Difference between revisions of "Team:Dundee/Modeling"

 
(44 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 
<html>
 
<html>
−
<style>container { text-align:center; min-width:80%; }
+
 
−
#pagebox { text-align:left; width:80%; margin-left:auto; margin-right:auto; }</style><!-- This style command adds margins to the page so that the content is all centred and easy to read. -->
+
  
 
<script>
 
<script>
Line 34: Line 33:
  
  
−
     <header>
+
     <header id="header-modelling">
 
     <a class="anchor" id="top"></a><!--This sets an anchor so that internal links can later be used to scroll back to this section quickly using #top reference.-->
 
     <a class="anchor" id="top"></a><!--This sets an anchor so that internal links can later be used to scroll back to this section quickly using #top reference.-->
 
         <center>
 
         <center>
 
             <h1><highlight class="highlight">Dry Lab</highlight></h1>
 
             <h1><highlight class="highlight">Dry Lab</highlight></h1>
 +
<br>
 
             <h3><highlight class="highlight">Introduction</highlight></h3>
 
             <h3><highlight class="highlight">Introduction</highlight></h3>
 
         </center>
 
         </center>
 +
 
       </header><!--The header(h1) and subheader(h3) is set with this command.-->
 
       </header><!--The header(h1) and subheader(h3) is set with this command.-->
−
<div id="pagebox"><!--This sets where the margined part of the pages is started.-->
+
<div class="container"><!--This sets where the margined part of the pages is started.-->
  
−
<font size="5" color="white"><!--The font size is set as 4 throughout and colour is white.-->
+
<font color="white"><!--The font size is set as 4 throughout and colour is white.-->
 
<a class="anchor" id="overview"></a><!--This sets an anchor so that internal links can later be used to scroll back to this section quickly using #overview reference.-->
 
<a class="anchor" id="overview"></a><!--This sets an anchor so that internal links can later be used to scroll back to this section quickly using #overview reference.-->
 
     <section id="overview"><!--Set the section name as overview.-->
 
     <section id="overview"><!--Set the section name as overview.-->
Line 49: Line 50:
 
         <div class="row"><!--set class as defined in the style.css file.-->
 
         <div class="row"><!--set class as defined in the style.css file.-->
 
          
 
          
−
           <div class="col-md-12 feature"  style=""><!--set class as defined in the style.css file.-->
+
           <div class="col-md-6 feature"  style=""><!--set class as defined in the style.css file.-->
 
             <div class="row"><!--set class as defined in the style.css file.-->
 
             <div class="row"><!--set class as defined in the style.css file.-->
 
                  
 
                  
−
               <h2><b>Introduction</b></h2><!--Set Introduction as a heading for the section.--><br><!--Adds a line break-->  <p><!--The p tag starts a new paragraph.-->In our project three approaches were taken within the dry lab; data analysis using PCA, modeling using ordinary differential equations (ODEs) and practical physics experiments. Mathematical modeling can be used within synthetic biology to reduce complex biological systems to their key components, allowing for a quantitative understanding of the reactions occurring. Models can then be considered in the lab to allow for optimisation of the techniques to produce the best end result.  ODEs were used to model the change in concentration of substances over time, this was implemented within all aspects of the project; the BioSpray, fingerprint aging and chromate detection.</p><!--End the paragraph.-->
+
               <h2><b>Introduction</b></h2><!--Set Introduction as a heading for the section.--><br><!--Adds a line break-->  <p><!--The p tag starts a new paragraph.-->In our project three approaches were taken within the dry lab; data analysis using principal component analysis (PCA), modelling using ordinary differential equations (ODEs) and practical physics experiments. Mathematical modelling can be used within synthetic biology to reduce complex biological systems to their key components, allowing for a quantitative understanding of the reactions occurring. Models can then be considered in the lab to allow for optimisation of the techniques to produce the best end result.  ODEs were used to model the change in concentration of substances over time, this was implemented within all aspects of the project; FluID, fingerprint ageing and the Chromate Biosensor.</p><!--End the paragraph.-->
 
<br><!--Adds a line break-->  
 
<br><!--Adds a line break-->  
−
<p> PCA is a statistical procedure whereby a dataset with many dimensions is simplified to its principal components in order to visualise hidden correlations. PCA was used to analyse the composition of fingerprints for the fingerprint aging. Physics experiments were used to investigate the incisions on bones by stainless steel knifes to complement the chromium biosensor part of the toolkit. </p>
+
<p> PCA is a statistical procedure whereby a dataset with many dimensions is simplified to its principal components in order to visualise hidden correlations. PCA was used to analyse the composition of fingerprints for the fingerprint ageing. Physics experiments were used to investigate the incisions on bones by stainless steel knives to complement the chromium biosensor part of the toolkit. </p>
 
<br><!--Adds a line break-->
 
<br><!--Adds a line break-->
−
<p>Click on the sections below to find out more about each part described. The development of software, such as MATLAB, has allowed for greater use of mathematical models across the whole of Synthetic Biology. MATLAB was used in all aspects of the dry lab work, all code used can be found in our appendix via links at the bottom of each section.</p>
+
<p> The development of software, such as MATLAB, has allowed for greater use of mathematical models across the whole of synthetic biology. MATLAB was used in all aspects of the dry lab work, all code used can be found in our appendix via links at the bottom of each section. Click on the buttons below to find out more about each section described.</p>
 
               </div><!--End the div class setting.-->   
 
               </div><!--End the div class setting.-->   
 
      
 
      
 
               </div><!--End the div class setting.-->  
 
               </div><!--End the div class setting.-->  
 +
<div class="col-md-6 feature"  style=""><!--set class as defined in the style.css file.-->
 +
            <div class="row">
 +
<br>
 +
 +
<center>
 +
<img src="https://static.igem.org/mediawiki/2015/b/b8/TeamDundee_keyboard_tiny2.png" width="90%" height="auto"/>
 +
<br>
 +
<br>
 +
<img src="https://static.igem.org/mediawiki/2015/f/fb/TeamDundee-Chrom-tiny2.png" width="90%" height="auto"/>
 +
</center>
 
             </div><!--End the div class setting.-->  
 
             </div><!--End the div class setting.-->  
 
              
 
              
Line 72: Line 83:
 
       <div class="row">
 
       <div class="row">
 
         <div class="col-lg-4">
 
         <div class="col-lg-4">
−
           <a href="https://2015.igem.org/Team:Dundee/Modeling/Biospray"> <span class="glyphicon glyphicon-tint" type="button"></span></a> <!--This button contains a link to the BioSpray models page.-->
+
           <a href="https://2015.igem.org/Team:Dundee/Modeling/FluID"> <span class="glyphicon glyphicon-tint" type="button"></span></a> <!--This button contains a link to the FluID models page.-->
−
           <h3>BioSpray</h3>
+
           <h3>FluID</h3>
−
           <p class="about-content">Find out more about the modeling for each of the components of the BioSpray.</p><!--This is the text displayed underneath the button.-->
+
           <p class="about-content">Find out more about the modelling for each of the components of FluID.</p><!--This is the text displayed underneath the button.-->
 
         </div>
 
         </div>
 
         <div class="col-lg-4">
 
         <div class="col-lg-4">
 
           <a href="https://2015.igem.org/Team:Dundee/Modeling/Fingerprints"><span class="glyphicon glyphicon-hand-down" type="button"></span></a><!--This button contains a link to the Fingerprints models page.-->
 
           <a href="https://2015.igem.org/Team:Dundee/Modeling/Fingerprints"><span class="glyphicon glyphicon-hand-down" type="button"></span></a><!--This button contains a link to the Fingerprints models page.-->
−
           <h3>Fingerprint Aging</h3>
+
           <h3>Fingerprint Ageing</h3>
−
           <p class="about-content">Find out more about principal component analysis and modeling of fingerprint aging.</p><!--This is the text displayed underneath the button.-->
+
           <p class="about-content">Find out more about principal component analysis (PCA) and modelling of fingerprint ageing.</p><!--This is the text displayed underneath the button.-->
 
         </div>
 
         </div>
 
         <div class="col-lg-4">
 
         <div class="col-lg-4">
 
           <a href="https://2015.igem.org/Team:Dundee/Modeling/Chromate"><span class="glyphicon glyphicon-pushpin" type="button"></span></a> <!--This button contains a link to the Chromate models page.-->
 
           <a href="https://2015.igem.org/Team:Dundee/Modeling/Chromate"><span class="glyphicon glyphicon-pushpin" type="button"></span></a> <!--This button contains a link to the Chromate models page.-->
−
           <h3>Chromate Sensor</h3>
+
           <h3>Chromate Biosensor</h3>
−
           <p class="about-content">Find out more about modeling of chromate and bone incision experiments.</p><!--This is the text displayed underneath the button.-->
+
           <p class="about-content">Find out more about modelling of chromate and bone incision experiments.</p><!--This is the text displayed underneath the button.-->
 
         </div>
 
         </div>
  

Latest revision as of 22:21, 18 September 2015

Dry Lab


Introduction

Introduction


In our project three approaches were taken within the dry lab; data analysis using principal component analysis (PCA), modelling using ordinary differential equations (ODEs) and practical physics experiments. Mathematical modelling can be used within synthetic biology to reduce complex biological systems to their key components, allowing for a quantitative understanding of the reactions occurring. Models can then be considered in the lab to allow for optimisation of the techniques to produce the best end result. ODEs were used to model the change in concentration of substances over time, this was implemented within all aspects of the project; FluID, fingerprint ageing and the Chromate Biosensor.


PCA is a statistical procedure whereby a dataset with many dimensions is simplified to its principal components in order to visualise hidden correlations. PCA was used to analyse the composition of fingerprints for the fingerprint ageing. Physics experiments were used to investigate the incisions on bones by stainless steel knives to complement the chromium biosensor part of the toolkit.


The development of software, such as MATLAB, has allowed for greater use of mathematical models across the whole of synthetic biology. MATLAB was used in all aspects of the dry lab work, all code used can be found in our appendix via links at the bottom of each section. Click on the buttons below to find out more about each section described.




FluID

Find out more about the modelling for each of the components of FluID.

Fingerprint Ageing

Find out more about principal component analysis (PCA) and modelling of fingerprint ageing.

Chromate Biosensor

Find out more about modelling of chromate and bone incision experiments.