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Commit 3b7500d9 authored by Aadityanshu Abhinav's avatar Aadityanshu Abhinav
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Merge branch 'main' into 'Aadityanshu' 

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2 merge requests!40Aadityanshu updated Results page,!39Main
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.gitignore
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......@@ -3,4 +3,6 @@ venv
igemEnv
.vscode
__pycache__
public
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public
.DS_Store
./static/.DS_Store
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static/scripts.js
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function darkModeFunc() {
var element = document.body;
element.classList.toggle("dark-mode");
}
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var toggler = document.getElementById("dark-mode-toggler");
if (toggler.innerHTML == "Dark Mode") {
toggler.innerHTML = "Light Mode";
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toggler.innerHTML = "Dark Mode";
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var toggler_2 = document.getElementById("dark-mode-toggler-2");
if (toggler_2.innerHTML == "Dark Mode") {
toggler_2.innerHTML = "Light Mode";
} else {
toggler_2.innerHTML = "Dark Mode";
}
}
document.addEventListener("DOMContentLoaded", function () {
var coll = document.getElementsByClassName("collapsible");
var i;
for (i = 0; i < coll.length; i++) {
var content = coll[i].nextElementSibling;
content.style.maxHeight = "7500px";
coll[i].classList.add("active"); // Add the "active" class
coll[i].addEventListener("click", function () {
this.classList.toggle("active");
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var arrowIcon = this.querySelector(".arrow-icon");
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content.style.maxHeight = "7500px";
content.style.transition = "max-height 0.5s ease-in";
arrowIcon.classList.remove("arrow-down");
arrowIcon.classList.add("arrow-up");
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static/style.css
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wiki/footer.html
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<footer>
<div class="sponsors p-5">
<h4 class="text-center">A heartful thanks to our title sponsors:</h4>
<div class="sponsors-images">
<a href="https://www.inito.com/">
<img src="https://static.igem.wiki/teams/4931/wiki/team-images/team-images/inito.jpeg" alt="inito" class="sponsors-image">
</a>
<a href="https://iitmaa.org/">
<img src="https://static.igem.wiki/teams/4931/wiki/iitmaa.png" alt="iitmaa" class="sponsors-image">
</a>
</div>
</div>
<hr>
<div class="main">
<div class="left-column p-5">
<div class="horizontal-logos">
<img src="https://static.igem.wiki/teams/4931/wiki/igem-logo.png" alt="Logo 1" class="footer-logo">
<img src="https://static.igem.wiki/teams/4931/wiki/igem-logo.png" alt="Logo 1" class="footer-logo bg-dark">
<img src="https://static.igem.wiki/teams/4931/wiki/iitm-logo.png" alt="Logo 2" class="footer-logo">
</div>
<img src="https://static.igem.wiki/teams/4931/wiki/g20-logo.png" alt="Large Logo" class="footer-large-logo">
......@@ -13,12 +25,12 @@
<h1 style=" margin-top: 0px; text-align: center;"><b>Address</b></h1>
<h3 style=" margin-top: 20px; text-align: center;" class="tab">Indian Institute of Technology Madras, Chennai, 600036</h3>
</div>
<p class="d-flex align-items-center">
<p class="d-flex justify-content-center">
<i class="fa fa-phone" style="font-size: 2em;"></i> &nbsp;
044 2257 8000
</p>
<br>
<p class="d-flex align-items-center">
<p class="d-flex justify-content-center">
<i class="fa fa-envelope-o" style="font-size: 2em;"></i> &nbsp;
igem@smail.iitm.ac.in
</p>
......
wiki/menu.html
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<nav class="navbar navbar-expand-lg navbar-dark bg-dark">
<nav class="navbar navbar-expand-lg navbar-dark">
<a class="navbar-brand nav-name" href="/">Synthopedia</a>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarNav"
aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse justify-content-center text-white" id="navbarNav">
<ul class="navbar-nav text-white">
<li class="nav-item text-white">
<ul class="navbar-nav">
<li class="nav-item">
<a class="nav-link text-white" href="{{ url_for('pages', page = '/') }}">Home</a>
</li>
<li class="nav-item dropdown text-white">
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle text-white" href="#" id="projectsDropdown" role="button"
data-bs-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Projects
Project
</a>
<div class="dropdown-menu bg-dark text-white" aria-labelledby="projectsDropdown">
<div class="dropdown-menu" aria-labelledby="projectsDropdown">
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/description') }}">Description</a>
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/contribution') }}">Contributions</a>
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/notebook') }}">Notebook</a>
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/experiments') }}">Experiments</a>
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/engineering') }}">Engineering Success</a>
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/safety') }}">Safety</a>
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/results') }}">Results</a>
</div>
</li>
<li class="nav-item dropdown text-white">
<a class="nav-link dropdown-toggle text-white" href="#" id="wetLabDropdown" role="button" data-bs-toggle="dropdown"
aria-haspopup="true" aria-expanded="false">
Wet lab
</a>
<div class="dropdown-menu bg-dark text-white" aria-labelledby="wetLabDropdown">
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/experiments') }}">Experiments</a>
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/measurement') }}">Measurements</a>
</div>
<li class="nav-item">
<a class="nav-link text-white" href="{{ url_for('pages', page = '/safety') }}">Safety</a>
</li>
<li class="nav-item dropdown text-white">
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle text-white" href="#" id="dryLabDropdown" role="button" data-bs-toggle="dropdown"
aria-haspopup="true" aria-expanded="false">
Dry lab
</a>
<div class="dropdown-menu bg-dark text-white" aria-labelledby="dryLabDropdown">
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/model') }}">Modelling</a>
<div class="dropdown-menu bg-dark" aria-labelledby="dryLabDropdown">
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/model') }}">Model</a>
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/software') }}">Software</a>
</div>
</li>
<li class="nav-item dropdown text-white">
<a class="nav-link dropdown-toggle text-white" href="#" id="humanPracticesDropdown" role="button"
data-bs-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Human Practices
</a>
<div class="dropdown-menu bg-dark" aria-labelledby="humanPracticesDropdown">
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/human-practices') }}">Integrated Human
Practices</a>
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/inclusivity') }}">Inclusivity</a>
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/education') }}">Public Engagement &
Education</a>
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/entrepreneurship') }}">Entrepreneurship</a>
</div>
<li class="nav-item">
<a class="nav-link text-white" href="{{ url_for('pages', page = '/human-practices') }}">Human Practices</a>
</li>
<li class="nav-item dropdown text-white">
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle text-white" href="#" id="teamDropdown" role="button"
data-bs-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Team
......@@ -67,10 +49,23 @@
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/attributions') }}">Attributions</a>
</div>
</li>
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle text-white" href="#" id="awardsDropdown" role="button" data-bs-toggle="dropdown"
aria-haspopup="true" aria-expanded="false">
Awards
</a>
<div class="dropdown-menu bg-dark" aria-labelledby="awardsDropdown">
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/education') }}">Education</a>
<a class="dropdown-item text-white" href="{{ url_for('pages', page = '/model') }}">Model</a>
<a class="dropdown-item text-white" href="#">Parts</a>
</div>
</li>
<li class="nav-item dark-mode-mobile">
<button onclick="darkModeFunc()" id="dark-mode-toggler" class="nav-link">Dark Mode</button>
</li>
</ul>
</div>
<div class="nav-logo">
<a href="{{ url_for('pages', page = '/') }}"><img src="https://static.igem.wiki/teams/4931/wiki/igem-logo.png"
alt="iGem IITM" /></a>
<div class="dark-mode-button">
<button onclick="darkModeFunc()" id="dark-mode-toggler-2">Dark Mode</button>
</div>
</nav>
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{% block lead %}Describe how and why you chose your iGEM project.{% endblock %}
{% block page_content %}
<div class="row text-white" style="background-image: url(https://static.igem.wiki/teams/4931/wiki/wiki-bg-images/bg-image.jpg);">
<div class="p-5">
<div class="row">
<div class="col-lg-12">
<h1 class="display-4 text-center">Project Description</h1>
</div>
<div class="description">
<div class="name">
<h1>PROJECT<br>DESCRIPTION</h1>
</div>
</div>
<div class="pb-5">
<div class="bg-dark bd-callout bd-callout-info font-futura">
<p>Synthetic biology envisions a bioengineering domain for designing new genetic parts and systems, or redesigning of existing ones. It has employed the design-build-test-learn iterative cycle for ushering major advancements in the fields of bioprocess engineering and bio-therapeutics. Until now, the most versatile workhorse of synthetic biology has been Escherichia coli. However, there is a need for exploring new chassis which can be naturally adapted to unique traits or metabolic pathways. </p>
<hr>
<p>Lactococcus lactis (L. lactis) is a ‘Generally Regarded As Safe’ (GRAS) organism. It is naturally found in milk products and is also known to colonize the human gut. Unlike E. coli, it does not have a lipopolysaccharide (endotoxin) layer, which requires extra measures for purification. The range of products it can be engineered to produce include lactic acid (for bioplastics), biofuels (ethanol, butanol), biopolymers (PHAs), polyols (mannitol, sorbitol), and food flavors (diacetyl). Due to its ability to use a wide range of substrates and tolerance for a wide range of conditions (pH, temperature, solvent concentration), L. lactis serves as an alternate bacterial model for metabolic and bioprocess engineering. However, the absence of genetic and regulatory libraries for this organism make genetic circuits design and assembly challenging in this chassis.</p>
<hr>
<p>The ability to fine-tune gene expression forms a cornerstone for the design and operation of genetic circuits. This optimization has not been fully carried out in non-traditional chassis like L. lactis. Our project is aimed at the construction and testing of a library of synthetic 5’ untranslated regions (UTR) containing ribosome binding sites (RBS) in L. lactis. Creating a well characterized library of RBS sequences would enable the rational engineering of this bacterium towards increased yield of products such as hyaluronic acid (HA) and in biomedical applications like probiotics.</p>
<hr>
<p>The group led by Howard M. Salis at the Pennsylvania State University has designed a web tool, called the RBS Calculator, for the design of RBS sequences. While this tool has been immensely useful for synthetic biologists, the creators, and others, have highlighted the model’s drawbacks. In addition to our lab work, we also plan to study these drawbacks and come up with potential improvements to the existing model. This would include studying the effect of temperature on mRNA folding, the interaction between the mRNA and the ribosomal S1 protein, the difference in optimal RBS-AUG spacing in Gram-positive and Gram-negative bacteria, and the effect of RNAse-mediated degradation of the transcript. Combining the (hopefully improved) model with an optimisation algorithm, we aim to rationally design the ‘best’ RBS for a given gene, in a given organism.</p>
<div class="container-description px-m-5 py-5">
<div class="motivation">
<p class="subtitles">Motivations</p>
<p class="motivationdata">
<i>Lactococcus Lactis (L. Lactis)</i> is a ‘Generally Regarded As Safe’ (GRAS) organism. It is naturally found in milk products and is also known to colonize the human gut. Unlike E. coli, it does not have an endotoxin layer, which requires extra measures for purification. Due to its ability to use a wide range of substrates and tolerance for a wide range of conditions (pH, temperature, solvent concentration), <i>L. Lactis</i> serves as an alternate bacterial model for metabolic and bioprocess engineering.
The range of products it can be engineered to produce include bioplastics, biofuels, biopolymers, polyols, and food flavors. However, the absence of genetic and regulatory libraries for this organism make genetic circuits design and assembly challenging in this chassis.
The ability to fine-tune gene expression forms a cornerstone for the design and operation of genetic circuits. This optimization has not been fully carried out in non-traditional chasses like <i>L. Lactis</i>.
</p>
</div>
<div class="rightdiv">
</div>
</div>
<div class="container-description px-m-5 py-5">
<div class="background">
<p class="backgrounddata">
Synthetic biology envisions a bioengineering domain for designing new genetic parts and systems, or redesigning of existing ones. Until now, the most versatile workhorse of synthetic biology has been Escherichia coli. However, there is a need for exploring new chassis which can be naturally adapted to unique traits or metabolic pathways.
</p>
<p class="subtitles">Background</p>
</div>
</div>
</div>
<div class="container-description px-m-5 py-5">
<div class="project">
<p class="subtitles">Project</p>
<p class="projectdata">
<b>Our project is aimed at the construction and testing of a library of synthetic 5’ untranslated regions (UTR) containing ribosome binding sites (RBS) in <i>L. Lactis</i>.</b><br><br>
In addition to our lab work, we also plan to study the drawbacks of existing models and come up with potential improvements. This would include studying the effect of temperature on mRNA folding, the interaction between the mRNA and the ribosomal S1 protein, the difference in optimal RBS-AUG spacing in Gram-positive and Gram-negative bacteria, and the effect of RNAse-mediated degradation of the transcript. Combining the model with an optimisation algorithm, we aim to rationally design the ‘best’ RBS for a given gene, in a given organism.
</p>
</div>
<div class="rightdiv3">
</div>
</div>
{% endblock %}
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......@@ -28,12 +28,8 @@ standardized genetic parts and systems in this beneficial chassis.{% endblock %}
<div class="box">
<p><br><br><br></p>
</div>
<div class="arrow">
<!-- <p>.</p> -->
<br>
</div>
<div class="arrow"></div>
<div class="arr">
<br><br>
<div class="line"></div>
<div class="point"></div>
</div>
......@@ -57,12 +53,8 @@ standardized genetic parts and systems in this beneficial chassis.{% endblock %}
<div class="box1">
<p><br><br><br></p>
</div>
<div class="arrow1">
<!-- <p>.</p> -->
<br>
</div>
<div class="arrow1"></div>
<div class="arr1">
<br><br>
<div class="line3"></div>
<div class="line1"></div>
<div class="line2"></div>
......@@ -102,8 +94,5 @@ standardized genetic parts and systems in this beneficial chassis.{% endblock %}
<div class="container">
<iframe></iframe>
</div>
<div class="container">
<div class="sponsors"></div>
</div>
{% endblock %}
\ No newline at end of file
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{% extends "layout.html" %}
{% block title %}Software{% endblock %}
{% block lead %}Software in iGEM should make synthetic biology based on standard parts easier, faster, better or more accessible to our community.{% endblock %}
{% block lead %}Software in iGEM should make synthetic biology based on standard parts easier, faster, better or more
accessible to our community.{% endblock %}
{% block page_content %}
<div class="row mt-4">
<div class="col">
<div class="bd-callout bd-callout-info">
<h4>Best Software Tool</h4>
<p>Regardless what's the topic, iGEM projects often create or adapt computational tools to move the bigger project forward. Because they are born out of a direct practical need, these software tools (or new computational methods) can even prove surprisingly useful for others. Without necessarily being big or complex, they can make the crucial difference to a project's success. This award tries to find and honor such "nuggets" of computational work. To be eligible, your software has to be documented and made available under an OSI-approved open source license. Teams nominating themselves for this prize must host the source code of their software on the dedicated repository on iGEM's GitLab.</p>
<p>To compete for the Best Software Tool prize, please describe your work on this page and also fill out the description on the <a href="https://competition.igem.org/deliverables/judging-form">judging form</a>.</p>
<hr>
<p>Please see the <a href="https://competition.igem.org/judging/awards">2023 Awards Page</a> for more information.</p>
</div>
</div>
<br>
<div class="model-subheading">
<h1>Software</h1>
</div>
<div class="row mt-4">
<div class="col">
<h2>Inspirations</h2>
<hr>
<ul>
<li><a href="https://2019.igem.org/Team:Sydney_Australia/Software">2019 Sydney Australia</a></li>
<li><a href="https://2019.igem.org/Team:SMMU-China/Software">2019 SMMU China</a></li>
<li><a href="https://2019.igem.org/Team:Grenoble-Alpes/Software">2019 Grenoble Alpes</a></li>
<li><a href="https://2020.igem.org/Team:DTU-Denmark/Software">2020 DTU Denmark</a></li>
<li><a href="https://2020.igem.org/Team:GunnVistaPingry_US/Software">2020 GunnVistaPingry US</a></li>
<li><a href="https://2020.igem.org/Team:Rochester/Software">2020 Rochester</a></li>
</ul>
</div>
<div class="Content">
<p>
We have developed a user-friendly website featuring a publicly accessible web tool that serves as the interface for
our dry-lab model and optimizer. Upon accessing the website, users are presented with a choice between two distinct
tools: the RBS Rate Prediction Tool and the RBS Optimization Tool.
<br><br>
The RBS Rate Prediction Tool accepts the following input parameters: RBS Sequence, Coding Sequence, Temperature,
Gram Stain of Chassis, 16S rRNA Sequence. It subsequently provides the relative expression level in terms of the RBS
rate, represented on a logarithmic scale.
<br><br>
On the other hand, the RBS Optimization Tool also receives the following inputs: RBS Sequence, Coding Sequence,
Target Relative Expression (expressed in terms of the RBS rate on a logarithmic scale), Temperature, Gram Stain of
Chassis, and 16S rRNA Sequence. This tool then furnishes the optimized RBS sequence along with its corresponding
predicted (logarithmically scaled) RBS rate.
<br><br>
<a href="https://synthopedia.igemiitm.in/myapp/">https://synthopedia.igemiitm.in/myapp/</a>
</p>
</div>
{% endblock %}
{% endblock %}
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