Difference between revisions of "Template:SYSU-Software/statics/html/Projects/Description.html"

 
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                 novel numerical simulation algorithm </a> </span>
 
                 novel numerical simulation algorithm </a> </span>
 
         for circuit）applied in CO-RAD was developed to predict the expression level of genetic circuits in no time.
 
         for circuit）applied in CO-RAD was developed to predict the expression level of genetic circuits in no time.
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         Through In addition, we incorporated self-designed <span class="bold"> <a href="javascript:void(0)" goto="Validation">
+
         Through in addition, we incorporated self-designed <span class="bold"> <a href="javascript:void(0)" goto="Validation">
 
                 wet-lab validation </a> </span>into
 
                 wet-lab validation </a> </span>into
 
         our project to validate the new results designed by our CO-RAD platform. In conclusion, by assisting in
 
         our project to validate the new results designed by our CO-RAD platform. In conclusion, by assisting in
 
         collaboration and inspiration, CO-RAD makes complex biological systems accessible to researchers who want
 
         collaboration and inspiration, CO-RAD makes complex biological systems accessible to researchers who want
 
         rapid, intuitive, and high-quality
 
         rapid, intuitive, and high-quality
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         accomplish their designs.
+
         accomplish their designs. Click here to design in <a href="http://www.sysu-corad.com/">CO-RAD</a> way.
−
 
+
 
     </div>
 
     </div>
  
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     <div class="header2"> Description </div>
+
    <img src="https://static.igem.org/mediawiki/2018/0/06/T--SYSU-Software--coEdit.png" />
 +
 
 +
     <div class="header2"> Background </div>
 
     <div class="content">
 
     <div class="content">
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         Groupwork is the bread and butter of biological system & circuit design, due to the complexity of this research
+
         The data shows a shift from single-investigator 'little science' to increasingly large, expensive,
−
        field. In consequence of the complexity of biological systems, genetic circuit design and the limited personal
+
        multinational, interdisciplinary and interdependent 'big science'. The scientific collaboration among
−
        experience, it is very difficult for individuals to design a viable circuit alone.This raises the demand of
+
        researchers becomes more pervasive and essential.
−
        effective collaboration methods. It would be better if the biologists can work face to face, in which way they
+
    </div>
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         can exchange ideas with absolute ease. However, in many cases we can't even make sure everyone works on the
+
    <div class="content">
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         same continent, let alone in the same room, so we need appropriate ways for tele-cooperation. Sadly,
+
        To synthetic biology, due to the natural complexity of biological systems, genetic circuit design and the
−
        traditional online tools don't satisfy biologists' needs. For example, genetic circuits and experimental
+
        limited personal experience, it is very difficult for individuals to design a viable circuit alone, raising the
−
        protocols cannot be precisely represented via Google Doc. Local designing software such as SBOLDesigner don't
+
        demand of effective collaboration methods. Interdisciplinary and engineering-oriented natures on scientific
−
         let scientists edit online cooperatively, which brings down efficiency a lot. Besides, creative ideas and
+
         research make it praticularly open to collaboration, while time and space issues would compromise the
−
        valuable suggestions are also important in collaboration, which will have a great influence in the final result
+
         convenience and the efficency to conduct a collaboration.
−
         of users' co-design.
+
    </div>
 +
    <div class="content">
 +
         In this case, we developed a software to improve the efficiency in collaboration and help inspire
 +
         synbiologists' ideas, assist their work and optimize their design.
 
     </div>
 
     </div>
  
−
     <img src="https://static.igem.org/mediawiki/2018/0/06/T--SYSU-Software--coEdit.png" />
+
     <div class="background-data">
 +
        <img src="https://static.igem.org/mediawiki/2018/8/85/T--SYSU-Software--backgrounddata1.png" />
 +
        <div class="caption">Figure 1: Percentage of multientity publications, 2000–2009 </div>
 +
        <img src="https://static.igem.org/mediawiki/2018/9/9f/T--SYSU-Software--backgrounddata2.png" />
 +
        <div class="caption">Figure 2: The percentage of multiinstitutional publications in 22 ESI fields</div>
 +
    </div>
  
 
     <div class="content">
 
     <div class="content">
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         <ol>
 
         <ol>
 
             <li>
 
             <li>
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                 How to make tele-cooperation as convenient as face-to-face collaboration.
+
                 How to make tele-cooperation as convenient as face-to-face collaboration?
 
             </li>
 
             </li>
 
             <li>
 
             <li>
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                 How to encourage users to think of and share more creative ideas while cooperating.
+
                 How to encourage users to come up with and share more creative ideas while designing genetic circuits?
 
             </li>
 
             </li>
 
         </ol>
 
         </ol>
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     <div class="header2"> Solution </div>
 
     <div class="header2"> Solution </div>
  
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     <div class="header3">Help users come up with more creative ideas</div>
+
     <div class="header3">Source of creative ideas</div>
 
     <div class="ui three cards">
 
     <div class="ui three cards">
 
         <div class="card wide-card">
 
         <div class="card wide-card">
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             </div>
 
             </div>
 
             <div class="content">
 
             <div class="content">
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                 <div class="ui header">Search & recommendaion</div>
+
                 <div class="ui header">Search & Recommendation</div>
 
             </div>
 
             </div>
−
             <div class="ui bottom attached button detail-btn" data-id="4">View Detail</div>
+
             <div class="ui bottom attached button detail-btn button-override" data-id="4">View Detail</div>
 
         </div>
 
         </div>
 
         <div class="card wide-card">
 
         <div class="card wide-card">
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             </div>
 
             </div>
 
             <div class="content">
 
             <div class="content">
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                 <div class="ui header">Analysis & simulation</div>
+
                 <div class="ui header">Analysis & Simulation</div>
 
             </div>
 
             </div>
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             <div class="ui bottom attached button detail-btn" data-id="5">View Detail</div>
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             <div class="ui bottom attached button detail-btn button-override" data-id="5">View Detail</div>
 
         </div>
 
         </div>
 
         <div class="card wide-card">
 
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             </div>
 
             </div>
 
             <div class="content">
 
             <div class="content">
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                 <div class="ui header">Guide the design</div>
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                 <div class="ui header">Guide the Design</div>
 
             </div>
 
             </div>
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             <div class="ui bottom attached button detail-btn" data-id="6">View Detail</div>
+
             <div class="ui bottom attached button detail-btn button-override" data-id="6">View Detail</div>
 
         </div>
 
         </div>
 
     </div>
 
     </div>
 
     <div class="ui modal" id="modal-4">
 
     <div class="ui modal" id="modal-4">
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         <div class="header">Search & recommendaion</div>
+
         <div class="header">Search & Recommendaion</div>
 
         <div class="image content">
 
         <div class="image content">
 
             <div class="ui medium image">
 
             <div class="ui medium image">
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             </div>
 
             </div>
 
             <div class="description">
 
             <div class="description">
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                 Given the experience of previous achievements provides valuable inspiration while cooperating, we
+
                 Search engine in CO-RAD is powerful for users to quickly gain their desired projects and papers, from which new and creative ideas originate.
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                developed this function to help users quickly find the project they need.
+
 
             </div>
 
             </div>
 
         </div>
 
         </div>
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     </div>
 
     </div>
 
     <div class="ui modal" id="modal-5">
 
     <div class="ui modal" id="modal-5">
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         <div class="header">Analysis & simulation</div>
+
         <div class="header">Analysis & Simulation</div>
 
         <div class="image content">
 
         <div class="image content">
 
             <div class="ui medium image">
 
             <div class="ui medium image">
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             </div>
 
             </div>
 
             <div class="description">
 
             <div class="description">
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                 Deeper understanding of the circuit design can help users make more hypothetical opinions. Our software
+
                 CO-RAD can not only analyses circuits and compute the values of CG and CAI, but builds mathematical models to simulate the circuits and predict the expression levels.
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                analyzes circuits and gives values for CG and CAI, and builds mathematical simulation models to predict
+
−
                expression levels.
+
 
             </div>
 
             </div>
 
         </div>
 
         </div>
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     </div>
 
     </div>
 
     <div class="ui modal" id="modal-6">
 
     <div class="ui modal" id="modal-6">
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         <div class="header">Guide the design</div>
+
         <div class="header">Guide the Design</div>
 
         <div class="image content">
 
         <div class="image content">
 
             <div class="ui medium image">
 
             <div class="ui medium image">
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             </div>
 
             </div>
 
             <div class="description">
 
             <div class="description">
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                 Through an algorithm that simulates evolution, users can get optimal kinetic parameters for circuits,
+
                 Through an algorithm that simulates evolution, users can get optimal kinetic parameters for circuits, which can assist users in modifying their circuits to reach the expected behavior.
−
                which can assist users in modifying their circuits to reach the expected behavior.
+
 
             </div>
 
             </div>
 
         </div>
 
         </div>
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         </div>
 
         </div>
 
     </div>
 
     </div>
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    <div class="header3">Solve the inconvenience of remote collaboration and communication</div>
 
 
     <br />
 
     <br />
 +
    <div class="header3">Enhancement on Collaboration</div>
 
     <div class="ui three cards">
 
     <div class="ui three cards">
 
         <div class="card wide-card">
 
         <div class="card wide-card">
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             </div>
 
             </div>
 
             <div class="content">
 
             <div class="content">
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                 <div class="ui header">Real-time collaboration</div>
+
                 <div class="ui header">Collaborative Platform</div>
 
             </div>
 
             </div>
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             <div class="ui bottom attached button detail-btn" data-id="1">View Detail</div>
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             <div class="ui bottom attached button detail-btn button-override" data-id="1">View Detail</div>
 
         </div>
 
         </div>
 
         <div class="card wide-card">
 
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             </div>
 
             </div>
 
             <div class="content">
 
             <div class="content">
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                 <div class="ui header">Synchronization sketchpad</div>
+
                 <div class="ui header">Synchronization Sketchpad</div>
 
             </div>
 
             </div>
−
             <div class="ui bottom attached button detail-btn" data-id="2">View Detail</div>
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             <div class="ui bottom attached button detail-btn button-override" data-id="2">View Detail</div>
 
         </div>
 
         </div>
 
         <div class="card wide-card">
 
         <div class="card wide-card">
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             </div>
 
             </div>
 
             <div class="content">
 
             <div class="content">
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                 <div class="ui header">SBOL support</div>
+
                 <div class="ui header">SBOL Support</div>
 
             </div>
 
             </div>
−
             <div class="ui bottom attached button detail-btn" data-id="3">View Detail</div>
+
             <div class="ui bottom attached button detail-btn button-override" data-id="3">View Detail</div>
 
         </div>
 
         </div>
 
     </div>
 
     </div>
 
     <div class="ui modal" id="modal-1">
 
     <div class="ui modal" id="modal-1">
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         <div class="header">Real-time collaboration</div>
+
         <div class="header">Collaborative Platform</div>
 
         <div class="image content">
 
         <div class="image content">
 
             <div class="ui medium image">
 
             <div class="ui medium image">
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             </div>
 
             </div>
 
             <div class="description">
 
             <div class="description">
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                 A real-time genetic circuit design platform where multiple users can edit one file at the same time,
+
                 A collaborative platform with visual circuit designer and management studio, where multiple users can work together, just like (and even better than!) working face to face.
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                just like (and even better than!) working on the same computer.
+
 
             </div>
 
             </div>
 
         </div>
 
         </div>
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     </div>
 
     </div>
 
     <div class="ui modal" id="modal-2">
 
     <div class="ui modal" id="modal-2">
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         <div class="header">Synchronization sketchpad</div>
+
         <div class="header">Synchronization Sketchpad</div>
 
         <div class="image content">
 
         <div class="image content">
 
             <div class="ui medium image">
 
             <div class="ui medium image">
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             </div>
 
             </div>
 
             <div class="description">
 
             <div class="description">
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                 A tool that simulates pen and paper, users can express their opinions by labeling or drawing during the
+
                 A magical board that connects everyone, with which users can share their real-time performances on visual designer.  
−
                communication process.
+
 
             </div>
 
             </div>
 
         </div>
 
         </div>
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     </div>
 
     </div>
 
     <div class="ui modal" id="modal-3">
 
     <div class="ui modal" id="modal-3">
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         <div class="header">SBOL support</div>
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         <div class="header">SBOL Support</div>
 
         <div class="image content">
 
         <div class="image content">
 
             <div class="ui medium image">
 
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             </div>
 
             </div>
 
             <div class="description">
 
             <div class="description">
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                 Our system is compatible with SBOL, the most common data format in the field of synthetic biology,
+
                 Our system is compatible to SBOL, the most common data format in the field of synthetic biology, which means circuits edited on other software can be quickly imported into our software without re-editing.
−
                which means circuits edited on other software can be quickly imported into our software without
+
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                re-editing.
+
 
             </div>
 
             </div>
 
         </div>
 
         </div>

Latest revision as of 22:26, 17 October 2018

Project
Welcome to CO-RAD!
       The complexity of genetic circuits has made it difficult for synthetic biologists to design the artificial
       biological systems. In our project, we developed CO-RAD, a Collaborative
           Optimization platform with multiple functions including Recommendation,
           Analysis and Design. With the help of CO-RAD, users can design genetic circuits easily and cooperate
       with remote partners in real time.
       More importantly, the search & recommendation system in CO-RAD were developed to
       inspire users with some previous projects and optimize their design with evolutionary
           algorithm. Moreover,  <a href="javascript:void(0)" goto="Simulation-Circuits"> a
               novel numerical simulation algorithm </a> 
       for circuit）applied in CO-RAD was developed to predict the expression level of genetic circuits in no time.
       Through in addition, we incorporated self-designed  <a href="javascript:void(0)" goto="Validation">
               wet-lab validation </a> into
       our project to validate the new results designed by our CO-RAD platform. In conclusion, by assisting in
       collaboration and inspiration, CO-RAD makes complex biological systems accessible to researchers who want
       rapid, intuitive, and high-quality
       accomplish their designs. Click here to design in <a href="http://www.sysu-corad.com/">CO-RAD</a> way.

   <img src="T--SYSU-Software--coEdit.png" />
Background 
       The data shows a shift from single-investigator 'little science' to increasingly large, expensive,
       multinational, interdisciplinary and interdependent 'big science'. The scientific collaboration among
       researchers becomes more pervasive and essential.

       To synthetic biology, due to the natural complexity of biological systems, genetic circuit design and the
       limited personal experience, it is very difficult for individuals to design a viable circuit alone, raising the
       demand of effective collaboration methods. Interdisciplinary and engineering-oriented natures on scientific
       research make it praticularly open to collaboration, while time and space issues would compromise the
       convenience and the efficency to conduct a collaboration.

       In this case, we developed a software to improve the efficiency in collaboration and help inspire
       synbiologists' ideas, assist their work and optimize their design.

       <img src="T--SYSU-Software--backgrounddata1.png" />
Figure 1: Percentage of multientity publications, 2000–2009 
       <img src="T--SYSU-Software--backgrounddata2.png" />
Figure 2: The percentage of multiinstitutional publications in 22 ESI fields
       Therefore, we're here to solve the following problems:
  1. How to make tele-cooperation as convenient as face-to-face collaboration?
  2. How to encourage users to come up with and share more creative ideas while designing genetic circuits?
Solution
Source of creative ideas
               <img src="T--SYSU-Software--Des4.png" />
Search & Recommendation
View Detail
               <img src="T--SYSU-Software--Des5.png" />
Analysis & Simulation
View Detail
               <img src="T--SYSU-Software--Des6.png" />
Guide the Design
View Detail
Enhancement on Collaboration
               <img src="T--SYSU-Software--Des1.png" />
Collaborative Platform
View Detail
               <img src="T--SYSU-Software--Des2.png" />
Synchronization Sketchpad
View Detail
               <img src="T--SYSU-Software--Des3.png" />
SBOL Support
View Detail

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