Team:SCUT/Model/Overview

From 2014.igem.org

(Difference between revisions)

Latest revision as of 15:05, 26 November 2014

Background

Carbon dioxide fixed part

n-butanol part

Introduction

Individual part

Complete Network

The function of Rubisco

Scaffold

Reference

Introduction

Simulation

Reference

Outline

Reference

Background

The design and redesign is one of the hallmarks of synthesis biology. In order to test the consistence of the pathway we designed and the function of scaffold we used, modeling is the most powerful tool to be used before doing experiments.

Carbon dioxide fixed part

For the carbon dioxide fixed part, we use ODEs (ordinary differential equations) to simulate the pathway and proof the function of RuBisCo. With the help of parameter sweep, we find out the optimal reaction rate ratio of the reactions involved in the scaffold. By the way ,we also use the“bottom-up” strategy, the most famous principle of Computer Science, to guide our work.

n-butanol part

For the n-butanol part, in order to simulate the n-butanol biosynthetic pathway in Saccharomyces cerevisiae mitochondria, we construct a model by using Michealis-Menton kinetics and ODEs (ordinary differential equations). The model shows that, with high concentrations of NADH and NADPH in mitochondria, the production of n-butanol will be greatly improved.

Besides, all of our programs run on the MATLAB.

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-body{height:1400px;text-align:center;}
+body{height:1520px;text-align:center;}
 #overview{position:absolute;height:auto;width:100%;top:300px;left:0px;}
+.mainbody1{height:390px;}
+#over_right{float:right;margin:35px;margin-top:0px;}
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@@ Line 18: / Line 21: @@
 <div class="navibody navibody1" id="show">
 <p onclick="scroll_1()">Background</p>
-<p onclick="scroll_2()">Rubisco simulation</p>
+<p onclick="scroll_2()">Carbon dioxide fixed part</p>
-<p onclick="scroll_3()">N-butanol simulation</p>
+<p onclick="scroll_3()">n-butanol part</p>
 </div>
-<div class="navihead navihead2"><a href="https://2014.igem.org/Team:SCUT/Model/Rubisco_simulation"><img src="https://static.igem.org/mediawiki/2014/0/0c/2-01.png"></a>
+<div class="navihead navihead2"><a href="https://2014.igem.org/Team:SCUT/Model/Rubisco_simulation"><img src="https://static.igem.org/mediawiki/2014/c/c6/Model2-01.png"></a>
 </div>
 <div class="navibody navibody2">
+<p>Introduction</p>
 <p>Individual part</p>
-<p>Combine part</p>
+<p>Complete Network</p>
 <p>The function of Rubisco</p>
 <p>Scaffold</p>
+<p>Reference</p>
 </div>
 <div class="navihead navihead3">
-<a href="https://2014.igem.org/Team:SCUT/Model/N-butanol_simulation"><img src="https://static.igem.org/mediawiki/2014/1/16/3-01.png"></a>
+<a href="https://2014.igem.org/Team:SCUT/Model/N-butanol_simulation"><img src="https://static.igem.org/mediawiki/2014/d/d2/Model3-01.png"></a>
 </div>
 <div class="navibody navibody3">
-<p>Background</p>
+<p>Introduction</p>
-<p>Rubisco simulation</p>
+<p>Simulation</p>
-<p>N-butanol simulation</p>
+<p>Reference</p>
-</div>
-<div class="navihead navihead4">
-<img src="https://static.igem.org/mediawiki/2014/a/ab/4-01.png">
-</div>
-<div class="navibody navibody4">
-<p>Background</p>
-<p>Rubisco simulation</p>
-<p>N-butanol simulation</p>
 </div>
 <div class="navihead navihead5">
-<a href="https://2014.igem.org/Team:SCUT/Model/Tips_for_other_teams"><img src="https://static.igem.org/mediawiki/2014/7/7f/5-01.png"></a>
+<a href="https://2014.igem.org/Team:SCUT/Model/Tips_for_other_teams"><img src="https://static.igem.org/mediawiki/2014/a/af/Model4-01.png"></a>
 </div>
 <div class="navibody navibody5">
-<p>Background</p>
+<p>Outline</p>
-<p>Rubisco simulation</p>
+<p>Reference</p>
-<p>N-butanol simulation</p>
 </div>
 </div>
@@ Line 63: / Line 59: @@
 <span>Background</span>
 </p>
-<p class="first">
+<p>
-The design and redesign is one of the hallmarks of synthesis biology. In order to test the consistence of the pathway we designed and the function of scaffold we used, modeling is the most powerful tool to be used before doing experiments.
+<img src="https://static.igem.org/mediawiki/2014/8/83/Model-outline.PNG" id="over_right">
+The design and redesign is one of the hallmarks of synthesis biology. In order to test the consistence of the pathway we designed and the function of scaffold we used, modeling is the most powerful tool to be used before doing experiments.<br/>
 </p>
 </div>
 <div class="mainbody" id="label_2">
 <p class="atop">
-<span>Rubisco part</span>
+<span>Carbon dioxide fixed part</span>
 </p>
 <p>
-For the Rubisco part, we use<span> ODEs (ordinary differential equations)</span> to <span>simulate the pathway</span> and proof <span>the function of Rubisco</span>. With the help of <span>parameter sweep</span>, we find out the <span>optimal reaction rate ratio</span> of the reactions involved in the scaffold. By the way ,we also use <span>the“bottom-up” strategy</span>, the most famous principle of Computer Science, to guide our work.
+For the  carbon dioxide fixed part, we use<span> ODEs (ordinary differential equations)</span> to <span>simulate the pathway</span> and proof <span>the function of RuBisCo</span>. With the help of <span>parameter sweep</span>, we find out the <span>optimal reaction rate ratio</span> of the reactions involved in the scaffold. By the way ,we also use <span>the“bottom-up” strategy</span>, the most famous principle of Computer Science, to guide our work.
 </p>
 </div>
 <div class="mainbody" id="label_3">
 <p class="atop">
-<span>N-butanol part</span>
+<span>n-butanol part</span>
 </p>
 <p>
-For the N-butanol part, in order to simulate the n-butanol biosynthetic pathway in Saccharomyces cerevisiae mitochondria, we construct a model by using <span>Michealis-Menton kinetics</span> and <span>ODEs (ordinary differential equations)</span>. The model shows that, with high concentrations of NADH and NADPH in mitochondria, the production of n-butanol will be greatly improved.
+For the n-butanol part, in order to simulate the n-butanol biosynthetic pathway in Saccharomyces cerevisiae mitochondria, we construct a model by using <span>Michealis-Menton kinetics</span> and <span>ODEs (ordinary differential equations)</span>. The model shows that, with high concentrations of NADH and NADPH in mitochondria, the production of n-butanol will be greatly improved.
 </p>
 <p>