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<h3>Lorem Ipsum dolor</h3>
<div class="post-info"><span>By John Smith</span><span>Jan 27, 2018</span></div>
<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc quam urna, dignissim nec auctor in, mattis vitae leo. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc quam urna, dignissim nec auctor in, mattis vitae leo. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc quam urna, dignissim nec auctor in, mattis vitae leo. Lorem ipsum dolor sit amet, consectetur adipiscing elit.</p>
<figure class="figure"><img class="rounded img-fluid figure-img figure-img" src="assets/img/scenery/image6.jpg" alt="A generic square placeholder image with rounded corners in a figure.">
<figcaption class="figure-caption">Lorem ipsum dolor</figcaption>
</figure>
<h4>Lorem Ipsum</h4>
<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc quam urna, dignissim nec auctor in, mattis vitae leo. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc quam urna, dignissim nec auctor in, mattis vitae leo. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc quam urna, dignissim nec auctor in, mattis vitae leo. Lorem ipsum dolor sit amet, consectetur adipiscing elit.</p>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc quam urna, dignissim nec auctor in, mattis vitae leo. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc quam urna, dignissim nec auctor in, mattis vitae leo. Lorem ipsum dolor sit amet, consectetur adipiscing elit.&nbsp;</p>
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<h4>Lorem Ipsum dolor</h4>
<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc quam urna, dignissim nec auctor in, mattis vitae leo. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc quam urna, dignissim nec auctor in, mattis vitae leo. Lorem ipsum dolor sit amet, consectetur adipiscing elit.</p>
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<p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc quam urna, dignissim nec auctor in, mattis vitae leo. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc quam urna, dignissim nec auctor in, mattis vitae leo. Lorem ipsum dolor sit amet, consectetur adipiscing elit.</p>
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<figcaption class="figure-caption">Lorem Ipsum dolor</figcaption>
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<h2 class="section-heading mb-4">
<span class="section-heading-lower"><strong>Award</strong></span>
</h2>
<span id="s1" class="section-heading-upper h3"><br />Bronze - All criteria have been met.</span>
<span id="s11" class="section-heading-upper h4"><br />B1 Competition Deliverables</span>
<p>We have already submitted the Wiki and Judging Form, and we will submit the Presentation
Video on time in early October. Additionally, we will attend the Jamboree in person in late
October.
</p>
<ol>
<li><a href="https://2024.igem.wiki/squirrel-shenzhen/b">Wiki</a></li>
<li>Presentation Video（Submitted）</li>
<li>Judging Form（Submitted）</li>
<li>Judging Session（Attending in person）</li>
</ol>
<span id="s12" class="section-heading-upper h4"><br />B2 Project Attributions</span>
<li><a href="https://2024.igem.wiki/squirrel-shenzhen/attributions">Attributions</a></li>
<p>We have clearly outlined the division of work and contributions of each team member, and have
also acknowledged our advisors, as well as all the experts, entrepreneurs, and the companies
and organizations that have provided us with support.</p>
<span id="s13" class="section-heading-upper h4"><br />B3 Project Description</span>
<li><a href="https://2024.igem.wiki/squirrel-shenzhen/descriptions">Descriptions</a></li>
<p>We developed a set of biosensors for detecting heavy metal ion pollution and validated their
functionality. This is the description of our project.</p>
<span id="s14" class="section-heading-upper h4"><br />B4 Contribution</span>
<li> <a href="https://parts.igem.org/Part:BBa_K1758320">BBa_K1758320</a>
</li>
<li><a href="https://2024.igem.wiki/squirrel-shenzhen/contribution">Contribution</a></li>
<p>We provided <b>additional data for previous parts (BBa_K1758320)</b> based on our
high-throughput screening, offering a large collection of reference sequences and promoter
performance data for future iGEM participants in promoter screening. Additionally, we
explored the effects of different metal ions (copper, zinc, etc.) on E. coli growth and
uploaded the related data.</p>
<span id="s2" class="section-heading-upper h3"><br />Silver - All criteria have been met.</span>
<span id="s21" class="section-heading-upper h4"><br />S1 Engineering Success</span>
<li><a href="https://parts.igem.org/Part:BBa_K5459002">BBa_K5459002</a>
</li>
<li><a href="https://2024.igem.wiki/squirrel-shenzhen/engineering">Engineering</a></li>
<span id="s22" class="section-heading-upper h4"><br />S2 Human Practices</span>
<li><a href="https://2024.igem.wiki/squirrel-shenzhen/human-practices">Human-Practices</a></li>
<span id="s3" class="section-heading-upper h3"><br />Gold - The selected criteria have been
met.</span>
<span id="s31" class="section-heading-upper h4"><br />G1 Excellence in Synthetic Biology</span>
<span id="s311" class="section-heading-upper h5"><br />New Composite Part</span>
<li><a href="https://parts.igem.org/Part:BBa_K5459002">BBa_K5459002</a>
</li>
<li><a href="https://2024.igem.wiki/squirrel-shenzhen/parts">Parts</a></li>
<p>We utilize this part as a promoter responsive to copper ions to initiate the expression of
downstream reporter genes. Furthermore, we have demonstrated with this example that
endogenous promoters from Escherichia coli can function independently within E. coli without
the need for additional expression of their corresponding transcriptional regulatory
proteins; they can directly use the proteins already present in the genome.</p>
<span id="s312" class="section-heading-upper h5"><br />Model</span>
<li><a href="https://2024.igem.wiki/squirrel-shenzhen/model">Model</a></li>
<p>In this study, we employed machine learning (ML) techniques to analyze the relationship
between sequences and responses using our experimental dataset of 88 samples. Our initial
objective was to establish a regression model to predict fluorescence intensity based on
sequence features. We implemented a feature extraction strategy focusing on k-mers,
constructing datasets from various k-mer lengths. However, we found that using 3-mers and
4-mers as features did not yield sufficient predictive power.</p>
<p>In response, we shifted our approach by changing the prediction target to classify promoters
into three categories based on fluorescence intensity: high, medium, and low. When utilizing
the k-mers feature extraction method for this classification task, we still encountered
limited success. Conversely, when we employed one-hot encoding for the promoter sequences,
we achieved notable results, with our logit boost model reaching an impressive
classification accuracy of 0.96 and an AUC greater than 0.9. This indicates that our refined
approach significantly improved the model's ability to predict promoter activity based on
sequence information, paving the way for more effective designs in synthetic biology
applications.</p>
<span id="s31" class="section-heading-upper h4"><br />G2 Specializations</span>
<span id="s311" class="section-heading-upper h5"><br />- Integrated Human Practices</span>
<li><a href="https://2024.igem.wiki/squirrel-shenzhen/human-practices">Human-Practices</a></li>
<p>Human Practices played a crucial role in our project. We implemented Human Practices through
the logic of the DBTL (Design-Build-Test-Learn) cycle, with HP and project design
alternating and advancing in conjunction. The project continuously evolved towards
practicality and responsible innovation under the guidance of stakeholders.</p>
</div>
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......@@ -86,20 +171,49 @@
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<h2 class="section-heading mb-4">
<span class="section-heading-lower"><strong>Modeling</strong></span>
</h2>
<span id="s1" class="section-heading-upper h3"><br />Overview</span>
<p>Machine learning (ML) has become an essential tool in modern biology, providing powerful
methods for analyzing large and complex datasets. In fields like genomics, transcriptomics,
and synthetic biology, ML algorithms enable researchers to uncover hidden patterns, make
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