url: https://github.com/CHTC/tutorial-python-environments
icon: "bi bi-github"
description: |
Compare the ways of bringing a Python environment along with your jobs,
from `conda-pack` tarballs to purpose-built Apptainer containers.
tags:
- python
- conda
- container
- beginner-friendly
- CHTC-created
- HTC
last updated: 2026-08-19

- text: Run MPI Simulations on the HPC Cluster
url: https://github.com/CHTC/tutorial-hpc-mpi
icon: "bi bi-github"
description: |
An introduction to compiling and running multi-node MPI codes with SLURM,
including how to scale up gradually and measure parallel efficiency.
tags:
- HPC
- MPI
- CHTC-created
last updated: 2026-03-08

- text: Introduction to High Throughput Computing
url: https://github.com/OSGConsortium/osg-school-materials
icon: "bi bi-github"
description: |
Lessons and exercises from OSG School covering the ideas behind
high throughput computing and the mechanics of submitting your first
workloads.
featured: true
tags:
- HTC
- beginner-friendly
- workshop
last updated: 2026-02-20

- text: Manage Multi-Step Workflows with DAGMan
url: https://github.com/CHTC/tutorial-dagman
icon: "bi bi-github"
description: |
Chain jobs together into a workflow so that pre-processing, analysis, and
aggregation steps run in the right order and recover from failures.
featured: true
tags:
- workflows
- HTC
- CHTC-created
last updated: 2026-01-27

- text: Analyze Large Datasets with Dask
url: https://github.com/CHTC/tutorial-dask
icon: "bi bi-github"
description: |
Scale pandas-style analysis beyond a single machine, and learn when a
Dask cluster is the right tool versus many independent HTC jobs.
tags:
- python
- data-analysis
- HTC
last updated: 2025-11-06

- text: Get Started with HTC in Ten Jobs
url: https://github.com/CHTC/tutorial-first-jobs
icon: "bi bi-github"
featured: true
description: |
The place to start if you have never submitted a job before: ten small
exercises that build up from a single "hello world" job to a batch of
hundreds.
tags:
- HTC
- beginner-friendly
- CHTC-created
- workshop
last updated: 2025-12-15

- text: Run MATLAB Jobs Without a License Server
url: https://github.com/CHTC/tutorial-matlab-compiler
icon: "/images/Matlab_Logo.png"
description: |
Compile MATLAB code into a standalone executable so that your jobs can run
anywhere in the pool, without needing to check out a license.
tags:
- MATLAB
- HTC
- CHTC-created
last updated: 2026-07-02

- text: Checkpoint Long-Running Jobs
url: https://github.com/CHTC/tutorial-self-checkpointing
icon: "bi bi-github"
description: |
Break a multi-day computation into restartable pieces so it survives
interruptions and makes steady progress on opportunistic capacity.
tags:
- HTC
- workflows
- CHTC-created
last updated: 2026-06-05

- text: Move Large Datasets In and Out of CHTC
url: https://github.com/CHTC/tutorial-data-transfer
icon: "bi bi-github"
description: |
Choose between HTCondor file transfer, staging space, and Globus for the
inputs and outputs your jobs produce, with examples of each.
tags:
- data-transfer
- HTC
- beginner-friendly
- CHTC-created
last updated: 2026-05-28
154 changes: 154 additions & 0 deletions _uw-research-computing/learning-materials.html
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---
layout: default
title: Learning Materials
description: A collection of tutorials, workshops, and example repositories for learning high throughput and high performance computing.
js_extension:
- src: "/assets/js/pages/learning-materials.js"
loading: defer
type: module
---

{% assign by_date = site.data.learning-materials | sort: "last updated" | reverse %}
{% assign featured_materials = by_date | where: "featured", true %}
{% assign other_materials = by_date | where_exp: "material", "material.featured != true" %}
{% comment %} Featured materials lead the default listing; JS drops the pin once a visitor sorts. {% endcomment %}
{% assign materials = featured_materials | concat: other_materials %}
{% assign all_tags = materials | map: "tags" | join: "," | split: "," | uniq | sort_natural %}

<div class="container-xxl pt-3" id="learning-materials">
{% include page-title.html title=page.title %}

<p class="lm-intro">
Tutorials, workshop materials, and example repositories for learning how to run
your research computing work at scale. Filter by topic using the tags, or search
for a keyword.
</p>

<div class="row">

<!-- Sidebar: tag selector -->
<div class="col-12 col-lg-3">
<button class="btn btn-outline-primary w-100 mb-3 d-lg-none" type="button"
data-bs-toggle="collapse" data-bs-target="#lm-tag-panel"
aria-expanded="false" aria-controls="lm-tag-panel">
Browse by tag
</button>

<div class="collapse d-lg-block" id="lm-tag-panel">
<div class="lm-sidebar mb-4">
<div class="lm-sidebar-header">
<h2 class="h6 mb-0">Tags</h2>
<button type="button" class="btn btn-link btn-sm p-0 lm-clear-tags" id="lm-clear-tags" hidden>
Clear
</button>
</div>

<ul class="lm-tag-list list-unstyled mb-0">
{% for tag in all_tags %}
{% assign tagged = materials | where_exp: "material", "material.tags contains tag" %}
<li>
<label class="lm-tag-option" for="lm-tag-{{ tag | slugify }}">
<input class="form-check-input" type="checkbox"
id="lm-tag-{{ tag | slugify }}"
value="{{ tag }}"
data-lm-tag="{{ tag }}">
<span class="lm-tag-name">{{ tag }}</span>
<span class="lm-tag-count" aria-label="{{ tagged.size }} {% if tagged.size == 1 %}guide{% else %}guides{% endif %}">{{ tagged.size }}</span>
</label>
</li>
{% endfor %}
</ul>
</div>
</div>
</div>

<!-- Cards, with filter + sort controls -->
<div class="col-12 col-lg-9">

<div class="lm-toolbar">
<div class="lm-search">
<label class="visually-hidden" for="lm-search-input">Search learning materials</label>
<i class="bi bi-search lm-search-icon" aria-hidden="true"></i>
<input type="search" class="form-control" id="lm-search-input"
placeholder="Search titles, descriptions, and tags" autocomplete="off">
</div>

<div class="lm-sort">
<label class="form-label mb-0" for="lm-sort-select">Sort by</label>
<select class="form-select" id="lm-sort-select">
<option value="updated-desc" selected>Recently updated</option>
<option value="updated-asc">Least recently updated</option>
<option value="title-asc">Title (A&ndash;Z)</option>
<option value="title-desc">Title (Z&ndash;A)</option>
</select>
</div>
</div>

<div class="lm-status">
<p class="mb-0 text-muted" id="lm-count" aria-live="polite">
Showing {{ materials.size }} of {{ materials.size }} guides
</p>
<div id="lm-active-tags" class="lm-active-tags"></div>
</div>

<div class="row" id="lm-grid">
{% for material in materials %}

{% assign updated = material.last_updated | default: material["last updated"] %}
{% assign icon = material.icon | default: "bi bi-github" %}
{% assign tag_string = material.tags | join: " " %}

<div class="col-12 col-md-6 col-xl-4 mb-4 lm-card-col"
data-tags="{{ material.tags | join: '|' }}"
data-featured="{% if material.featured %}true{% else %}false{% endif %}"
data-updated="{% if updated %}{{ updated | date: '%Y-%m-%d' }}{% endif %}"
data-title="{{ material.text | escape }}"
data-search="{{ material.text | append: ' ' | append: material.description | append: ' ' | append: tag_string | normalize_whitespace | escape }}">
<div class="lm-card{% if material.featured %} lm-card-featured{% endif %}">
<div class="lm-card-head">
{% if icon contains "bi " %}
<i class="{{ icon }} lm-card-icon" aria-hidden="true"></i>
{% elsif icon contains "//" %}
<img class="lm-card-icon-img" src="{{ icon }}" alt="">
{% else %}
<img class="lm-card-icon-img" src="{{ icon | relative_url }}" alt="">
{% endif %}
<h3 class="lm-card-title">
{% if material.featured %}
<span class="lm-featured-label">
<i class="bi bi-star-fill" aria-hidden="true"></i>Featured
</span>
{% endif %}
<a href="{{ material.url }}">{{ material.text }}</a>
</h3>
</div>

<div class="lm-card-description">
{{ material.description | markdownify }}
</div>

<div class="lm-card-tags">
{% for tag in material.tags %}
<button type="button" class="lm-tag-badge" data-lm-tag-toggle="{{ tag }}">{{ tag }}</button>
{% endfor %}
</div>

<div class="lm-card-footer">
<span class="lm-card-host">{{ material.url | remove: "https://" | remove: "http://" | remove_first: "www." }}</span>
{% if updated %}
<span class="lm-card-updated">Updated {{ updated | date: "%b %-d, %Y" }}</span>
{% endif %}
</div>
</div>
</div>
{% endfor %}
</div>

<div id="lm-no-results" class="lm-no-results" hidden>
<p class="mb-2"><strong>No learning materials match your filters.</strong></p>
<button type="button" class="btn btn-outline-primary btn-sm" id="lm-reset-all">Clear all filters</button>
</div>

</div>
</div>
</div>
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