Difference between revisions of "Team:NUDT CHINA/Model/Overview"

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  <p style="font-size:36px;margin: 0 0%;padding: 8% 0 0 10%;color: white;">Development of A Novel</p>
 
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<p style="font-size:36px;margin: 0 0%;padding: 0 0 0 10%;color: white;">Blood-MicroRNA Handy Detection System with CRISPR</p></div>
 
  
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      <h1 style="font-size: 40px;font-weight: 900">Our Work</h1>
 
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                                      <h2 style="font-size: 32px;margin-bottom: 10px;margin-top: 15px;">Our Work</h2>
 
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<p alt="content_add" style="font-size: 18px;">hello everyone this is the another example-content part for more imformation. Hello everyone this is the another example-content part for more imformation.Donec id elit non mi porta gravida at eget metus. Fusce dapibus, tellus ac cursus commodo, tortor mauris condimentum nibh, ut fermentum massa justo sit amet risus. Etiam porta sem malesuada magna mollis euismod. Donec sed odio dui. </p>
 
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<p alt="content_add" style="font-size: 18px;">hello everyone this is the another example-content part for more imformation. Hello everyone this is the another example-content part for more imformation.Donec id elit non mi porta gravida at eget metus. Fusce dapibus, tellus ac cursus commodo, tortor mauris condimentum nibh, ut fermentum massa justo sit amet risus. Etiam porta sem malesuada magna mollis euismod. Donec sed odio dui. </p>
 
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<p alt="content_add" style="font-size: 18px;">hello everyone this is the another example-content part for more imformation. Hello everyone this is the another example-content part for more imformation.Donec id elit non mi porta gravida at eget metus. Fusce dapibus, tellus ac cursus commodo, tortor mauris condimentum nibh, ut fermentum massa justo sit amet risus. Etiam porta sem malesuada magna mollis euismod. Donec sed odio dui. </p>
 
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<p alt="content_add" style="font-size: 18px;">hello everyone this is the another example-content part for more imformation. Hello everyone this is the another example-content part for more imformation.Donec id elit non mi porta gravida at eget metus. Fusce dapibus, tellus ac cursus commodo, tortor mauris condimentum nibh, ut fermentum massa justo sit amet risus. Etiam porta sem malesuada magna mollis euismod. Donec sed odio dui. </p>
 
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Example block-level help text here.There are several variants of  derived from different organisms. In our project, we  . The structure of this protein has been determined with and without  The  a  lobe. The two lobes are positively charged towards the protein core to accommodate the negatively charged RNA. Each of these two lobes contains an RNase domain. At the  main is responsible for target cleavage. In contrast to other  two RNase domains of the NUC lobe are located at the outside of the protein, which is likely the reason collateral cleavage upon activation by binding to a matching target. These two domains have been labeled as red spots in Figure 2 and can be found at the interface between the green and pink domain.
 
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<h3>More details</h3>
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<a href="#model1"><img class="model1" src="https://static.igem.org/mediawiki/2016/c/c1/T--Manchester--modelling1_pic.png" alt="What were we modelling?"></img></a>
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<a class="panel-title collapsed " data-toggle="collapse" data-parent="#panel-1" href="#panel-element-1"  style="color: #079209; font-size: 20px;text-decoration:none;">Question 1: What does the structure of domains look like?</a>
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There are several variants of  derived from different organisms. In our project, we  . The structure of this protein has been determined with and without  The  a  lobe. The two lobes are positively charged towards the protein core to accommodate the negatively charged RNA. Each of these two lobes contains an RNase domain. At the  main is responsible for target cleavage. In contrast to other  two RNase domains of the NUC lobe are located at the outside of the protein, which is likely the reason collateral cleavage upon activation by binding to a matching target. These two domains have been labeled as red spots in Figure 2 and can be found at the interface between the green and pink domain.
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<a class="panel-title collapsed" data-toggle="collapse" data-parent="#panel-1" href="#panel-element-2" style="color: #079209; font-size: 20px;text-decoration:none;">Collapsible Group Item #2</a>
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<a href="#model2"><img class="model1" src="https://static.igem.org/mediawiki/2016/a/a3/T--Manchester--modelling2_pic.png" alt="What is esemble modelling?"></img></a>
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<a href="#model3"><img class="model1" src="https://static.igem.org/mediawiki/2016/4/46/T--Manchester--modelling3_pic.png" alt="What does our modelling achieve?"></img></a>
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<p style="border-bottom: 1px black solid ;font-size:25px;text-weight:bold;display:inline-block">What did our model achieve?</p>
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<p style="font-size:1.2em;">
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We achieved 3 main aims in our modelling work:
 +
 +
 +
</br> We introduced a novel <a href="https://2016.igem.org/Team:Manchester/Model/ModelExplorer">ensemble modelling</a> approach to iGEM and made this approach accessible to other iGEM teams by sharing <a target="_Blank" href="https://github.com/Manchester-iGem-2016/Ensemble-Modelling">our code.</a>
 +
<br />
 +
We improved our understanding of our system and used real experimental data to improve our model, using <a href="https://2016.igem.org/Team:Manchester/Model/MechanismUncertainty">network mechanism analysis </a> and <a href="https://2016.igem.org/Team:Manchester/Model/ParameterRelationships">parameter relationship analysis</a>. <br />
 +
We answered key questions that arose during our <a href="https://2016.igem.org/Team:Manchester/Model/hp"> integrated human practices</a> work, helping to improve the design of our system using <a href="https://2016.igem.org/Team:Manchester/Model/Costing">cost analysis</a>.
 +
 +
 +
</br></br>
 +
All of our models are available on <a target="_Blank" href="https://github.com/Manchester-iGem-2016/Ensemble-Modelling">our Github page</a>
 +
 +
</p>
 +
 +
<table>
 +
      <th><a href="https://2016.igem.org/Team:Manchester/Model/MechanismUncertainty">Network Mechanism Analysis </a></th>
 +
      <th><a href="https://2016.igem.org/Team:Manchester/Model/ParameterRelationships">Parameter Relationship Analysis</a></th>
 +
      <th><a href="https://2016.igem.org/Team:Manchester/Model/Costing">Cost Analysis</a></th>
 +
<tr>
 +
    <td>Comparing model predictions with experimental data for different potential circuit topologies. <a href="https://2016.igem.org/Team:Manchester/Model/MechanismUncertainty">read more</a></td>
 +
    <td>Assessing the interlinking nature of specific parameter pairings on the outcomes of the system. <a href="https://2016.igem.org/Team:Manchester/Model/ParameterRelationships"> read more </a></td>
 +
    <td>Predicting the costs for a range of different system specifications by varying the amount of enzymes based on experimental data. <a href="https://2016.igem.org/Team:Manchester/Model/Costing">read more</a></td>
 +
</tr>
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</table>
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<div class="modelling_info1">
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<center>
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<p style="font-size:1.2em;">
 +
We found great inspiration from our <a href="https://2016.igem.org/Team:Manchester/Human_Practices/Industries">human practices</a> and guidance working both ways with the experiments. Click <a href="https://2016.igem.org/Team:Manchester/Model/hp"> here</a> to see a summary.
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</p>
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<div id="model1">
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</div>
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<div class="modelling_info1">
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<p style="border-bottom: 1px black solid ;font-size:25px;text-weight:bold;display:inline-block">What were we modelling?</p>
 +
<p style="font-size:1.2em;">
 +
We focused on modelling the <a href="https://2016.igem.org/Team:Manchester/Description/mechanism1">Cell-free Mechanism</a>. The short version is the AlcoPatch relies on alcohol, alcohol oxidase (AOx), horseradish peroxidase (HRP) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) to detect and quantify alcohol levels. The ABTS<sub>Oxidised</sub> produced in the prescence of alcohol is dark green and can be detected spectophotometrically or visually.
 +
</br></br>
 +
We focused on this small system because it was possible to obtain a large amount of <a href="https://2016.igem.org/Team:Manchester/Notebook">experimental data</a> for model validation, and because it allowed us to establish and illustrate the <a href="https://2016.igem.org/Team:Manchester/Model/ModelExplorer">ensemble modelling</a> process.
 +
</p>
 +
<p style="font-size:1.2em;">
 +
The majority of our experimental data came from the <a href="https://2016.igem.org/Team:Manchester/Proof">proof-of-concept</a> study of the analogous system of glucose and glucose oxidase (GOx) rather than alcohol and AOx. The reaction network of the two sytems is the same and only some kinetic parameters differ.
 +
</p>
 +
<p style="font-size:1.2em;">
 +
A schematic diagram of the final circuit of our detection system is given below. </br>
 +
<b> For more information about the individual reactions click on the blue enzyme boxes. </b>
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</p>
 +
<img class="full" src="https://static.igem.org/mediawiki/2016/0/04/T--Manchester--ModellingNetworkDiagram.png" alt="Reaction Network Diagram used in the modelling" usemap="#diagramclick" />
 +
 +
<map name="diagramclick">
 +
<area shape="rect" coords="195,120,255,175" href="https://2016.igem.org/Team:Manchester/Model/GlucoseOxidaseReaction" title="Glucose Oxidase Reaction">
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<area shape="rect" coords="505,155,566,210" href="https://2016.igem.org/Team:Manchester/Model/HorseRadishPeroxidaseReaction" title="HorseRadish Peroxidase Reaction">
 +
</map>
 +
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</br>
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<p style="font-size:1.2em;">
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Alternatively you can click on the enzyme name below:
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</p>
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<p style="font-size:1.2em;">
 +
<a href="https://2016.igem.org/Team:Manchester/Model/GlucoseOxidaseReaction">Glucose Oxidase</a>
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</br>
 +
<a href="https://2016.igem.org/Team:Manchester/Model/HorseRadishPeroxidaseReaction">Horseradish Peroxidase</a>
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</p>
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</div>
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<div id="model2">
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</div>
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<div  class="modelling_info1">
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<p style="border-bottom: 1px black solid ;font-size:25px;text-weight:bold;display:inline-block">What is Ensemble Modelling?</p>
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<p style="font-size:1.2em;">
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Incomplete and uncertain knowledge of kinetic parameters is a common problem when building models for synthetic biology. Ensemble modelling is one strategy to deal with this problem. Instead of running our model with a single set of specific parameters (for example rate constants), we run our model multiple times using different sets of plausible parameter values and analyse the predictions as an ensemble. We collected all the available parameter values from published literature and took into account the uncertainties that are associated with them. The resulting confidence in our parameter values was then described by <a href="https://2016.igem.org/Team:Manchester/Model/PDF">probability density functions</a>. </br>
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This has created probabilistic outputs allowing us to make rigorous conclusions about our reaction mechanism – and to assess which predictions are reliable, and where we are lacking information. </br> </br>
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<b>To explore the theory of this process please click the boxes on the diagram below.</b>
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</p>
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<img class="full" src="https://static.igem.org/mediawiki/2016/a/a9/T--Manchester--ModelFlowchart.jpg" alt="Overview flowchart of ensemble modelling" / usemap="#diagram1click">
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<area shape="rect" coords="70,82,413,190" href="https://2016.igem.org/Team:Manchester/Model/ParameterSelection" title="Parameter Selection">
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<area shape="rect" coords="635,305,850,411" href="https://2016.igem.org/Team:Manchester/Model/Simulate" title="system Simulate">
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<area shape="rect" coords="338,307,553,412" href="https://2016.igem.org/Team:Manchester/Model/result" title="Result Analysis">
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<area shape="rect" coords="50,298,265,400" href="https://2016.igem.org/Team:Manchester/Model/Story" title="Update Model">
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Alternatively you can click on the step name below:
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<p  style="font-size:1.2em;">
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<a href="https://2016.igem.org/Team:Manchester/Model/ParameterSelection">Collecting and Processing Data</a> </br>
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<a href="https://2016.igem.org/Team:Manchester/Model/PDF">Generating Probability Density Functions</a> </br>
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<a href="https://2016.igem.org/Team:Manchester/Model/Simulate">Simulate the System</a> </br>
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<a href="https://2016.igem.org/Team:Manchester/Model/result">Analyse the Results</a> </br>
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<a href="https://2016.igem.org/Team:Manchester/Model/Story">Story of the Model</a> </br>
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<a class="projectlink" href="https://2016.igem.org/Team:Manchester"><< Main Page</a>
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Revision as of 01:44, 22 September 2018

Modelling Banner
What were we modelling?
What is esemble modelling?
What does our modelling achieve?

What did our model achieve?

We achieved 3 main aims in our modelling work:
We introduced a novel ensemble modelling approach to iGEM and made this approach accessible to other iGEM teams by sharing our code.
We improved our understanding of our system and used real experimental data to improve our model, using network mechanism analysis and parameter relationship analysis.
We answered key questions that arose during our integrated human practices work, helping to improve the design of our system using cost analysis.

All of our models are available on our Github page

Network Mechanism Analysis Parameter Relationship Analysis Cost Analysis
Comparing model predictions with experimental data for different potential circuit topologies. read more Assessing the interlinking nature of specific parameter pairings on the outcomes of the system. read more Predicting the costs for a range of different system specifications by varying the amount of enzymes based on experimental data. read more

We found great inspiration from our human practices and guidance working both ways with the experiments. Click here to see a summary.

What were we modelling?

We focused on modelling the Cell-free Mechanism. The short version is the AlcoPatch relies on alcohol, alcohol oxidase (AOx), horseradish peroxidase (HRP) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) to detect and quantify alcohol levels. The ABTSOxidised produced in the prescence of alcohol is dark green and can be detected spectophotometrically or visually.

We focused on this small system because it was possible to obtain a large amount of experimental data for model validation, and because it allowed us to establish and illustrate the ensemble modelling process.

The majority of our experimental data came from the proof-of-concept study of the analogous system of glucose and glucose oxidase (GOx) rather than alcohol and AOx. The reaction network of the two sytems is the same and only some kinetic parameters differ.

A schematic diagram of the final circuit of our detection system is given below.
For more information about the individual reactions click on the blue enzyme boxes.

Reaction Network Diagram used in the modelling

Alternatively you can click on the enzyme name below:

Glucose Oxidase
Horseradish Peroxidase

What is Ensemble Modelling?

Incomplete and uncertain knowledge of kinetic parameters is a common problem when building models for synthetic biology. Ensemble modelling is one strategy to deal with this problem. Instead of running our model with a single set of specific parameters (for example rate constants), we run our model multiple times using different sets of plausible parameter values and analyse the predictions as an ensemble. We collected all the available parameter values from published literature and took into account the uncertainties that are associated with them. The resulting confidence in our parameter values was then described by probability density functions.
This has created probabilistic outputs allowing us to make rigorous conclusions about our reaction mechanism – and to assess which predictions are reliable, and where we are lacking information.

To explore the theory of this process please click the boxes on the diagram below.

Overview flowchart of ensemble modelling

Alternatively you can click on the step name below:

Collecting and Processing Data
Generating Probability Density Functions
Simulate the System
Analyse the Results
Story of the Model

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