Difference between revisions of "Team:Washington/Modeling"

(Prototype team page)
 
 
(29 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 
{{Washington}}
 
{{Washington}}
 +
 
<html>
 
<html>
 +
    <div id="menuContainer">
 +
        <!-- This list is your menu, every list item is a menu button and nested listed become submenu buttons -->
 +
        <ul>
 +
            <a href="https://2015.igem.org/Team:Washington">
 +
                <li>Home
 +
                  <ul>
 +
                    <li><a href="https://2014.igem.org/Team:Washington">UW 2014</a></li>
 +
                    <li><a href="https://2013.igem.org/Team:Washington">UW 2013</a></li>
 +
                    <li><a href="https://2012.igem.org/Team:Washington">UW 2012</a></li>
 +
                    <li><a href="https://2011.igem.org/Team:Washington">UW 2011</a></li>
 +
                    <li><a href="https://2010.igem.org/Team:Washington">UW 2010</a></li>
 +
                    <li><a href="https://2009.igem.org/Team:Washington">UW 2009</a></li>
 +
                    <li><a href="https://2008.igem.org/Team:University_of_Washington">UW 2008</a></li>
 +
                    <li><a href="https://2013.igem.org/Main_Page">iGEM Homepage</a></li>
 +
                  </ul>
 +
</li>
 +
            </a>
 +
            <a href="https://2015.igem.org/Team:Washington/Auxin">
 +
                <li>Auxin
 +
                        <ul>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Washington/Auxin#Introduction">Introduction</a>
 +
                            </li>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Washington/Auxin#Methods">Methods</a>
 +
                            </li>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Washington/Auxin#Results">Results</a>
 +
                            </li>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Washington/Auxin#Conclusion">Conclusion</a>
 +
                            </li>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Washington/Auxin#Future_Direction">Future Direction</a>
 +
                            </li>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Washington/Parts#Auxin">Biobrick</a>
 +
                            </li>
 +
                        </ul>
 +
                </li>
 +
            </a>
 +
            <a href="https://2015.igem.org/Team:Washington/Aptazyme">
 +
                <li>Aptazyme                             
 +
                    <ul>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Washington/Aptazyme#Introduction">Introduction</a>
 +
                            </li>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Washington/Aptazyme#Methods">Methods</a>
 +
                            </li>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Washington/Aptazyme#Results">Results</a>
 +
                            </li>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Washington/Aptazyme#Conclusion">Conclusion</a>
 +
                            </li>
 +
                            <li>
 +
                                <a href=https://2015.igem.org/Team:Washington/Parts#Aptazyme">Biobrick</a>
 +
                            </li>
 +
                    </ul>
 +
                </li>
 +
            </a>
 +
            <a href="https://2015.igem.org/Team:Washington/Paper_Device">
 +
                <li>Paper Device             
 +
                    <ul>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:Washington/Paper_Device#Introduction">Introduction</a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:Washington/Paper_Device#Methods">Methods</a>
 +
                        </li>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Washington/Design">Design</a>
 +
                            </li>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Washington/Paper_Device#Results">Results</a>
 +
                            </li>
 +
                            <li>
 +
                                <a href="https://2015.igem.org/Team:Washington/Paper_Device#Conclusion">Conclusion</a>
 +
                            </li>
 +
                    </ul>
 +
                </li>
 +
            </a>
 +
            <a href="https://2015.igem.org/Team:Washington/Modeling">
 +
                <li>Modeling             
 +
                  <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
 +
                    <ul class="nav navbar-nav">
 +
                            <li>
 +
                                <a href="#" class="scroll-link" data-id="Paper_Device">Paper Device</a>
 +
                            </li>
  
−
<h2> Modeling</h2>
+
                            <li>
 +
                                <a href="#" class="scroll-link" data-id="Aptazyme">Aptazyme</a>
 +
                            </li>
 +
                    </ul>
 +
</div>
 +
                </li>
 +
            </a>
 +
            <a href="https://2015.igem.org/Team:Washington/Practices">
 +
                <li>Human Practices             
 +
                    <ul>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:Washington/Practices#Outreach">Outreach</a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:Washington/Practices#Integrated">Integrated</a>
 +
                        </li>
 +
                    </ul>
 +
                </li>
 +
            </a>
 +
            <a href="https://2015.igem.org/Team:Washington/Protocols">
 +
                <li>Protocols
 +
                    <ul>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:Washington/Protocols#Experiments">Experiments</a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:Washington/Protocols#Safety">Safety</a>
 +
                        </li>
 +
                    </ul>
 +
                </li>
 +
            </a>
 +
            <a href="https://2015.igem.org/Team:Washington/Team">
 +
                <li>Team                       
 +
                    <ul>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:Washington/Team#Members">Members</a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:Washington/Attributions">Attributions</a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:Washington/Team#Sponsors">Sponsors</a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:Washington/Team#Judging_Form">Judging Form</a>
 +
                        </li>
 +
                    </ul>
 +
                </li>
 +
            </a>
 +
        </ul>
 +
    </div>
 +
    <!-- End of menu  -->
 +
    <!-- Start of content -->
  
 +
    <div id="main">
 +
        <div class="container clearfix">
 +
            <div id="sidebar">
 +
                <div id="nav-anchor"></div>
 +
                <nav>
 +
                    <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
 +
                        <ul class="nav navbar-nav" style="list-style-type: none;">
 +
                            <li>
 +
                                <a href="#" class="scroll-link" data-id="Paper_Device">Paper Device</a>
 +
                            </li>
 +
                            <li>
 +
                                <a href="#" class="scroll-link" data-id="Aptazyme">Aptazyme</a>
 +
                            </li>
 +
                            <li>
 +
                                <a href="#" class="scroll-link" data-id="nav-anchor">Top</a>
 +
                            </li>
 +
                        </ul>
 +
                    </div>
 +
                </nav>
 +
            </div>
 +
<div id="contentContainer">
  
−
<div class="highlightBox">
+
<h2> Modeling </h2>
−
<h4>Note</h4>
+
 
−
<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best Model award</a>, you must fill out this page.</p>
+
<p> In our project we developed a novel paper microfluidic device for accomodating two biological detection systems. Both for the paper device and the apatazyme detection system, we constructed computational models to provide a theoretical framework for our experimental findings.</p>
 +
 
 +
<h2 id="Paper_Device"> Paper Device </h2>
 +
 
 +
<p> To model the functionality of the paper device, we developed a spatial model for fluid forces on a strip of paper and implemented it in COMSOL. The model simulates the material properties of the paper used in our experiments – represented by a rectangular prism – while submerged in fluid. We were able to calculate the magnitude of the fluid forces on the paper over time, which allowed insights on the influence of fluid forces on the device’s structural integrity. </p>
 +
 
 +
<div style="width: 500px; margin-left: auto; margin-right: auto;">
 +
<img src="https://static.igem.org/mediawiki/2015/a/a5/Modeling_paper.png" width="500" height="400" style="align:center;">
 
</div>
 
</div>
  
 +
<h2 id="Aptazyme"> Aptazyme </h2>
  
−
<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
+
<p> For the aptamer system, we constructed a time-dependent ODE model for protein expression resulting from an aptazyme-based genetic pathway (1). It describes the level of protein expression over time as a function of various system parameters, including transcription, aptazyme folding and cleavage, translation and degradation of RNA fragments and proteins. </p>
  
−
<p>
+
<div style=" width: 400px; margin-left: auto; margin-right: auto;">
−
Here are a few examples from previous teams:
+
<img src="https://static.igem.org/mediawiki/2015/c/c7/Modeling_aptazyme_pathway.jpeg" width="400" height="400" style="align:center;">
−
</p>
+
</div>
−
<ul>
+
<div style="margin-left: 420px">(Carothers 2011)</div>
−
<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
+
−
<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
+
−
</ul>
+
  
 +
<p> We implemented the model in Python using Tellurium (2) and theoretically predicted results for various conditions. A comparison with literature data indicated a good fit between the computational model and the experimental setting. </p>
  
 +
<div style="width: 600px; margin-left: auto; margin-right: auto;">
 +
<img src="https://static.igem.org/mediawiki/2015/f/f5/Modeling_aptazyme_results_new.jpeg" width="600" height="400" style="align:center;">
 
</div>
 
</div>
  
−
</html>
+
<p> The experimental ratio between the steady-state expression levels of the RED13 and RED6 plasmids is 1.21.  In our model, the ratio is 1.30.  The model accurately reproduces the experimentally determined relative levels of aptazyme activity. </p>
 +
 
 +
<h2> References </h2>
 +
<p>(1) Carothers JM et. al. (2011): Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression; Science, vol. 334(6063), pp. 1716-1719 </p>
 +
<p>(2) Tellurium. Python enviroment for Systems Biology developed and maintained at UW Seattle. (http://tellurium.analogmachine.org)</p>
 +
<br><br></br></br>
 +
           
 +
            </div>
 +
        </div>
 +
        <!--These are the closing tags for div id="mainContainer" and div id="contentContainer". The corresponding opening tags appear in the template that is {{included}} at the top of this page.-->
 +
    </html>

Latest revision as of 03:28, 19 September 2015



Modeling

In our project we developed a novel paper microfluidic device for accomodating two biological detection systems. Both for the paper device and the apatazyme detection system, we constructed computational models to provide a theoretical framework for our experimental findings.

Paper Device

To model the functionality of the paper device, we developed a spatial model for fluid forces on a strip of paper and implemented it in COMSOL. The model simulates the material properties of the paper used in our experiments – represented by a rectangular prism – while submerged in fluid. We were able to calculate the magnitude of the fluid forces on the paper over time, which allowed insights on the influence of fluid forces on the device’s structural integrity.

Aptazyme

For the aptamer system, we constructed a time-dependent ODE model for protein expression resulting from an aptazyme-based genetic pathway (1). It describes the level of protein expression over time as a function of various system parameters, including transcription, aptazyme folding and cleavage, translation and degradation of RNA fragments and proteins.

(Carothers 2011)

We implemented the model in Python using Tellurium (2) and theoretically predicted results for various conditions. A comparison with literature data indicated a good fit between the computational model and the experimental setting.

The experimental ratio between the steady-state expression levels of the RED13 and RED6 plasmids is 1.21. In our model, the ratio is 1.30. The model accurately reproduces the experimentally determined relative levels of aptazyme activity.

References

(1) Carothers JM et. al. (2011): Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression; Science, vol. 334(6063), pp. 1716-1719

(2) Tellurium. Python enviroment for Systems Biology developed and maintained at UW Seattle. (http://tellurium.analogmachine.org)