Team:SYSU-Software/designer

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    <img src="https://static.igem.org/mediawiki/2013/7/77/Cast-header-image.png">
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    CAST (Computer Aided Synbio Tool)- An Integrated Tool<br>
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<!-- <img src="https://static.igem.org/mediawiki/2013/7/77/Cast-header-image.png"> -->
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    for Synthetic Biology
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CAST (Computer Aided Synbio Tool)- An Integrated Tool<br>
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for Synthetic Biology</h1>
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          <span id="cast-intruction-image">
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</div>
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            <img src="https://static.igem.org/mediawiki/2013/4/41/Cast-intruction-image.png">
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<div class="introduction">
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<span class="cast-introduction-text-header">Gene circuit</span>
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<span>Followed by Regulation network part, CAST will generate default gene circuits automatically. Also, the circuits can be optimized by users according to special demand of materials or methods. Simultaneously, the simulation of this network will be displayed. The parameters of proteins can be adjusted by dragging the columns, and thus, the model will be real-time adjusted. Furthermore, we can view the model by detail; in the simulation window, users can compare some curves they concentrate, or view the model influenced by stochastic noise or time delay. Inducers' effects will be also reflected in the model.</span>
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<div><img src="https://static.igem.org/mediawiki/2013/f/fb/SYSU-Gene_circuit.png"></div>
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            <span id="cast-intruction-text-header">Introduction</span><br>
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<div class="shots">
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            Accurate simulation and gene circuit design are essential but difficult parts in synthetic biology.Here, we designed CAST to cover the workflow from beginning to end, users can focus on function design and the gene circuit would be automatically designed. Furthermore, we developed a new simulation model that work with standard dynamic characteristic and verified by wetlab experiments. Moreover, we build an expandable database that users can contribute their own dynamic information which would lead to more accurate and sufficient dynamic information of all the Biobricks. Finally, our software is designed as an easy deployed server so that it can be used on personal purpose or shared by a whole lab or institution.
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<div><img src="https://static.igem.org/mediawiki/2013/1/1d/SYSU-Regulation_network.png"></div>
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<div><img src="https://static.igem.org/mediawiki/2013/6/6e/SYSU-Regulation_network1.png"></div>
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<div class="introduction">
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<span class="cast-introduction-text-header">Regulation network:</span>
 +
<span>Protein is the basic functional unit of all purpose of life. We can programme the mechanism among proteins by constructing regulation network; meanwhile, this is also the step that users initially organize their ideas. In the Regulation network part, users can search all kinds of proteins that relates to synthetic biology and drag them in the blank and then arrange the regulatory relationship. Clicking on Protein A, three icons will show on other proteins (for example, protein B) that can be regulated by A. To click on the up arrow means A stimulate the expression of B (up-regulation) while the down arrow means repression (down-regulation). The chain icon means A and B are programmed to be co-expressed. Different regulatory factors are provided to meet the demand of regulatory method. Users can design their functional network but not gene circuits thus they can focus on the ideas without the bothering of technical questions.</span>
 +
</div>
 +
</div>
 +
</div>
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<div id="part3" name="part3"class="cast-introduction-part cast-introduction-part1">
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<div class="introduction-content">
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<div class="shots">
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<div><img src="https://static.igem.org/mediawiki/2013/b/bf/SYSU-Simulation1.png"></div>
 +
</div>
 +
<div class="introduction">
 +
<span class="cast-introduction-text-header">Simulation:</span>
 +
<span>We can view the model by detail. In the simulation window, users can focus on the interested protein and trace its change; or compare some curves they concentrate on. Furthermore, users may view the model influenced by stochastic noise or time delay.</span>
 +
</div>
 +
</div>
 +
</div>
-
  <div id="cast-introduction-part2" class="cast-introduction-part">
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    <table>
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<div class="introduction-content">
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<div class="introduction">
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<span class="cast-introduction-text-header">Plasmid:</span>
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          <span id="cast-intruction-text">
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<span>As automation is our soul, the plasmid is constructed without your worrying. The plasmid will be presented intuitively and detailedly. Even better, you can select different assembly standard as you wish.</span>
-
            <span id="cast-intruction-text-header">Introduction</span><br>
+
</div>
-
            Accurate simulation and gene circuit design are essential but difficult parts in synthetic biology.Here, we designed CAST to cover the workflow from beginning to end, users can focus on function design and the gene circuit would be automatically designed. Furthermore, we developed a new simulation model that work with standard dynamic characteristic and verified by wetlab experiments. Moreover, we build an expandable database that users can contribute their own dynamic information which would lead to more accurate and sufficient dynamic information of all the Biobricks. Finally, our software is designed as an easy deployed server so that it can be used on personal purpose or shared by a whole lab or institution.
+
<div class="shots">
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          </span>
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<div><img src="https://static.igem.org/mediawiki/2013/4/45/Cast-Plasmid03.png"></div>
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<div id="part5" name="part5"class="cast-introduction-part cast-introduction-part1">
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          <span id="cast-intruction-image">
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<div class="introduction-content">
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            <img src="https://static.igem.org/mediawiki/2013/4/41/Cast-intruction-image.png">
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<div class="shots">
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<div><img src="https://static.igem.org/mediawiki/2013/7/7d/Cast_Protocol.png"></div>
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</div>
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      </tr>  
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<div class="introduction">
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    </table>
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<span class="cast-introduction-text-header">Protocol:</span>
-
  </div>
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<span>Being a amateur and find it hard to begin? Do not worry! CAST is a considerable assistant. Your can accomplish your synthetic biology design under our detailed direction.</span>
 +
</div>
 +
</div>
 +
</div>
-
  <div id="cast-introduction-part1" class="cast-introduction-part">
+
<div id="part6" name="part6"class="cast-introduction-part cast-introduction-part2">
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    <table>
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<div class="introduction-content">
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<div class="introduction">
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        <td>
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<span class="cast-introduction-text-header">Other functions:</span>
-
          <span id="cast-intruction-image">
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<span>Aside from the basic functions listed above, there are some auxiliary functions which help a lot.</span>
-
            <img src="https://static.igem.org/mediawiki/2013/4/41/Cast-intruction-image.png">
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</div>
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<div><img src="https://static.igem.org/mediawiki/2013/4/41/Cast-intruction-image.png"></div>
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</div>
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</div>
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</div>
-
        <td>
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<div id="part7" name="part7"class="cast-introduction-part cast-introduction-part1">
-
          <span id="cast-intruction-text">
+
<div class="introduction-content">
-
            <span id="cast-intruction-text-header">Introduction</span><br>
+
<div class="introduction">
-
            Accurate simulation and gene circuit design are essential but difficult parts in synthetic biology.Here, we designed CAST to cover the workflow from beginning to end, users can focus on function design and the gene circuit would be automatically designed. Furthermore, we developed a new simulation model that work with standard dynamic characteristic and verified by wetlab experiments. Moreover, we build an expandable database that users can contribute their own dynamic information which would lead to more accurate and sufficient dynamic information of all the Biobricks. Finally, our software is designed as an easy deployed server so that it can be used on personal purpose or shared by a whole lab or institution.
+
<span><b>Introduce Biobrick.</b> In the interface of user account, entering "my files", people can build and upload their novel biobricks by typing in the sequence and describe the parameters and type. These data can be edited and managed online.</span>
-
          </span>
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</div>
-
        </td>
+
-
      </tr>
+
-
    </table>
+
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  </div>
+
 +
<div class="shots">
 +
<div><img src="https://static.igem.org/mediawiki/2013/9/95/Cast-Introbiobrick.png"></div>
 +
</div>
 +
</div>
 +
</div>
-
  <div id="cast-introduction-part2" class="cast-introduction-part">
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<div id="part8" name="part8"class="cast-introduction-part cast-introduction-part2">
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    <table>
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<div class="introduction-content">
-
      <tr >
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<div class="introduction">
-
        <td>
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<!-- <span class="cast-introduction-text-header">Other functions:</span> -->
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          <span id="cast-intruction-text">
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<span><b>Output SBOL file.</b> The created biobricks will be compiled into SBOL automatically and thus users can get the file according to the information of the biobrick.</span>
-
            <span id="cast-intruction-text-header">Introduction</span><br>
+
</div>
-
            Accurate simulation and gene circuit design are essential but difficult parts in synthetic biology.Here, we designed CAST to cover the workflow from beginning to end, users can focus on function design and the gene circuit would be automatically designed. Furthermore, we developed a new simulation model that work with standard dynamic characteristic and verified by wetlab experiments. Moreover, we build an expandable database that users can contribute their own dynamic information which would lead to more accurate and sufficient dynamic information of all the Biobricks. Finally, our software is designed as an easy deployed server so that it can be used on personal purpose or shared by a whole lab or institution.
+
<div class="shots">
-
          </span>
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<div><img src="https://static.igem.org/mediawiki/2013/5/57/Cast_Output_SBOL_file.png"></div>
-
        </td>
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</div>
 +
</div>
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</div>
-
        <td>
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<div id="part9" name="part9"class="cast-introduction-part cast-introduction-part1">
-
          <span id="cast-intruction-image">
+
<div class="introduction-content">
-
            <img src="https://static.igem.org/mediawiki/2013/4/41/Cast-intruction-image.png">
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<div class="introduction">
-
          </span>
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<!-- <span class="cast-introduction-text-header">Plasmid & protocol</span> -->
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        </td>
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<span><b>File sharing.</b> Not only the biobricks, but also the ideas can be shared by CAST. Users' result of their ideas: regulation network, plasmid constructed and simulation can be stored on CAST and shared between researchers.</span>
-
      </tr>  
+
</div>
-
    </table>
+
-
  </div>
+
 +
<div class="shots">
 +
<div><img src="https://static.igem.org/mediawiki/2013/8/8d/Cast_File_sharing.png"></div>
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    <img id="bottom-image" src="https://static.igem.org/mediawiki/2013/d/d9/Sysu-footer.png">
 
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 +
<div id="part10" name="part8"class="cast-introduction-part cast-introduction-part2">
 +
<div class="introduction-content">
 +
<div class="introduction">
 +
<!-- <span class="cast-introduction-text-header">Other functions:</span> -->
 +
<span><b>Clotho apps</b>For clotho users, we have created a clotho app to open our software. The interface in clotho allow users open the server and web page at the same time.</span>
 +
</div>
 +
<div class="shots">
 +
<div><img src="https://static.igem.org/mediawiki/2013/8/86/SYSU-Clotho.png"></div>
 +
</div>
 +
</div>
 +
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 +
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<div id="sysu-footer">
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<img id="bottom-image" src="https://static.igem.org/mediawiki/2013/d/d9/Sysu-footer.png">
 +
</div>
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</div>
</body>
</body>
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</html>

Latest revision as of 23:19, 28 October 2013

Team:SYSU-Software new

CAST (Computer Aided Synbio Tool)- An Integrated Tool
for Synthetic Biology

Gene circuit Followed by Regulation network part, CAST will generate default gene circuits automatically. Also, the circuits can be optimized by users according to special demand of materials or methods. Simultaneously, the simulation of this network will be displayed. The parameters of proteins can be adjusted by dragging the columns, and thus, the model will be real-time adjusted. Furthermore, we can view the model by detail; in the simulation window, users can compare some curves they concentrate, or view the model influenced by stochastic noise or time delay. Inducers' effects will be also reflected in the model.
Regulation network: Protein is the basic functional unit of all purpose of life. We can programme the mechanism among proteins by constructing regulation network; meanwhile, this is also the step that users initially organize their ideas. In the Regulation network part, users can search all kinds of proteins that relates to synthetic biology and drag them in the blank and then arrange the regulatory relationship. Clicking on Protein A, three icons will show on other proteins (for example, protein B) that can be regulated by A. To click on the up arrow means A stimulate the expression of B (up-regulation) while the down arrow means repression (down-regulation). The chain icon means A and B are programmed to be co-expressed. Different regulatory factors are provided to meet the demand of regulatory method. Users can design their functional network but not gene circuits thus they can focus on the ideas without the bothering of technical questions.
Simulation: We can view the model by detail. In the simulation window, users can focus on the interested protein and trace its change; or compare some curves they concentrate on. Furthermore, users may view the model influenced by stochastic noise or time delay.
Plasmid: As automation is our soul, the plasmid is constructed without your worrying. The plasmid will be presented intuitively and detailedly. Even better, you can select different assembly standard as you wish.
Protocol: Being a amateur and find it hard to begin? Do not worry! CAST is a considerable assistant. Your can accomplish your synthetic biology design under our detailed direction.
Other functions: Aside from the basic functions listed above, there are some auxiliary functions which help a lot.
Introduce Biobrick. In the interface of user account, entering "my files", people can build and upload their novel biobricks by typing in the sequence and describe the parameters and type. These data can be edited and managed online.
Output SBOL file. The created biobricks will be compiled into SBOL automatically and thus users can get the file according to the information of the biobrick.
File sharing. Not only the biobricks, but also the ideas can be shared by CAST. Users' result of their ideas: regulation network, plasmid constructed and simulation can be stored on CAST and shared between researchers.
Clotho appsFor clotho users, we have created a clotho app to open our software. The interface in clotho allow users open the server and web page at the same time.

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