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        <a href="index.html" class="nav__brand">Bioinformatics Field Guide</a>
        <div class="nav__links" id="nav-links">
          <a href="#field-map">Field map</a>
          <a href="#guides">Guides</a>
          <a href="#resources">Resources</a>
          <a href="https://github.com/Caffeinated-Code/Bioinformatics-Field-Guide" target="_blank" rel="noreferrer">GitHub</a>
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          <div>
            <p class="eyebrow">Practical bioinformatics, from setup to interpretation</p>
            <h1>Bioinformatics Field Guide</h1>
            <p class="hero__subtitle">
              A technical learning map for bioinformatics: start with setup and languages,
              then move quickly into real files, workflows, analysis, and research-grade judgment.
            </p>
            <div class="hero__actions">
              <a class="button" href="#field-map">
                Explore the field map <i class="ri-arrow-right-line" aria-hidden="true"></i>
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              <a class="button button--ghost" href="week-03-bioinformatics-file-types.html">
                Jump to real files
              </a>
            </div>
          </div>
          <aside class="hero-panel">
            <span class="hero-panel__label">What makes this useful</span>
            <h2>Short guides with reusable mental models.</h2>
            <ul>
              <li>Beginner routes for setup, languages, and first notebooks.</li>
              <li>Technical routes for file formats, RNA-seq workflows, and differential expression statistics.</li>
              <li>New guides are published only after review, testing, and cleanup.</li>
              <li>Reusable notebooks, checklists, maps, and reproducible resources.</li>
            </ul>
          </aside>
        </div>
      </section>

      <section class="section" id="field-map">
        <div class="container">
          <div class="section__heading">
            <p class="eyebrow">Learning map</p>
            <h2>Pick a route through the field.</h2>
            <p>
              This is not only a chronological blog. Use it like a map: enter at your level,
              explore by domain, or return when the next reviewed guide is published.
            </p>
          </div>
          <div class="topic-map" aria-label="Bioinformatics learning map">
            <article class="map-node map-node--foundation">
              <span>Beginner</span>
              <h3>Setup and languages</h3>
              <p>Build the local stack, learn Bash/Python/R/SQL, and use a local AI assistant as a tutor.</p>
              <a href="week-01-laptop-setup-for-bioinformatics.html">Start setup</a>
              <a href="week-02-languages-for-bioinformatics.html">Choose languages</a>
            </article>
            <article class="map-node map-node--core">
              <span>Core technical</span>
              <h3>Files and public-data practice</h3>
              <p>Learn the formats that real bioinformatics work keeps returning to.</p>
              <a href="week-03-bioinformatics-file-types.html">Read file types</a>
            </article>
            <article class="map-node map-node--analysis">
              <span>Bulk RNA-seq</span>
              <h3>From FASTQ to statistical decisions</h3>
              <p>Connect Nextflow and nf-core/rnaseq pipeline execution to count matrices, QC reports, DESeq2 models, replicates, assumptions, and outlier checks.</p>
              <a href="week-04-bulk-rnaseq-differential-expression.html">Read bulk RNA-seq</a>
              <a href="week-05-nextflow-nfcore-rnaseq.html">Read Nextflow deep dive</a>
            </article>
            <article class="map-node map-node--frontier">
              <span>Later</span>
              <h3>More guides are in review</h3>
              <p>Future topics will appear here only after they are polished, tested, and ready for readers.</p>
              <a href="#resources">Project resources</a>
            </article>
          </div>
        </div>
      </section>

      <section class="section section--soft" id="guides">
        <div class="container">
          <div class="section__heading">
            <p class="eyebrow">Foundation Series</p>
            <h2>Follow the linear path when you want structure.</h2>
            <p>
              Start here if you want a clean sequence. These are the guides currently published and reviewed.
            </p>
          </div>
          <div class="series-path" aria-label="Foundation Series linear path">
            <a class="series-step" href="week-01-laptop-setup-for-bioinformatics.html">
              <span>01</span>
              <strong>Set Up Your Laptop</strong>
              <em>Conda, Docker, JupyterLab, VS Code, Ollama, BioChatter</em>
            </a>
            <a class="series-step" href="week-02-languages-for-bioinformatics.html">
              <span>02</span>
              <strong>Pick Your Languages</strong>
              <em>Bash, Python, R, SQL, notebooks, AI-assisted learning</em>
            </a>
            <a class="series-step" href="week-03-bioinformatics-file-types.html">
              <span>03</span>
              <strong>Learn Real File Types</strong>
              <em>FASTQ, BAM, VCF, GTF, count matrices, metadata</em>
            </a>
            <a class="series-step" href="week-04-bulk-rnaseq-differential-expression.html">
              <span>04</span>
              <strong>Understand Bulk RNA-seq</strong>
              <em>nf-core/rnaseq, count matrices, DESeq2 designs, outliers, caveats</em>
            </a>
            <a class="series-step series-step--active" href="week-05-nextflow-nfcore-rnaseq.html">
              <span>05</span>
              <strong>Run Reproducible RNA-seq Pipelines</strong>
              <em>Nextflow channels, processes, profiles, nf-core/rnaseq structure, MultiQC handoff</em>
            </a>
          </div>
        </div>
      </section>

      <section class="section" id="resources">
        <div class="container">
          <div class="section__heading">
            <p class="eyebrow">Reusable resources</p>
            <h2>Run the examples, not just the articles.</h2>
          </div>
          <div class="card-grid">
            <article class="resource-card">
              <h3>Environment</h3>
              <p>Conda environment file for the starter bioinformatics stack.</p>
              <a href="content/resources/week-01/environment.yml">environment.yml</a>
            </article>
            <article class="resource-card">
              <h3>Docker</h3>
              <p>Dockerfile and Compose setup for the JupyterLab workspace.</p>
              <a href="content/resources/week-01/docker-compose.yml">docker-compose.yml</a>
            </article>
            <article class="resource-card">
              <h3>BioChatter demo</h3>
              <p>A tiny local BioChatter + Ollama example for explaining observed output.</p>
              <a href="content/resources/week-01/biochatter_ollama_demo.py">demo script</a>
            </article>
            <article class="resource-card">
              <h3>Week 2 notebooks</h3>
              <p>Bash, Python, R, and SQL confidence labs with tiny bioinformatics data.</p>
              <a href="content/resources/week-02/README.md">open resources</a>
            </article>
            <article class="resource-card">
              <h3>Week 3 file lab</h3>
              <p>FASTQ, SAM/BAM, VCF, GTF, BED, bedGraph, bigWig, public-file drill, and expected outputs.</p>
              <a href="content/resources/week-03/README.md">open resources</a>
            </article>
            <article class="resource-card">
              <h3>Week 4 RNA-seq designs</h3>
              <p>nf-core samplesheet, DESeq2 design cheat sheet, and runnable design-matrix demo.</p>
              <a href="content/resources/week-04/README.md">open resources</a>
            </article>
            <article class="resource-card">
              <h3>Week 5 Nextflow</h3>
              <p>nf-core/rnaseq test runner, samplesheet template, syntax cheat sheet, and output folder map.</p>
              <a href="content/resources/week-05/README.md">open resources</a>
            </article>
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