Difference between revisions of "Team:XMU-China/Software"

 
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     <meta name="x5-page-mode" content="app"><!-- QQ应用模式 -->
 
     <meta name="x5-page-mode" content="app"><!-- QQ应用模式 -->
 
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     <title>Team:XMU-China/Description - 2018.igem.org</title>
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     <title>Team:XMU-China/Software - 2018.igem.org</title>
     <link rel="stylesheet" href="css/desciption.css">
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     <link rel="stylesheet" href="css/interlab.css">
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    <link rel="stylesheet" href="css/font.css">
 
     <link href="http://cdn.bootcss.com/font-awesome/4.7.0/css/font-awesome.min.css" rel="stylesheet">
 
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     <link rel="stylesheet" href="https://2018.igem.org/Team:XMU-China/css/cover?action=raw&ctype=text/css">
 
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     <link rel="stylesheet" href="https://2018.igem.org/Team:XMU-China/css/interlab?action=raw&ctype=text/css">
    <link rel="stylesheet" href="https://2018.igem.org/Team:XMU-China/css/desciption?action=raw&ctype=text/css">
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     <link rel="stylesheet" href="https://2018.igem.org/Team:XMU-China/css/font?action=raw&ctype=text/css">
 
     <link rel="stylesheet" href="https://2018.igem.org/Team:XMU-China/css/font?action=raw&ctype=text/css">
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    <link rel="stylesheet" href="https://2018.igem.org/Team:XMU-China/css/nav_mobile?action=raw&ctype=text/css">
 
     <link rel="stylesheet" href="https://2018.igem.org/Team:XMU-China/css/material-scrolltop?action=raw&ctype=text/css">
 
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</head>
 
</head>
  
 
<body>
 
<body>
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    <header></header>
 
     <div id="container">
 
     <div id="container">
 
         <header>
 
         <header>
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                                 <li><a href="https://2018.igem.org/Team:XMU-China/Description">Description</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Description">Description</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Design">Design</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Design">Design</a></li>
                                <li><a href="https://2018.igem.org/Team:XMU-China/Demonstrate">Demonstrate</a></li>
 
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Results">Results</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Results">Results</a></li>
 +
                                <li><a href="https://2018.igem.org/Team:XMU-China/Demonstrate">Demonstrate</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Parts">Parts</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Parts">Parts</a></li>
 
                             </ul>
 
                             </ul>
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                             <ul>
 
                             <ul>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Hardware">Overview</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Hardware">Overview</a></li>
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Hardware/Microfluidic_Chips">Microfluidic chips</a></li>
+
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Hardware#Microfluidic_Chips">Microfluidic Chips</a></li>
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Hardware/Fluorescenc_Detection">Fluorescence Detection</a></li>
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                                 <li><a href="https://2018.igem.org/Team:XMU-China/Hardware#Fluorescence_Detection">Fluorescence Detection</a></li>
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Hardware/Straberry_Pi">Straberry Pi</a></li>
+
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Hardware#Raspberry_Pi">Raspberry Pi</a></li>
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Applied_Design">Applied Design</a></li>
+
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Hardware#Application">Application</a></li>
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Software">APP</a></li>
+
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Software">Software</a></li>
 +
                                <li><a href="https://2018.igem.org/Team:XMU-China/Applied_Design">Product Design</a></li>
 
                             </ul>
 
                             </ul>
 
                         </li>
 
                         </li>
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                             <a href="#">Model</a>
 
                             <a href="#">Model</a>
 
                             <ul>
 
                             <ul>
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Model">Overview</a></li>
+
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Model#Summary">Summary</a></li>
 +
                                <li><a href="https://2018.igem.org/Team:XMU-China/Model#Thermodynamic_model">Thermodynamic Model</a></li>
 +
                                <li><a href="https://2018.igem.org/Team:XMU-China/Model#Fluid_dynamics_model">Fluid dynamics Model</a></li>
 +
                                <li><a href="https://2018.igem.org/Team:XMU-China/Model#Molecular_docking_model">Molecular Docking Model</a></li>
 +
                                <li><a href="https://2018.igem.org/Team:XMU-China/Model#The_dynamic_model">Derivation of Rate Equation</a></li>
 
                             </ul>
 
                             </ul>
 
                         </li>
 
                         </li>
 
                         <li class="Human_Practice">
 
                         <li class="Human_Practice">
                             <a href="#">Human Practice</a>
+
                             <a href="#">Social Works</a>
 
                             <ul>
 
                             <ul>
                                 <li><a href="https://2018.igem.org/Te
+
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Human_Practices">Human Practice</a></li>
                                am:XMU-China/Human_Practices">Overview</a></li>
+
                                <li><a href="https://2018.igem.org/Team:XMU-China/HP/Silver">Silver</a></li>
+
                                <li><a href="https://2018.igem.org/Team:XMU-China/HP/Gold_Integrated">Gold</a></li>
+
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Public_Engagement">Engagement</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Public_Engagement">Engagement</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Collaborations">Collaborations</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Collaborations">Collaborations</a></li>
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                                 <li><a href="https://2018.igem.org/Team:XMU-China/Notebook">Notebook</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Notebook">Notebook</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Experiments">Experiments</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Experiments">Experiments</a></li>
 +
                                <li><a href="https://2018.igem.org/Team:XMU-China/Engineering">Engineering</a></li>
 
                             </ul>
 
                             </ul>
 
                         </li>
 
                         </li>
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                                 <li><a href="https://2018.igem.org/Team:XMU-China/Attributions">Attributions</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Attributions">Attributions</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Judging">Judging</a></li>
 
                                 <li><a href="https://2018.igem.org/Team:XMU-China/Judging">Judging</a></li>
 +
                                <li><a href="https://2018.igem.org/Team:XMU-China/After_iGEM">After iGEM</a></li>
 
                             </ul>
 
                             </ul>
 
                         </li>
 
                         </li>
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     </div>
 
     </div>
 
     <script src="js/jquery-1.11.0.min.js"></script>
 
     <script src="js/jquery-1.11.0.min.js"></script>
    <!-- <script src="js/hc-mobile-nav.js"></script> -->
 
 
     <script src="https://2018.igem.org/Team:XMU-China/js/hc-mobile-nav?action=raw&ctype=text/javascript"></script>
 
     <script src="https://2018.igem.org/Team:XMU-China/js/hc-mobile-nav?action=raw&ctype=text/javascript"></script>
 
     <div class="header">
 
     <div class="header">
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                         <li><a href="https://2018.igem.org/Team:XMU-China/Attributions">Attributions</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Attributions">Attributions</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Judging">Judging</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Judging">Judging</a></li>
 +
                        <li><a href="https://2018.igem.org/Team:XMU-China/After_iGEM">After iGEM</a></li>
 
                     </ul>
 
                     </ul>
 
                 </div>
 
                 </div>
 
                 <div id="Notebook">
 
                 <div id="Notebook">
                     <div>
+
                     <div class="nav-word">Notebook</div>
                        <div class="nav-word">Notebook</a></div>
+
                    </div>
+
 
                     <ul>
 
                     <ul>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Notebook">Notebook</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Notebook">Notebook</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Experiments">Experiments</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Experiments">Experiments</a></li>
 +
                        <li><a href="https://2018.igem.org/Team:XMU-China/Engineering">Engineering</a></li>
 
                     </ul>
 
                     </ul>
 
                 </div>
 
                 </div>
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                 </div>
 
                 </div>
 
                 <div id="Human_Practice">
 
                 <div id="Human_Practice">
                     <div class="nav-word">Human Practice</div>
+
                     <div class="nav-word">Social Works</div>
 
                     <ul>
 
                     <ul>
                         <li><a href="https://2018.igem.org/Team:XMU-China/Human_Practices">Overview</a></li>
+
                         <li><a href="https://2018.igem.org/Team:XMU-China/Human_Practices">Human Practice</a></li>
                        <li><a href="https://2018.igem.org/Team:XMU-China/HP/Silver">Silver</a></li>
+
                        <li><a href="https://2018.igem.org/Team:XMU-China/HP/Gold_Integrated">Gold</a></li>
+
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Public_Engagement">Engagement</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Public_Engagement">Engagement</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Collaborations">Collaborations</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Collaborations">Collaborations</a></li>
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                     <div class="nav-word">Model</div>
 
                     <div class="nav-word">Model</div>
 
                     <ul>
 
                     <ul>
                         <li><a href="https://2018.igem.org/Team:XMU-China/Model">Overview</a></li>
+
                         <li><a href="https://2018.igem.org/Team:XMU-China/Model">Summary</a></li>
 +
                        <li><a href="https://2018.igem.org/Team:XMU-China/Model#Thermodynamic_model">Thermodynamic Model</a></li>
 +
                        <li><a href="https://2018.igem.org/Team:XMU-China/Model#Fluid_dynamics_model">Fluid dynamics Model</a></li>
 +
                        <li><a href="https://2018.igem.org/Team:XMU-China/Model#Molecular_docking_model">Molecular Docking Model</a></li>
 +
                        <li><a href="https://2018.igem.org/Team:XMU-China/Model#The_dynamic_model">Derivation of Rate Equation</a></li>
 
                     </ul>
 
                     </ul>
 
                 </div>
 
                 </div>
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                     <ul>
 
                     <ul>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Hardware">Overview</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Hardware">Overview</a></li>
                         <li><a href="https://2018.igem.org/Team:XMU-China/Hardware/Microfluidic_Chips">Microfluidic chips</a></li>
+
                         <li><a href="https://2018.igem.org/Team:XMU-China/Hardware#Microfluidic_Chips">Microfluidic Chips</a></li>
                         <li><a href="https://2018.igem.org/Team:XMU-China/Hardware/Fluorescenc_Detection">Fluorescence Detection</a></li>
+
                         <li><a href="https://2018.igem.org/Team:XMU-China/Hardware#Fluorescence_Detection">Fluorescence Detection</a></li>
                         <li><a href="https://2018.igem.org/Team:XMU-China/Hardware/Straberry_Pi">Straberry Pi</a></li>
+
                         <li><a href="https://2018.igem.org/Team:XMU-China/Hardware#Raspberry_Pi">Raspberry Pi</a></li>
                         <li><a href="https://2018.igem.org/Team:XMU-China/Applied_Design">Applied Design</a></li>
+
                         <li><a href="https://2018.igem.org/Team:XMU-China/Hardware#Application">Application</a></li>
                         <li><a href="https://2018.igem.org/Team:XMU-China/Software">APP</a></li>
+
                         <li><a href="https://2018.igem.org/Team:XMU-China/Software">Software</a></li>
 +
                        <li><a href="https://2018.igem.org/Team:XMU-China/Applied_Design">Product Design</a></li>
 
                     </ul>
 
                     </ul>
 
                 </div>
 
                 </div>
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                         <li><a href="https://2018.igem.org/Team:XMU-China/Description">Description</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Description">Description</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Design">Design</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Design">Design</a></li>
                        <li><a href="https://2018.igem.org/Team:XMU-China/Demonstrate">Demonstrate</a></li>
 
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Results">Results</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Results">Results</a></li>
 +
                        <li><a href="https://2018.igem.org/Team:XMU-China/Demonstrate">Demonstrate</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Parts">Parts</a></li>
 
                         <li><a href="https://2018.igem.org/Team:XMU-China/Parts">Parts</a></li>
 
                     </ul>
 
                     </ul>
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         <div class="clear"></div>
 
         <div class="clear"></div>
 
         <div class="description_banner">
 
         <div class="description_banner">
             <div class="word">Description</div>
+
             <div class="word">Software</div>
 
         </div>
 
         </div>
 
         <nav class="Quick-navigation">
 
         <nav class="Quick-navigation">
 
             <div class="Quick-navigation_word">
 
             <div class="Quick-navigation_word">
                 <img  src="https://static.igem.org/mediawiki/2018/f/f5/T--XMU-China--right0.png">
+
                 <img  src="https://static.igem.org/mediawiki/2018/e/e6/T--XMU-China--right50.png">
                 <a href="#ABCDsystem" class="Quick-navigation-item">
+
                 <a href="#Function_introduction" class="Quick-navigation-item" >
                     <img id="turn_img" src="https://static.igem.org/mediawiki/2018/d/db/T--XMU-China--right1.png">
+
                     <img id="turn_img" src="https://static.igem.org/mediawiki/2018/5/50/T--XMU-China--right51.png">
                     <a href="#ABCDsystem"id="Quick_A">ABCDsystem</a></a>
+
                     <a href="#Function_introduction" id="Quick_A">Function introduction</a></a>
                 <a href="#OMVs" class="Quick-navigation-item" >
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                 <a href="#Software_design" class="Quick-navigation-item">
                     <img id="turn_img" src="https://static.igem.org/mediawiki/2018/c/cd/T--XMU-China--right2.png">
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                     <img id="turn_img" src="https://static.igem.org/mediawiki/2018/0/04/T--XMU-China--right52.png">
                     <a href="#OMVs" id="Quick_B">OMVs</a></a>
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                     <a href="#Software_design" id="Quick_B">Software design</a></a>
                 <a href="#Supporting" class="Quick-navigation-item">
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                 <a href="#Picture_analysis_process" class="Quick-navigation-item">
                     <img id="turn_img" src="https://static.igem.org/mediawiki/2018/1/1c/T--XMU-China--right3.png">
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                     <img id="turn_img" src="https://static.igem.org/mediawiki/2018/d/d0/T--XMU-China--right53.png">
                     <a href="#Supporting" id="Quick_C">Supporting</a></a>
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                     <a href="#Picture_analysis_process"id="Quick_C">Picture analysis process</a></a>
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                <a href="#Block_chain" class="Quick-navigation-item">
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                    <img id="turn_img" src="https://static.igem.org/mediawiki/2018/1/11/T--XMU-China--right54.png">
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                    <a href="#Block_chain"id="Quick_D">Block chain</a></a>
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                <a href="#Application" class="Quick-navigation-item">
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                    <img id="turn_img" src="https://static.igem.org/mediawiki/2018/b/ba/T--XMU-China--right55.png">
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                    <a href="#Application"id="Quick_F">Application</a></a>
 
             </div>
 
             </div>
 
         </nav>
 
         </nav>
         <div class="main">
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         <div class="main software">
             <section id="ABCDsystem" class="js-scroll-step">
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             <section id="Summary" class="js-scroll-step">
 
                 <div class="headline">
 
                 <div class="headline">
                     ABCDsystem
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                     Summary
 
                 </div>
 
                 </div>
                 <h1>Background</h1>
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                 <p>Our team has developed an app, which makes a combination of AI algorithm and blockchain. It is designed in order to better control the hardware, making it more convenient and handy for grass-root hospitals and their patients, and facilitate the doctors' diagnosis. More details about the principle of the software, please switch to our code on <a class="click_here" href="https://github.com/igemsoftware2018/Team_XMU_China">the Github.</a></p>
                 <p>Protein plays a significant role in performing physiological functions<sup>[1]</sup>. However, in diseased cells, protein carrying out a certain function may indicate the proceedings of disease. Such protein could be sorted to biomarkers, which have been regarded as the targets of disease detection and treatment in recent years.<sup>[2]-[4]</sup> Therefore, detecting those biomarkers of protein-type becomes more and more critical to biological and medical fields.
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                 <p class="F3"><img src="https://static.igem.org/mediawiki/2018/e/e0/T--XMU-China--lunbotu3333333.jpg">
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                    <p class="Figure_word"><strong>Figure1.</strong> App interface</p>
 
                 </p>
 
                 </p>
                 <p>There are two main detecting approaches to detect a particular protein in a complex sample. One is direct determination of the content after purification, and the other is binding assays which include a target recognition probe and a signal transducer. The former approach includes gel filtration chromatography, ion exchange chromatography, nickel column and more. While on the down side, these methods involve high costs, strict equipment requirements and other drawbacks, which are not suitable for promotion and application. The enzyme-linked immunosorbent assay (ELISA) is a typical representative of the latter approach, nevertheless, such assays using antibodies as affinity ligands have cross-reactivity of antibodies compromising the specificity to the target of interest.<sup>[5]</sup> What’s worse, the premise of using ELISA is to find the corresponding antibodies, but the fact is that not all proteins can find their specific antibody protein. That is to say, the use of ELISA is also limited.
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            </section>
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            <section id="Function_introduction" class="js-scroll-step">
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                 <div class="headline">
 +
                    Function introduction
 +
                </div>
 +
                <h1>1.   The Hardware Control</h1>
 +
                <p class="reference">The first model mainly targets for the specific operations of the hardware. <br>
 +
                    <strong>                    (1) Engine Start Stop:  </strong> <br>Users could click the button, “Engine Start Stop”, to automatically start the hardware, and complete a series of tasks including centrifugation and pictures-taking. <br>
 +
                    <strong>(2) Step – Control:  <br></strong>
 +
                    a. Two-Sliders Controller: Being used to set the time and speed of the hardware engines. <br>
 +
                    b. The On-off Controller: Being used to start the hardware and send the speed and time the hardware needed for operating. <br>
 +
                    c. The Pictures-taking Controller: used to control the pick-up head of the camera to take photos. <br>
 +
                    <strong>(3) Show the real-time speed of the engine.</strong> <br>
 
                 </p>
 
                 </p>
                 <p>In terms of binding assays, using aptamers as affinity ligands to recognize specific proteins are better than those using antibodies. Aptamers are short, synthetic single stranded oligonucleotides (DNA or RNA) that can bind to target molecules with high affinity and specificity.<sup>[6]-[9]</sup> They are commonly selected from random sequence libraries, using the systematic evolution of ligands by exponential enrichment (SELEX) techniques.<sup>[10]</sup> Advantages of aptamers over antibodies include longer shelflife, improved thermal stability and ease of modification and conjugation.<sup>[11]</sup>
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                 <h1>2. The detection of the images</h1>
 +
                <p class="reference">The second model is mainly responsible for the analysis of pictures taken by the camera. <br>
 +
                    <strong>(1) The Loading Controller:  </strong> <br>
 +
                    Showing the pictures taken after the operation of the hardware. <br>
 +
                    <strong>(2) Analysis Controller: </strong> <br>Obtain the aperture gaps of the fluorescence and corresponding diseases’ information through analyzing those taken pictures.
 
                 </p>
 
                 </p>
                 <p>An interesting binding assay is to use aptamers as the target recognition probes and CRISPR-Cas12a (Cpf1) as the signal amplifier, which is called Aptamer Based Cell-free Detection system(ABCD system, Figure 1). We developed this system to detect those biomarkers of protein-type for the purpose of disease detection or staging.
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                <h1>3.  Diagnosis</h1>
 +
                 <p class="reference">The third model mainly serves to deploy the cases of patients, let doctors check those cases and give diagnoses in time. <br>
 +
                    <strong>(1) Setting an Account: </strong> <br>Establish blockchain accounts, and input the names、keywords and identities. After that, users can obtain the addresses of their accounts on Ethereum. <br>
 +
                    <strong>(2) Buying currencies and check the balance: </strong> <br>Which is used for the consumption of deploying cases for miners. <br>
 +
                    <strong>(3) Deploying cases: </strong> <br>Fill in related information according to all the intelligent-treaty-templets of cases, so that the information in cases could be published on Ethereum in the form of intelligent treaty. <br>
 +
                    <strong>(4) Check the Cases: </strong> <br>Doctor users can check all the cases deployed by patients, and make diagnoses accordingly. <br>
 
                 </p>
 
                 </p>
                <p class="F1">
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            </section>
                    <img src="https://static.igem.org/mediawiki/2018/e/e2/T--XMU-China--ABCD_system.png">
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            <section id="Software_design" class="js-scroll-step">
                    <p class="Figure_word">Figure 1. <strong>A</strong>ptamer <strong>B</strong>ased <strong>C</strong>ell-free <strong>D</strong>etection system.</p>
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                <div class="headline">
                 </p>
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                    Software design
                <h1>Abstract</h1>
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                </div>
                <p>The core of the ABCD system is the specific binding of the aptamer and its target protein. We immobilize the aptamer-“complementary strand” complex on a solid phase, using a “competitive” approach to free the “complementary strand”; then the “complementary strand” was detected using the trans-cleavage property of the Cpf1 protein, which allows the fluorescence recovery of the static quenched complex whose fluorophore and quencher are linked by a ssDNA. In summary, we initially transform the protein signal to the acid signal, then transform the nucleic acid signal to the fluorescence signal. We use aptamer SYL3C<sup>[12]</sup> against EpCAM, an epithelial cell adhesion molecule that is highly expressed on the surface of adenocarcinoma cells, to test the feasibility of our system.</p>
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                <p>Based on the improved C/S(Client/Server) structure, we set up a cloud server for exchanging information between software and hardware, storing database information and realizing related functions. With the rapid development of the Internet, mobile office and distributed office are becoming more and more popular. </p>
                <h1 class="reference">Reference</h1>
+
                 <p>Considering that the scale of our hardware will involve grassroots hospitals in towns and villages, it is a necessity for our system to be more scalable. In order to avoid the limitations of being applicable to LAN only, and to enhance the universality of software applications, we put the server in the cloud. Through the cloud LAN, terminals from LANs in different networks can be connected to form a new LAN, so that all internal connections are made. </p>
                 <p>
+
                 <p>The terminal devices can access on another, which enables remote control of the hardware by our software. Different from the traditional C/S structure, we put the data in the cloud server. The business logic of the software is also implemented only by the server. </p>
                    [1] Janet Iwasa, Wallace Marshall. Karp's Cell and Molecular Biology: Concepts and Experiments (8th ed.). <i>Wiley: Hoboken, NJ.</i> <strong>2016</strong>, 48-49.
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                <p>The app client does not save any business data and database connection information, which ensures the security to some extent, and also ensures the real-time and consistency of the data. In the future, if the number of users increases gradually, we can increase the number of servers by establishing a cluster server system smoothly. During this process, what we need to do is only realizing the load balance between each server, and it is unnecessary to give up the original server. The App is written with the react native framework, which supports android and ios, and has strong compatibility.</p>
                    <br>[2] J. K. Aronson. Biomarkers and surrogate endpoints. <i>British Journal of Clinical Pharmacology.</i> <strong>2005</strong>, 59, 491-494.
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                <p class="F25"><img src="https://static.igem.org/mediawiki/2018/c/c7/T--XMU-China--software_1.png">
                    <br>[3] Kyle Strimbu, Jorge A. Tavel. What are biomarkers? <i>Current Opinion in HIV and AIDS.</i> <strong>2010</strong>, 5, 463–466.
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                     <p class="Figure_word"><strong>Figure2</strong>. The communication structure </p>
                    <br>[4] Biomarkers Definitions Working Group. Biomarkers and surrogate endpoints: Preferred definitions and conceptual framework. <i>Clin. Pharmacol. Ther.</i> <strong>2001</strong>, 69, 89-95.
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                    <br>[5] Hongquan Zhang, Feng Li, Brittany Dever, Xing-Fang Li, X. Chris Le. DNA-Mediated Homogeneous Binding Assays for Nucleic Acids and Proteins. <i>Chem. Rev.</i> <strong>2013</strong>, 113, 2812-2841.
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                    <br>[6] Larry Gold, Barry Polisky, Olke Uhlenbeck, Michael Yarus. Diversity of Oligonucleotide Functions. <i>Annu. Rev. Biochem.</i> <strong>1995</strong>, 64, 763-797.
+
                    <br>[7] Camille L.A. Hamula, Jeffrey W. Guthrie, Hongquan Zhang, Xing-Fang Li, X. Chris Le. Selection and analytical applications of aptamers. <i>Trends Anal. Chem.</i> <strong>2006</strong>, 25, 681-691.
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                    <br>[8] Renee K. Mosing, Shaun D. Mendonsa, Michael T. Bowser. Capillary Electrophoresis-SELEX Selection of Aptamers with Affinity for HIV-1 Reverse Transcriptase. <i>Anal. Chem.</i> <strong>2005</strong>, 77, 6107-6112.
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                    <br>[9] Maxim Berezovski, Andrei Drabovich, Svetlana M. Krylova, Michael Musheev, Victor Okhonin, Alexander Petrov, Sergey N. Krylov. Nonequilibrium Capillary Electrophoresis of Equilibrium Mixtures: A Universal Tool for Development of Aptamers. <i>J. Am. Chem. Soc.</i> <strong>2005</strong>, 127, 3165-3171.
+
                    <br>[10] M Darmostuk, S Rimpelova, H Gbelcova, T Ruml. Current approaches in SELEX: an update to aptamer selection technology. <i>Biotechnology Advances.</i> <strong>2015</strong>, 33, 1141-1161.
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                     <br>[11] Sumedha D. Jayasena. Aptamers: an emerging class of molecules that rival antibodies in diagnostics. <i>Clin. Chem.</i> <strong>1999</strong>, 45, 1628-1650.
+
                    <br>[12] Yanling Song, Zhi Zhu, Yuan An, Weiting Zhang, Huimin Zhang, Dan Liu, Chundong Yu, Wei Duan, Chaoyong James Yang. Selection of DNA Aptamers against Epithelial Cell Adhesion Molecule for Cancer Cell Imaging and Circulating Tumor Cell Capture. <i>Anal Chem.</i> <strong>2013</strong>, 85, 4141-4149.
+
 
                 </p>
 
                 </p>
 +
                <p>Hardware control communication: Both the app part and the hardware part communicate with the server by using the web-socket protocol. The control messages are sent to the hardware from the app end, and the hardware realizes the function after being transmitted to the hardware module by the server. After that, the corresponding results are returned to the server. And a series of analyses and operations are carried out on the server side before finally transmitting back to the app.</p>
 
             </section>
 
             </section>
             <section id="OMVs" class="js-scroll-step">
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             <section id="Picture_analysis_process" class="js-scroll-step">
 
                 <div class="headline">
 
                 <div class="headline">
                     OMVs
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                     Picture analysis process
 
                 </div>
 
                 </div>
                 <h1>Background</h1>
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                 <p class="video"><video src="https://static.igem.org/mediawiki/2018/a/a9/T--XMU-China--software2.mp4" controls></video></p>
                 <p>Outer-membrane vesicles (OMVs) are lipid vesicles commonly produced by Gram-negative bacteria, which are filled with periplasmic content and are 20-250 nm in diameters (Figure 1). The production of OMVs allows bacteria to interact with their environment, and OMVs have been found to mediate diverse functions, including promoting pathogenesis, and enabling bacterial delivery of nucleic acids and proteins. A recent paper by Kojima R et al. 2018, demonstrated an EXOtic device that can produce exosomes with specific nucleic acids cargo (Figure 2). We were impressed by the amazing OMVs and EXOtic device and came up with an idea to design a cell-free system to enable specific siRNA to be encapsulated into OMVs for cancer treatment.
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                 <p>Image recognition algorithm: We used Convolutional neural network CNN algorithm in deep learning algorithm. Through the picture taken by the hardware, we need to analyze which holes fluoresce in the picture to determine the corresponding diseases. </p>
 +
                <p class="F3"><img src="https://static.igem.org/mediawiki/2018/7/72/T--XMU-China--software_2.png">
 +
                    <p class="Figure_word"><strong>Figure3</strong>. Pictures' transfer and conversion process</p>
 +
                </p>
 +
                <p>Firstly, we trained through the data sets which we had collected and got the model in advance. Then, we used the model to classify the photo taken by the hardware to obtain the specific pathological types to which the photo belonged. Because there were too many parameters in the fully connected layer of the fully connected neural network, not only will the calculation speed slow down, but also the over-fitting problem will occur. Therefore, we used the convolutional neural network structure to classify the image. The convolutional neural network architecture which we used is shown in the following picture:</p>
 +
                <p class="F1"><img src="https://static.igem.org/mediawiki/2018/d/d0/T--XMU-China--software_3.png">
 +
                    <p class="Figure_word"><strong>Figure4</strong>. The convolutional neural network architecture</p>
 
                 </p>
 
                 </p>
                 <p class="F2">
+
                <p>First, the input layer. We transformed the captured image on the server and converted the pixel to 32*32. Since it was the RGB color mode, we inputted a 32*32*3 three-dimensional matrix. Starting from the input layer, the three-dimensional matrix of the previous layer will be transformed into the next-level three-dimensional matrix through the neural network structure, and will finally reach connection layer. </p>
                    <img src="https://static.igem.org/mediawiki/2018/4/43/T--XMU-China--OMVs11.png">
+
                <p>After that, we performed a four-layer convolution operation. Through the convolution layer processing, the depth of the node matrix will increase. When it came to the corresponding pooling layer, the size of the matrix would be reduced, which further reduced the number of nodes in the last fully connected layer, thereby reducing the parameters in the entire nerve network. </p>
                     <p class="Figure_word">Figure 2. The cell envelope of Gram-negative bacteria consists of two membranes, the outer membrane and the cytoplasmic membrane. Envelope stability comes from various crosslinks including the non-covalent interactions between the PG and the porin outer-membrane protein A (OmpA).</p>
+
                <p>Then, the features of the image were extracted through two fully connected layers, and the final classification result was given. Finally, the probability distributions of the pictures’ belonging to the different examples was obtained through the softmax layer. </p>
 +
                <p>Convolution layer. In the convolutional layer, we used a filter to convert a sub-node matrix of the current layer neural network into a unit node matrix of the next layer of neural networks. This simulated the operating process of a convolutional layer:</p>
 +
                 <p class="F3"><img src="https://static.igem.org/mediawiki/2018/b/ba/T--XMU-China--software_4.png">
 +
                     <p class="Figure_word"><strong>Figure5</strong>. The operating process of a convolutional layer</p>
 
                 </p>
 
                 </p>
                 <p class="F2">
+
                 <p class="F3">$g(i)=f(\sum_{x=1}^{X}\sum_{y=1}^{Y}\sum_{z=1}^{Z}a_{x,y,z}\times w^{i}_{x,y,z}+b^i)$</p>
                    <img src="https://static.igem.org/mediawiki/2018/c/c0/T--XMU-China--OMVs12.png">
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                <p>The value of the i-th node in the identity matrix is $g(i), w^{i}_{x, y, z}$,which represents the filter input node for the i-th node in the output unit node matrix (x, y, z). b^i represents the offset term parameter corresponding to the i-th output node. And f is the activation function. In this project we choose 5*5 and 3*3 filter size and used ReLU as the activation function.</p>
                     <p class="Figure_word">Figure 3. Schematic illustration of the EXOtic devices. Exosomes are nanoscale extracellular lipid bilayer vesicles of endocytic origin, and they are secreted by nearly all cell types in physiological and pathological conditions. Exosomes containing the RNA packaging device (CD63-L7Ae) and mRNA (e.g., nluc-C/Dbox) can efficiently deliver specific nucleic acids.</p>
+
                <p>Pool layer. The pooling layer can effectively reduce the size of the matrix, thereby reducing the parameters in the final fully connected layer. Using a pooled layer can both speed up calculations and prevent overfitting problems. The pooling layer that uses the maximum operation is called the max pooling layer. In this project we used the max pooling layer.</p>
 +
                <p class="F3"><img src="https://static.igem.org/mediawiki/2018/7/77/T--XMU-China--software_5.png">
 +
                     <p class="Figure_word"><strong>Figure6</strong>. The operating process of a pooling layer</p>
 
                 </p>
 
                 </p>
                <h1>Abstract</h1>
+
                 <p>Through training, we can see that the loss value of the model is convergent, the accuracy rate can reach 99.90%, and the model is reliable.</p>
                 <p>Not only eukaryotes but also prokaryotes can produce nanoscale bubbles to fulfill diverse functions, such as cellular communication, surface modifications and the elimination of undesired components. Additionally, because of this functional versatility, OMVs have been explored as a platform for bioengineering applications. This year, we XMU-China decide to utilize OMVs as a cell-free platform to deliver our nucleic acids agents to facilitate therapeutic targeting of oncogenic KRAS in pancreatic cancer.</p>
+
 
                 <p class="F3">
 
                 <p class="F3">
                     <img src="https://static.igem.org/mediawiki/2018/9/9d/T--XMU-China--OMVs13.png">
+
                     <img src="https://static.igem.org/mediawiki/2018/1/10/T--XMU-China--software_6.png">
                     <p class="Figure_word">Figure 4. We utilize a split protein SpyTag/SpyCatcher (ST/SC) bioconjugation system to create a synthetic linkage between protein OmpA and archaeal ribosomal protein L7Ae. We fuse SpyTag with OmpA at its C-termini and N-termini respectively.</p>
+
                     <p class="Figure_word"><strong>Figure7</strong>. Model's training process</p>
 
                 </p>
 
                 </p>
 
                 <p class="F3">
 
                 <p class="F3">
                     <img src="https://static.igem.org/mediawiki/2018/d/da/T--XMU-China--OMVs14.png">
+
                     <img src="https://static.igem.org/mediawiki/2018/1/1a/T--XMU-China--software_7.png">
                     <p class="Figure_word">Figure 5. After the induction of IPTG and Arabinose, we can get L7Ae-SpyCatcher and siRNA-C/Dbox. Archaeal ribosomal protein L7Ae owns the ability to bind with C/Dbox RNA structure.</p>
+
                     <p class="Figure_word"><strong>Figure8</strong>. Loss function curve</p>
                </p>
+
                <p class="F4">
+
                    <img src="https://static.igem.org/mediawiki/2018/9/97/T--XMU-China--OMVs15.png">
+
                    <p class="Figure_word">Figure 6. With the interaction between SpyTag and SpyCatcher, and the ability of L7Ae to be bind with C/Dbox, we can produce customizable and cell-free OMVs containing specific siRNA to traget for oncogenic gene.</p>
+
                </p>
+
                <h1 class="reference">Reference</h1>
+
                <p>
+
                    [1] Kojima R, Bojar D, Rizzi G, et al. Designer exosomes produced by implanted cells intracerebrally deliver therapeutic cargo for Parkinson’s disease treatment[J]. <i>Nature Communications.</i> <strong>2018</strong>, 9(1):1305. <br>
+
                    [2] Alves N J, Turner K B, Medintz I L, et al. Protecting enzymatic function through directed packaging into bacterial outer membrane vesicles: [J]. <i>Scientific Reports</i>, <strong>2016</strong>, 6:24866. <br>
+
                    [3] Schwechheimer C, Kuehn M J. Outer-membrane vesicles from Gram-negative bacteria: biogenesis and functions. [J]. <i>Nature Reviews Microbiology</i>, <strong>2015</strong>, 13(10):605-19. <br>
+
                    [4] Vanaja S K, Russo A J, Behl B, et al. Bacterial Outer Membrane Vesicles Mediate Cytosolic Localization of LPS and Caspase-11 Activation. [J]. <i>Cell</i>, <strong>2016</strong>, 165(5):1106-1119. <br>
+
                    [5] Kamerkar S, Lebleu V S, Sugimoto H, et al. Exosomes facilitate therapeutic targeting of oncogenic KRAS in pancreatic cancer[J]. <i>Nature</i>, <strong>2017</strong>, 546(7659):498-503. <br>
+
                    [6] https://en.wikipedia.org/wiki/Pancreatic_cancer<br>
+
 
                 </p>
 
                 </p>
 
             </section>
 
             </section>
             <section id="Supporting" class="js-scroll-step">
+
             <section id="Block_chain" class="js-scroll-step">
                 <div class="headline">
+
                <div class="headline">Block chain</div>
                     Supporting
+
                <p>Why did we choose block chain technology?</p>
 +
                <p>The block chain accelerates the arrival of the“digital credit society” with its characteristics of decentral, reliable, immutable, trustworthy and anonymous. In the medical industry, what we need more is a highly trusted mechanism to protect the rights of the patients. Therefore, we chose block chain technology which enabled the patients to deploy their own medical records, and according to which doctors carried out the diagnoses. </p>
 +
                <p>Based on the block chain technology under Ethereum, the pow consensus mechanism was used. When generating a block, the system allows all the nodes to calculate a random number fairly. The node of the random number which was found first will be the producer of the block, and will get the corresponding block reward. Since the hash function is a hash function, the only way to solve a random number mathematically is through the method of exhaustion. The randomness is very good, and everyone can participate in the execution of the protocol. </p>
 +
                <p>Due to the setting of the Merkel tree’s root, the verification process of the solution of the hash function can also be implemented quickly. Therefore, everyone can participate without the permission of a centralized authority, and each participant does not need identity authentication. It can be said that the pow consensus mechanism algorithm is simple and easy to implement. The nodes can also enter freely and decentralize to a high extent. Destroying the system requires a huge investment. Therefore, the system could be said as extremely safe. The seletion of the block producer is realized by solving the hash function by the node. The final process of generating and verifying the proposal to the consensus is purely a mathematical problem, and the nodes can reach a consensus without exchanging additional information.</p>
 +
            </section>
 +
            <section id="Application" class="js-scroll-step">
 +
                 <div class="headline ">
 +
                     Application
 
                 </div>
 
                 </div>
                <h1>Background</h1>
+
                 <p>We set up an Ethereum private chain belonging to our system on the server. Every doctor and patient acts as an account on the block chain node. Everyone will get an address on the private chain of Ethereum through the passwords set by themselves. The process of generating this address is generating a private key from the secp256k1 curve first, which is composed of random 256 bits, and then use the elliptic curve digital signature algorithm (ECDSA) to map the private key into a public key. After that, the public key becomes 256bit through the Keccak-256 one-way hash function, and then takes 160 bits as the address.</p>
                 <p>Tardigrades are able to tolerate almost complete dehydration by reversibly switching to an ametabolic state. This ability is called anhydrobiosis.<sup>[1]</sup>Tardigrade-specific intrinsically disordered proteins (TDPs) are essential for desiccation olerance.<sup>[2]</sup>2012, Takekazu Kunieda and his team identified five abundant heat-soluble proteins in the tardigrades, which can prevent protein-aggregation in dehydrated conditions in other anhydrobiotic organisms.<sup>[1]</sup>
+
                 <p class="video"><video src="https://static.igem.org/mediawiki/2018/b/b1/T--XMU-China--software.mp4" controls></video></p>
                </p>
+
                 <p>Smart contracts can be deployed to private chains through addresses. The smart contract is a computer protocol designed to disseminate, verify or execute contracts in an informational way. In our system, we wrote the medical record in the form of a smart contract as a template, and the users can fill in personal information and medical record information. Therefore, the doctors can view all the medical records deployed to the private chain. That is to say, the doctors and can even choose from the medical records to make diagnoses, and write their diagnosing results into the medical records deployed by the patients. In intelligence contracts, we have written a one-on-one mechanism for doctors and patients, that is, one patient can only have one doctor to receive the consultation. Once the patient is admitted, other doctors will not be able to modify the diagnoses. </p>
                 <p class="F4">
+
                <p>In block chain technology, the hash algorithm is mainly used to receive a plaintext and convert it into an output hash with a short length and a fixed number of bits in an irreversible way. Because this encryption process is irreversible, it means that no information related to the original text can be inferred by outputting the contents of the hash. Any change in the input information, even a single change of the digit, will result in a significant change in the hash result. Based on the one-to-one correspondence between the output hash and the input text, the hash algorithm can be used to verify whether the information has been modified.</p>
                    <img src="https://static.igem.org/mediawiki/2018/2/2d/T--XMU-China--TDP1.png">
+
                 <p>Due to fact that the block chain technology could not be modified, once the case is viewed, the authenticity and accuracy of the case information can be guaranteed. Once there is a doctor-patient conflict or a medical consultation, we can refer to the accountability system, and therefore protect the rights of both the doctors and the patients. The information of each user and case address, together with related information is stored in the server's levedb database. In the future, we can also access the public health system database to realize the popularization.</p>
                    <p class="Figure_word">Figure 7. Stage Photo of Tardigrades in Ant-Man 2.</p>
+
                 <p class="F3"><img src="https://static.igem.org/mediawiki/2018/1/1f/T--XMU-China--software_8.png">
                </p>
+
                     <p class="Figure_word"><strong>Figure9</strong>. Interactive process</p>
                 <p>In 2017, Thomas C. Boothby and his team segregated three TDP proteins in the water bears and explored their mechanism of action<sup>[3]</sup>. This is a schematic diagram of the mechanism they have done so far. At the same time, one of the 2017 iGEM teams <a href="https://2017.igem.org/Team:TUDelft/Design"><span class="click_here">TUDelft</span></a>, attempted to preserve the Cas13a protein using the TDP proteins, and they also tried to preserve the bacteria with the TDP proteins and obtained amazing outcome.
+
                    In our project, we are going to use TDPs to help preserve the protein Cas12a and OMVs.
+
                </p>
+
                <h1>Abstract</h1>
+
                 <p>We have carried out research on TDP proteins this year. On the one hand, we plan to preserve the Cas12a required for protein detection and OMVs required for treatment with TDPs. On the other hand, as the wiki says, TDP is a new biological activity protector with great potential. So we are going to use TDP proteins to simplify existing methods of preserving proteins and bacteria.
+
                    There are two novel protein families with distinct subcellular localizations named Cytoplasmic Abundant Heat Soluble (CAHS) and Secretory Abundant Heat Soluble (SAHS) protein families, according to their localization. In our project, SAHS1 was used to preserve the proteins and CAHS1 was used for the preservation of the bacteria.
+
                </p>
+
                 <p class="F4">
+
                    <img src="https://static.igem.org/mediawiki/2018/a/aa/T--XMU-China--TDP2.png">
+
                     <p class="Figure_word">Figure 8. The Expression of TDPs When The Tardigrades Suffer Form Fast Drying and Slow Drying.(Thomas C. Boothby et al. 2017).</p>
+
                </p>
+
                <h1>Reference</h1>
+
                <p class="reference">
+
                    [1]. Yamaguchi A. Two Novel Heat-Soluble Protein Families Abundantly Expressed in an Anhydrobiotic Tardigrade. <i>PLoS ONE</i>, <strong>2012</strong>;7(8):e44209. <br>
+
[2]. Boothby TC. Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation. <i>Mol Cell</i>. <strong>2017</strong> Mar16;65(6):975-984.e5.
+
 
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Latest revision as of 02:47, 18 October 2018

Team:XMU-China/Software - 2018.igem.org

Software
Summary

Our team has developed an app, which makes a combination of AI algorithm and blockchain. It is designed in order to better control the hardware, making it more convenient and handy for grass-root hospitals and their patients, and facilitate the doctors' diagnosis. More details about the principle of the software, please switch to our code on the Github.

Figure1. App interface

Function introduction

1. The Hardware Control

The first model mainly targets for the specific operations of the hardware.
(1) Engine Start Stop:
Users could click the button, “Engine Start Stop”, to automatically start the hardware, and complete a series of tasks including centrifugation and pictures-taking.
(2) Step – Control:
a. Two-Sliders Controller: Being used to set the time and speed of the hardware engines.
b. The On-off Controller: Being used to start the hardware and send the speed and time the hardware needed for operating.
c. The Pictures-taking Controller: used to control the pick-up head of the camera to take photos.
(3) Show the real-time speed of the engine.

2. The detection of the images

The second model is mainly responsible for the analysis of pictures taken by the camera.
(1) The Loading Controller:
Showing the pictures taken after the operation of the hardware.
(2) Analysis Controller:
Obtain the aperture gaps of the fluorescence and corresponding diseases’ information through analyzing those taken pictures.

3. Diagnosis

The third model mainly serves to deploy the cases of patients, let doctors check those cases and give diagnoses in time.
(1) Setting an Account:
Establish blockchain accounts, and input the names、keywords and identities. After that, users can obtain the addresses of their accounts on Ethereum.
(2) Buying currencies and check the balance:
Which is used for the consumption of deploying cases for miners.
(3) Deploying cases:
Fill in related information according to all the intelligent-treaty-templets of cases, so that the information in cases could be published on Ethereum in the form of intelligent treaty.
(4) Check the Cases:
Doctor users can check all the cases deployed by patients, and make diagnoses accordingly.

Software design

Based on the improved C/S(Client/Server) structure, we set up a cloud server for exchanging information between software and hardware, storing database information and realizing related functions. With the rapid development of the Internet, mobile office and distributed office are becoming more and more popular.

Considering that the scale of our hardware will involve grassroots hospitals in towns and villages, it is a necessity for our system to be more scalable. In order to avoid the limitations of being applicable to LAN only, and to enhance the universality of software applications, we put the server in the cloud. Through the cloud LAN, terminals from LANs in different networks can be connected to form a new LAN, so that all internal connections are made.

The terminal devices can access on another, which enables remote control of the hardware by our software. Different from the traditional C/S structure, we put the data in the cloud server. The business logic of the software is also implemented only by the server.

The app client does not save any business data and database connection information, which ensures the security to some extent, and also ensures the real-time and consistency of the data. In the future, if the number of users increases gradually, we can increase the number of servers by establishing a cluster server system smoothly. During this process, what we need to do is only realizing the load balance between each server, and it is unnecessary to give up the original server. The App is written with the react native framework, which supports android and ios, and has strong compatibility.

Figure2. The communication structure

Hardware control communication: Both the app part and the hardware part communicate with the server by using the web-socket protocol. The control messages are sent to the hardware from the app end, and the hardware realizes the function after being transmitted to the hardware module by the server. After that, the corresponding results are returned to the server. And a series of analyses and operations are carried out on the server side before finally transmitting back to the app.

Picture analysis process

Image recognition algorithm: We used Convolutional neural network CNN algorithm in deep learning algorithm. Through the picture taken by the hardware, we need to analyze which holes fluoresce in the picture to determine the corresponding diseases.

Figure3. Pictures' transfer and conversion process

Firstly, we trained through the data sets which we had collected and got the model in advance. Then, we used the model to classify the photo taken by the hardware to obtain the specific pathological types to which the photo belonged. Because there were too many parameters in the fully connected layer of the fully connected neural network, not only will the calculation speed slow down, but also the over-fitting problem will occur. Therefore, we used the convolutional neural network structure to classify the image. The convolutional neural network architecture which we used is shown in the following picture:

Figure4. The convolutional neural network architecture

First, the input layer. We transformed the captured image on the server and converted the pixel to 32*32. Since it was the RGB color mode, we inputted a 32*32*3 three-dimensional matrix. Starting from the input layer, the three-dimensional matrix of the previous layer will be transformed into the next-level three-dimensional matrix through the neural network structure, and will finally reach connection layer.

After that, we performed a four-layer convolution operation. Through the convolution layer processing, the depth of the node matrix will increase. When it came to the corresponding pooling layer, the size of the matrix would be reduced, which further reduced the number of nodes in the last fully connected layer, thereby reducing the parameters in the entire nerve network.

Then, the features of the image were extracted through two fully connected layers, and the final classification result was given. Finally, the probability distributions of the pictures’ belonging to the different examples was obtained through the softmax layer.

Convolution layer. In the convolutional layer, we used a filter to convert a sub-node matrix of the current layer neural network into a unit node matrix of the next layer of neural networks. This simulated the operating process of a convolutional layer:

Figure5. The operating process of a convolutional layer

$g(i)=f(\sum_{x=1}^{X}\sum_{y=1}^{Y}\sum_{z=1}^{Z}a_{x,y,z}\times w^{i}_{x,y,z}+b^i)$

The value of the i-th node in the identity matrix is $g(i), w^{i}_{x, y, z}$,which represents the filter input node for the i-th node in the output unit node matrix (x, y, z). b^i represents the offset term parameter corresponding to the i-th output node. And f is the activation function. In this project we choose 5*5 and 3*3 filter size and used ReLU as the activation function.

Pool layer. The pooling layer can effectively reduce the size of the matrix, thereby reducing the parameters in the final fully connected layer. Using a pooled layer can both speed up calculations and prevent overfitting problems. The pooling layer that uses the maximum operation is called the max pooling layer. In this project we used the max pooling layer.

Figure6. The operating process of a pooling layer

Through training, we can see that the loss value of the model is convergent, the accuracy rate can reach 99.90%, and the model is reliable.

Figure7. Model's training process

Figure8. Loss function curve

Block chain

Why did we choose block chain technology?

The block chain accelerates the arrival of the“digital credit society” with its characteristics of decentral, reliable, immutable, trustworthy and anonymous. In the medical industry, what we need more is a highly trusted mechanism to protect the rights of the patients. Therefore, we chose block chain technology which enabled the patients to deploy their own medical records, and according to which doctors carried out the diagnoses.

Based on the block chain technology under Ethereum, the pow consensus mechanism was used. When generating a block, the system allows all the nodes to calculate a random number fairly. The node of the random number which was found first will be the producer of the block, and will get the corresponding block reward. Since the hash function is a hash function, the only way to solve a random number mathematically is through the method of exhaustion. The randomness is very good, and everyone can participate in the execution of the protocol.

Due to the setting of the Merkel tree’s root, the verification process of the solution of the hash function can also be implemented quickly. Therefore, everyone can participate without the permission of a centralized authority, and each participant does not need identity authentication. It can be said that the pow consensus mechanism algorithm is simple and easy to implement. The nodes can also enter freely and decentralize to a high extent. Destroying the system requires a huge investment. Therefore, the system could be said as extremely safe. The seletion of the block producer is realized by solving the hash function by the node. The final process of generating and verifying the proposal to the consensus is purely a mathematical problem, and the nodes can reach a consensus without exchanging additional information.

Application

We set up an Ethereum private chain belonging to our system on the server. Every doctor and patient acts as an account on the block chain node. Everyone will get an address on the private chain of Ethereum through the passwords set by themselves. The process of generating this address is generating a private key from the secp256k1 curve first, which is composed of random 256 bits, and then use the elliptic curve digital signature algorithm (ECDSA) to map the private key into a public key. After that, the public key becomes 256bit through the Keccak-256 one-way hash function, and then takes 160 bits as the address.

Smart contracts can be deployed to private chains through addresses. The smart contract is a computer protocol designed to disseminate, verify or execute contracts in an informational way. In our system, we wrote the medical record in the form of a smart contract as a template, and the users can fill in personal information and medical record information. Therefore, the doctors can view all the medical records deployed to the private chain. That is to say, the doctors and can even choose from the medical records to make diagnoses, and write their diagnosing results into the medical records deployed by the patients. In intelligence contracts, we have written a one-on-one mechanism for doctors and patients, that is, one patient can only have one doctor to receive the consultation. Once the patient is admitted, other doctors will not be able to modify the diagnoses.

In block chain technology, the hash algorithm is mainly used to receive a plaintext and convert it into an output hash with a short length and a fixed number of bits in an irreversible way. Because this encryption process is irreversible, it means that no information related to the original text can be inferred by outputting the contents of the hash. Any change in the input information, even a single change of the digit, will result in a significant change in the hash result. Based on the one-to-one correspondence between the output hash and the input text, the hash algorithm can be used to verify whether the information has been modified.

Due to fact that the block chain technology could not be modified, once the case is viewed, the authenticity and accuracy of the case information can be guaranteed. Once there is a doctor-patient conflict or a medical consultation, we can refer to the accountability system, and therefore protect the rights of both the doctors and the patients. The information of each user and case address, together with related information is stored in the server's levedb database. In the future, we can also access the public health system database to realize the popularization.

Figure9. Interactive process