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wiki/pages/contribution.html
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{% extends "layout.html" %}
{% block title %}CONTRIBUTION{% endblock %}
{% block lead %}OUR POTENTIAL CONTRIBUTION TO THE FUTURE{% endblock %}
{% block page_content %}
<head>
</head>
<body>
<div class="row mt-4">
@@ -16,26 +18,13 @@
<h5>Overview</h5>
<ul class="nav flex-column"> <!--YOU CAN ADD MORE OVERVIEW LINKS HERE, SIMPLY DUPLICATE AN UNORDERED LIST-->
<li class="nav-item">
<a class="nav-link" href="#EDIT-ID">EDIT OVERVIEW TEXT</a>
<ul class="nav flex-column ml-3">
<li class="nav-item">
<a class="nav-link" href="#EDIT-ID-1">EDIT SUBHEADING 1</a>
<ul class="nav flex-column ml-3">
<li class="nav-item">
<a class="nav-link" href="#cool">EDIT SUB SUBHEADING 1</a>
</li>
<li class="nav-item">
<a class="nav-link" href="#cool2">EDIT SUB SUB HEADING 2</a>
</li>
</ul>
</li>
<li class="nav-item">
<a class="nav-link" href="#EDIT-ID-2">EDIT SUBHEADING 2</a>
</li>
<li class="nav-item">
<a class="nav-link" href="#Vcell">Vcell Contributions</a>
</li>
</ul>
<a class="nav-link" href="#parts">Parts Contribution</a>
</li>
<li class="nav-item">
<a class="nav-link" href="#md">MD Contribution</a>
</li>
<li class="nav-item">
<a class="nav-link" href="#Vcell">Vcell Contribution</a>
</li>
</ul>
</div>
@@ -43,298 +32,92 @@
<div class="col-lg-9">
<div id="EDIT-ID" class="mt-4">
<h2>EDIT HEADER</h2>
<p>EDIT TEXT</p>
<div id="parts" class="mt-4">
<h2>Parts</h2>
<hr>
<div id="EDIT-ID-1">
<h3>EDIT SUBHEADING</h3>
<p>EDIT TEXT</p>
</div>
<div id="parts">
<h4>EDIT SUB SUBHEADING</h4>
<p>EDIT TEXT</p>
</div>
<div id="parts">
<h4>Parts</h4>
<table>
<tr>
<th>Part link</th>
<th>Description</th>
</tr>
<tr>
<td>https://parts.igem.org/Part:BBa_K5114823</td>
<td>Device encoding superfolder GFP under prmA. After transforming into E. coli and not observing fluorescence, it is our hypothesis that the prmA promoter does not work in E. coli, likely due to lack of transcriptional machinery specific to Rhodococcus jostii.</td>
</tr>
<tr>
<td>https://parts.igem.org/Part:BBa_K5114227</td>
<td>Coding sequence for human liver fatty acid binding protein conjugated with circularly permuted GFP (hlFAB-GFP or FAB-GFP).</td>
</tr>
<tr>
<td>https://parts.igem.org/Part:BBa_K5114228</td>
<td>Expression Device for hlFAB-GFP</td>
</tr>
<tr>
<td>TBD</td>
<td>Coding sequence for a synthetic, estradiol-induced transcription factor that binds to the LexA operator DNA region. </td>
</tr>
<tr>
<td>TBD</td>
<td>Expression device for the synthetic transcription factor</td>
</tr>
<tr>
<td>TBD</td>
<td>GFP with RBS and Terminator under control of synthetic promoter bound by the synthetic transcription factor</td>
</tr>
</table>
</div>
<div id="MD">
<h3>Molecular Dynamics</h5>
<p>Using Amber, ChimeraX, and AutoDock Vina, we engineered and tested various mutations on hlFAB to enhance its lower detection limit. To streamline the calculation of the dissociation constant (Kd) using MMPBSA, we developed an automated pipeline. This pipeline outputs an Excel-compatible data file and a PDB file from the final simulation step, allowing for easy visualization of charge contributions. It integrates all critical steps of molecular dynamics simulation, including LEaP for system parameterization, a minimization step using steepest descent, a heating phase to bring the system to 300K, a density equilibration step to stabilize the system and allows for RMSD tracking, followed by equilibration, and finally, a 10-nanosecond production run, from which data for MMPBSA analysis is extracted. The pipeline also includes MMPBSA calculations, and a custom Python script that formats the raw output data into a user-friendly format. It is available in our team's software repository along with all prerequisite files. This pipeline is free to use and can assist teams in determining the effectiveness of ligand-receptor interactions. Additionally, it is fully customizable, making it adaptable for use with other ligands beyond PFOA.
<br>
Instructions to download and use the pipeline can be found on our wiki and our software tools repository:
https://gitlab.igem.org/2024/software-tools/gcm-ky
</p>
</div>
<table>
<tr>
<th>Part link</th>
<th>Description</th>
</tr>
<tr>
<td>https://parts.igem.org/Part:BBa_K5114823</td>
<td>Device encoding superfolder GFP under prmA. After transforming into E. coli and not observing
fluorescence, it is our hypothesis that the prmA promoter does not work in E. coli, likely due to lack of
transcriptional machinery specific to Rhodococcus jostii.</td>
</tr>
<tr>
<td>https://parts.igem.org/Part:BBa_K5114227</td>
<td>Coding sequence for human liver fatty acid binding protein conjugated with circularly permuted GFP
(hlFAB-GFP or FAB-GFP).</td>
</tr>
<tr>
<td>https://parts.igem.org/Part:BBa_K5114228</td>
<td>Expression Device for hlFAB-GFP</td>
</tr>
<tr>
<td>TBD</td>
<td>Coding sequence for a synthetic, estradiol-induced transcription factor that binds to the LexA operator
DNA region. </td>
</tr>
<tr>
<td>TBD</td>
<td>Expression device for the synthetic transcription factor</td>
</tr>
<tr>
<td>TBD</td>
<td>GFP with RBS and Terminator under control of synthetic promoter bound by the synthetic transcription
factor</td>
</tr>
</table>
</div>
<div id="MD" class="mt-4">
<h2>Molecular Dynamics</h2>
<hr>
<p>Using Amber, ChimeraX, and AutoDock Vina, we engineered and tested various mutations on hlFAB to enhance its
lower detection limit. To streamline the calculation of the dissociation constant (Kd) using MMPBSA, we
developed an automated pipeline. This pipeline outputs an Excel-compatible data file and a PDB file from the
final simulation step, allowing for easy visualization of charge contributions. It integrates all critical
steps of molecular dynamics simulation, including LEaP for system parameterization, a minimization step using
steepest descent, a heating phase to bring the system to 300K, a density equilibration step to stabilize the
system and allows for RMSD tracking, followed by equilibration, and finally, a 10-nanosecond production run,
from which data for MMPBSA analysis is extracted. The pipeline also includes MMPBSA calculations, and a custom
Python script that formats the raw output data into a user-friendly format. It is available in our team's
software repository along with all prerequisite files. This pipeline is free to use and can assist teams in
determining the effectiveness of ligand-receptor interactions. Additionally, it is fully customizable, making
it adaptable for use with other ligands beyond PFOA.</p>
<p><strong>Instructions to download and use the pipeline can be found on our wiki and our software tools
repository:</strong></p>
<a href="https://gitlab.igem.org/2024/software-tools/gcm-ky"
target="_blank">https://gitlab.igem.org/2024/software-tools/gcm-ky</a>
</div>
<div id="Vcell" class="mt-4">
<h2>Vcell Contribution</h2>
<hr>
<p>We have created a VCell BioModel that simulates our entire gene circuit. This model includes all components
for the pRMA_GFP, FAB_GFP, and the Synt_Tran factor construct, all extremely valuable systems in synthetic
biology that do not yet have a VCell model. With a few modifications, our model can be used to model different
types of genetic circuits involving the LuxR-LuxI gene regulatory system.</p>
<img src="https://static.igem.wiki/teams/5114/images-arjun/hefiefbiruebf.png" alt="Vcell_Contributions_Image">
<p>The models are hosted on VCell servers and are shared publicly in the “Uncurated” folder. They are completely
free to use and modify for anyone with VCell.</p>
<p>Our most up-to-date models can be found in a table on the experiments page. These models are free for anyone
to tinker with and use.
<div id="Vcell">
<hr>
<h3>Vcell Contribution</h3>
<p>We have created a VCell BioModel that simulates our entire gene circuit. This model includes all components for the pRMA_GFP, FAB_GFP, and the Synt_Tran factor construct, all extremely valuable systems in synthetic biology that do not yet have a VCell model. With a few modifications, our model can be used to model different types of genetic circuits involving the LuxR-LuxI gene regulatory system.</p>
<img src="https://static.igem.wiki/teams/5114/images-arjun/hefiefbiruebf.png" alt="Vcell_Contributions_Image">
<p>The models are hosted on VCell servers and are shared publicly in the “Uncurated” folder. They are completely free to use and modify for anyone with VCell.</p>
<p>Our most up-to-date models can be found in a table on the experiments page. These models are free for anyone to tinker with and use.
Additionally, with the help of the VCell support team, we debugged VCell’s ability to export and import simulation data. This allows future users to pick up where they left off on previous simulations.
A document that outlines how to do so is attached below:
</p>
<div id="Tutorial_to_access_vcell_models">
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<body>
<h2 style="text-align:center">How to Access Our Vcell Models</h2>
<div class="container">
<div class="mySlides">
<div class="numbertext">1 / 9</div>
<img src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-114425.png" style="width:50%">
</div>
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<img src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-114725.png" style="width:50%">
</div>
<div class="mySlides">
<div class="numbertext">3 / 9</div>
<img src="https://static.igem.wiki/teams/5114/images-arjun/hefiefbiruebf.png" style="width:50%">
</div>
<div class="mySlides">
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<img src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-115146.png" style="width:50%">
</div>
<div class="mySlides">
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<img src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-115341.png" style="width:50%">
</div>
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<img src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-115555.png" style="width:50%">
</div>
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<img src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-115736.png" style="width:50%">
</div>
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<img src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-115856.png" style="width:50%">
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<img src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-120005.png" style="width:50%">
</div>
<a class="prev" onclick="plusSlides(-1)">❮</a>
<a class="next" onclick="plusSlides(1)">❯</a>
<div class="caption-container">
<p id="caption"></p>
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<div class="row">
<div class="column">
<img class="demo cursor" src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-114425.png" style="width:50%" onclick="currentSlide(1)" alt="Go to vcell.org and download the latest version of Vcell that is compatible with your device">
</div>
<div class="column">
<img class="demo cursor" src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-114725.png" style="width:50%" onclick="currentSlide(2)" alt="Once you download Vcell and signed in go to the bottom left hand box and click the plus sign, and input the username of the creator of the biomodel you wish to see">
</div>
<div class="column">
<img class="demo cursor" src="https://static.igem.wiki/teams/5114/images-arjun/hefiefbiruebf.png" style="width:50%" onclick="currentSlide(3)" alt="After putting in the username click on the Uncurated folder near the bottom on the box">
</div>
<div class="column">
<img class="demo cursor" src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-115146.png" style="width:50%" onclick="currentSlide(4)" alt="Click on the folder with the same username as the one you searched for & then click the biomodel you wish to see">
</div>
<div class="column">
<img class="demo cursor" src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-115341.png" style="width:50%" onclick="currentSlide(5)" alt="You can now look at the reaction diagram and simulation results but if you wish to have a copy of this biomodel you need to click on file(top left) and then click save as">
</div>
<div class="column">
<img class="demo cursor" src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-115555.png" style="width:50%" onclick="currentSlide(6)" alt="A window will then pop up and simply input the name you wish to call the biomodel in the text bar near the bottom and then click save">
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<div class="column">
<img class="demo cursor" src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-115736.png" style="width:50%" onclick="currentSlide(7)" alt="If you wish to see simulation data click on application(shown in image) and then click on simulation. ">
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<div class="column">
<img class="demo cursor" src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-115856.png" style="width:50%" onclick="currentSlide(8)" alt="To access to data you need to click on the simulation you wish to see the data for and the click the graph icon on the top right">
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<div class="column">
<img class="demo cursor" src="https://static.igem.wiki/teams/5114/images-arjun/2/screenshot-2024-09-29-120005.png" style="width:50%" onclick="currentSlide(9)" alt="Finally if you wish to see the data in a table format click on the table icon near the bottom right(shown in image)">
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<p> </p>
<p> </p>
<p>Our most up-to-date models can be found in a table on the experiments page. These models are free for anyone to tinker with and use.</p>
</div>
<hr>
</div>
Additionally, with the help of the VCell support team, we debugged VCell’s ability to export and import
simulation data. This allows future users to pick up where they left off on previous simulations.
A document that outlines how to do so is attached below:
</p>
<hr>
<p>Our most up-to-date models can be found in a table on the experiments page. These models are free for anyone
to tinker with and use.</p>
</div>
</div>
</div>
</body>
{% endblock %}
{% endblock %}
\ No newline at end of file