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<li class="toctree-l2"><a class="reference internal" href="auto_examples/hurdle_api_example.html">Hurdle InflammAge API Example</a></li>
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<article role="main" id="furo-main-content">
<section id="using-hurdle-s-inflammage-model-in-biolearn">
<h1>Using Hurdle’s InflammAge Model in Biolearn<a class="headerlink" href="#using-hurdle-s-inflammage-model-in-biolearn" title="Link to this heading">¶</a></h1>
<section id="non-commercial-use-only">
<h2>Non-Commercial Use Only<a class="headerlink" href="#non-commercial-use-only" title="Link to this heading">¶</a></h2>
<p><strong>Important Notice:</strong>
This inflammaging calculation is provided for personal and educational purposes only.</p>
<p>Any commercial use, distribution, or resale of this information is strictly prohibited without prior written agreement from Chronomics Limited. See https://hurdle.bio/ for further commercial information.</p>
</section>
<hr class="docutils" />
<section id="quick-start">
<h2>Quick Start<a class="headerlink" href="#quick-start" title="Link to this heading">¶</a></h2>
<ol class="arabic">
<li><p><strong>Get API Credentials</strong></p>
<ul class="simple">
<li><p>Register at: https://dashboard.hurdle.bio/register</p></li>
<li><p>Navigate to Developer > API keys</p></li>
<li><p>Save your API key securely</p></li>
</ul>
</li>
<li><p><strong>Set Up Your API Key</strong></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">HURDLE_API_KEY</span><span class="o">=</span><span class="s2">"your_api_key_here"</span>
</pre></div>
</div>
</li>
<li><p><strong>Use the Model</strong></p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span><span class="w"> </span><span class="nn">biolearn.model_gallery</span><span class="w"> </span><span class="kn">import</span> <span class="n">ModelGallery</span>
<span class="n">gallery</span> <span class="o">=</span> <span class="n">ModelGallery</span><span class="p">()</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">gallery</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"HurdleInflammAge"</span><span class="p">)</span>
<span class="c1"># Make predictions</span>
<span class="n">predictions</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">methylation_data</span><span class="p">)</span>
</pre></div>
</div>
</li>
</ol>
</section>
<section id="privacy-notice">
<h2>Privacy Notice<a class="headerlink" href="#privacy-notice" title="Link to this heading">¶</a></h2>
<p>⚠️ <strong>Data Privacy Warning</strong>: Using this model will send your methylation data to Hurdle Bio’s servers. You will be asked for explicit consent before any data is transmitted. Ensure you have permission to share genomic data with third parties.</p>
</section>
<section id="detailed-setup">
<h2>Detailed Setup<a class="headerlink" href="#detailed-setup" title="Link to this heading">¶</a></h2>
<section id="getting-your-api-key">
<h3>Getting Your API Key<a class="headerlink" href="#getting-your-api-key" title="Link to this heading">¶</a></h3>
<ol class="arabic simple">
<li><p>Visit https://dashboard.hurdle.bio/register</p></li>
<li><p>Create an account</p></li>
<li><p>Navigate to Developer > API keys</p></li>
<li><p>Generate a new API key</p></li>
<li><p>Store it securely (never commit to version control)</p></li>
</ol>
</section>
<section id="setting-your-api-key">
<h3>Setting Your API Key<a class="headerlink" href="#setting-your-api-key" title="Link to this heading">¶</a></h3>
<p><strong>Option 1: Environment Variable (Recommended)</strong></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">HURDLE_API_KEY</span><span class="o">=</span><span class="s2">"your_api_key_here"</span>
</pre></div>
</div>
<p><strong>Option 2: Direct Input</strong></p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span><span class="w"> </span><span class="nn">biolearn.model</span><span class="w"> </span><span class="kn">import</span> <span class="n">HurdleAPIModel</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">HurdleAPIModel</span><span class="p">(</span><span class="n">api_key</span><span class="o">=</span><span class="s2">"your_api_key_here"</span><span class="p">)</span>
</pre></div>
</div>
</section>
</section>
<section id="usage-examples">
<h2>Usage Examples<a class="headerlink" href="#usage-examples" title="Link to this heading">¶</a></h2>
<section id="basic-usage">
<h3>Basic Usage<a class="headerlink" href="#basic-usage" title="Link to this heading">¶</a></h3>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span><span class="w"> </span><span class="nn">biolearn.model_gallery</span><span class="w"> </span><span class="kn">import</span> <span class="n">ModelGallery</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">biolearn.data_library</span><span class="w"> </span><span class="kn">import</span> <span class="n">DataLibrary</span>
<span class="c1"># Load data</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">DataLibrary</span><span class="p">()</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"YourDataset"</span><span class="p">)</span><span class="o">.</span><span class="n">load</span><span class="p">()</span>
<span class="c1"># Get model</span>
<span class="n">gallery</span> <span class="o">=</span> <span class="n">ModelGallery</span><span class="p">()</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">gallery</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"HurdleInflammAge"</span><span class="p">)</span>
<span class="c1"># Make predictions (you'll be asked for consent)</span>
<span class="n">predictions</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">data</span><span class="o">.</span><span class="n">dnam</span><span class="p">)</span>
</pre></div>
</div>
</section>
<section id="with-metadata">
<h3>With Metadata<a class="headerlink" href="#with-metadata" title="Link to this heading">¶</a></h3>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># If your data includes age and sex information,</span>
<span class="c1"># the model will use this for more accurate predictions</span>
<span class="n">predictions</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> <span class="c1"># Uses both dnam and metadata</span>
</pre></div>
</div>
</section>
</section>
<section id="data-requirements">
<h2>Data Requirements<a class="headerlink" href="#data-requirements" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><p><strong>Input</strong>: DNA methylation beta values (0-1 range)</p></li>
<li><p><strong>Format</strong>: Pandas DataFrame with CpG sites as rows, samples as columns</p></li>
<li><p><strong>Tissue</strong>: Blood samples recommended</p></li>
<li><p><strong>CpG Sites</strong>: Requires all 62,000+ specific CpG sites (no missing values allowed)</p></li>
<li><p><strong>Optional</strong>: Age and sex metadata improve accuracy</p></li>
</ul>
<section id="missing-value-handling">
<h3>Missing Value Handling<a class="headerlink" href="#missing-value-handling" title="Link to this heading">¶</a></h3>
<p>The model requires approximately 62,000 specific CpG sites. If your data is missing any of these sites, you’ll get an error listing the missing CpGs. You must impute missing values before calling the model. Use biolearn’s built-in imputation:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Option 1: Use ModelGallery's imputation</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">gallery</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"HurdleInflammAge"</span><span class="p">,</span> <span class="n">imputation_method</span><span class="o">=</span><span class="s2">"averaging"</span><span class="p">)</span>
<span class="c1"># Option 2: Impute your data beforehand</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">biolearn.imputation</span><span class="w"> </span><span class="kn">import</span> <span class="n">hybrid_impute</span>
<span class="n">imputed_data</span> <span class="o">=</span> <span class="n">hybrid_impute</span><span class="p">(</span><span class="n">your_data</span><span class="p">,</span> <span class="n">reference_values</span><span class="p">,</span> <span class="n">required_cpgs</span><span class="p">)</span>
</pre></div>
</div>
</section>
</section>
<section id="troubleshooting">
<h2>Troubleshooting<a class="headerlink" href="#troubleshooting" title="Link to this heading">¶</a></h2>
<section id="common-errors">
<h3>Common Errors<a class="headerlink" href="#common-errors" title="Link to this heading">¶</a></h3>
<p><strong>“API key required”</strong></p>
<ul class="simple">
<li><p>Set your API key using one of the methods above</p></li>
<li><p>Verify the key is correct</p></li>
</ul>
<p><strong>“Failed to get upload URL: 401”</strong></p>
<ul class="simple">
<li><p>Your API key may be invalid or expired</p></li>
<li><p>Verify you’re using a production API key from https://dashboard.hurdle.bio</p></li>
</ul>
<p><strong>“Missing X/Y required CpG sites”</strong></p>
<ul class="simple">
<li><p>Your data is missing some required CpG sites</p></li>
<li><p>The error will show examples of missing sites</p></li>
<li><p>Use one of biolearn’s imputation methods before calling predict()</p></li>
</ul>
<p><strong>“No required CpG sites found in data”</strong></p>
<ul class="simple">
<li><p>Your methylation data doesn’t contain any of the required CpG sites</p></li>
<li><p>Ensure your data uses Illumina array probe IDs (e.g., “cg00000029”)</p></li>
</ul>
<p><strong>“User consent required to send data to external API”</strong></p>
<ul class="simple">
<li><p>You must type “yes” when prompted to consent to sending data</p></li>
<li><p>This ensures you’re aware that data will be transmitted to external servers</p></li>
</ul>
<p><strong>Network Errors</strong></p>
<ul class="simple">
<li><p>Check your internet connection</p></li>
<li><p>Verify firewall settings allow HTTPS connections to hurdle.bio</p></li>
</ul>
</section>
</section>
<section id="best-practices">
<h2>Best Practices<a class="headerlink" href="#best-practices" title="Link to this heading">¶</a></h2>
<ol class="arabic simple">
<li><p><strong>Test First</strong>: Verify your API credentials work with a small subset of samples</p></li>
<li><p><strong>Batch Processing</strong>: For large datasets, consider processing in smaller batches</p></li>
<li><p><strong>Error Handling</strong>: Always wrap API calls in try-except blocks</p></li>
<li><p><strong>Data Security</strong>: Ensure you have consent to share genomic data before using this model</p></li>
<li><p><strong>Save Results</strong>: Cache predictions locally to avoid redundant API calls</p></li>
</ol>
</section>
<section id="support">
<h2>Support<a class="headerlink" href="#support" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><p><strong>Biolearn Issues</strong>: Open an issue on the <a class="reference external" href="https://github.com/bio-learn/biolearn">biolearn GitHub repository</a></p></li>
<li><p><strong>API Access</strong>: Contact Hurdle Bio support via https://hurdle.bio</p></li>
<li><p><strong>Commercial Use</strong>: Contact Chronomics Limited for licensing inquiries</p></li>
</ul>
</section>
<section id="example-script">
<h2>Example Script<a class="headerlink" href="#example-script" title="Link to this heading">¶</a></h2>
<p>See <code class="docutils literal notranslate"><span class="pre">examples/hurdle_api_example.py</span></code> for a complete working example.</p>
</section>
<section id="technical-details">
<h2>Technical Details<a class="headerlink" href="#technical-details" title="Link to this heading">¶</a></h2>
<ul class="simple">
<li><p><strong>Model Type</strong>: Third-party API integration</p></li>
<li><p><strong>Output</strong>: InflammAge score (inflammation-based biological age)</p></li>
<li><p><strong>API Endpoint</strong>: https://api.hurdle.bio/predict/v1/</p></li>
<li><p><strong>Timeout</strong>: 30 seconds default</p></li>
<li><p><strong>Consent</strong>: Required once per session</p></li>
</ul>
</section>
</section>
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<ul>
<li><a class="reference internal" href="#">Using Hurdle’s InflammAge Model in Biolearn</a><ul>
<li><a class="reference internal" href="#non-commercial-use-only">Non-Commercial Use Only</a></li>
<li><a class="reference internal" href="#quick-start">Quick Start</a></li>
<li><a class="reference internal" href="#privacy-notice">Privacy Notice</a></li>
<li><a class="reference internal" href="#detailed-setup">Detailed Setup</a><ul>
<li><a class="reference internal" href="#getting-your-api-key">Getting Your API Key</a></li>
<li><a class="reference internal" href="#setting-your-api-key">Setting Your API Key</a></li>
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