Team:UCSD Software/Teaml

From 2014.igem.org

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and open the template in the editor.
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<html>
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    <head>
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        <title>About</title>
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        <meta charset="UTF-8">
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        <meta name="viewport" content="width=device-width, initial-scale=1.0">
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        <link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
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        <script src="https://code.jquery.com/jquery-2.1.1.min.js"></script>
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        <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js"></script>
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        <script src="http://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
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        <script>
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          $(document).ready(function(){
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    //redirecting to other pages
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    $("#home").click(function(){
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      window.location.href="index.html";
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    });
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    $("#about").click(function(){
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      window.location.href="AboutPage.html";
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    });
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    $("#documentation").click(function(){
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      window.location.href="sampleHome.html";
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    });
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    $("#wiki").click(function(){
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      window.location.href="https://2014.igem.org/Team:UCSD_Software";
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    });
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    $("#app").click(function(){
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      window.location.href="AppPage.html";
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    });
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    $("#thumbThree").click(function(){
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      window.location.href="AppPage.html";
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    });
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    $("#contact").click(function(){
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      window.location.href="contactPage.html";
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    });
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    //server functions
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      //contactUs page
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      $('#submitContact').click(function(){
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      alert("your information is getting sent");
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      var name = $("#name").val();
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      var email = $('#email').val();
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      var affiliation = $('#affiliation').val();
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      var message = $('#message').val();
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      var data = {name:name, email:email, affiliation:affiliation,message: message, command:"contactUs"};
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      $.get("AuthenticationServlet", data, function(done){
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          alert(done);
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      });
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    }); 
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      $('#register').click(function(){
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          alert("clicked");
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          var name = $("#newName").val();
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          var email = $("#newPassword").val();
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          alert(name + email);
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          var data = {name: name, email:email, command:"register"};
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          $.get("AuthenticationServlet", data, function(done){
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              alert(done);
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          });
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      });
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}); 
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<hl> Name of person </hl>
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        </script>
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    <style>
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body{
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  background-color: white;
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}
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#nav{
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  background-color: #003D99;
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  color: white;
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  box-sizing: border-box;
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}
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#nav .btn:hover{
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<ol>
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  color: gold;
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}
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#nav .btn:active{
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<li> what they did </li>
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  color: white;
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  background-color: rgba(204,204,204,0.5);
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}
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#mainPic{
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  border: none;
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  color:#00004C;
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  font-size: 25px;
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}
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#mainPic .img-responsive{
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<li> </li>
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    height: 600px;
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    width: 100%;
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    border: 2px solid blue;
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}
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#underPic{
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    height:300px;
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    width: 350px;
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    background-color:white;
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    color: #00004C;
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    text-decoration: none;
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    border: none;
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    text-align: center;
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}
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#underPic:hover{
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}
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#underPic .img-circle{
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</ol>
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    border: 2px solid #00004C;
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    height: 200px;
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}
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#underPic .img-circle:hover{
 
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    border: 2px solid blue;
 
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}
 
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#gradPic{
 
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    height:300px;
 
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    width: 350px;
 
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    background-color:white;
 
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    color: #00004C;
 
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    text-decoration: none;
 
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    border: none;
 
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}
 
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#gradPic:hover{
 
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}
 
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#gradPic .img-circle:hover{
 
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    //border: 2px solid blue;
 
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}
 
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#gradPic .img-circle{
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<Div>
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    border: 2px solid gold;
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    width: 200px;
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li{
 
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    list-style: none;
 
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.row{
 
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    margin: 40px;
 
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}
 
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h1{
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<Div class = "container-fluid" id = "one">
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    margin-bottom: 30px;
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}
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 +
<hl> Kwat </hl>
 +
<ol>
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<li> Generated Pydoc </li>
 +
<li> Learnt SQL </li>
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//modal
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<li> Learnt Petri Nets </li>
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//modal stuff
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#modalBodyLogin{
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}
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#loginModal{
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</ol>
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    border: 2px solid white;
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    margin: auto;
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    background-image: url("ProfilePics/network.png");
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    background-repeat: no-repeat;
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    background-size: 100%;
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    text-align: center;
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    //opacity: .9;
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    height: 100%;
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    background-color: white;
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}
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#modalInput{
 
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    padding: 10px;
 
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    margin: auto;
 
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    height: 250px;
 
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    border: 2px solid black;
 
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logger{
 
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    height: 400px;
 
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    width: auto;
 
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    margin: auto;
 
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    border: none;
 
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}
 
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.logger:hover{
 
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    background-color: gold;
 
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}
 
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#registration{
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<hl> Lauren </hl>
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    padding: 10px;
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    margin: 15px;
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}
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#registration input{
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    margin: 5px;
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    border-radius: 15px;
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}   
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}
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 +
<ol>
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.logger{
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<li> Did Learn Python the Hard Way </li>
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    height: 400px;
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    width: auto;
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    margin: auto;
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    border: none;
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}
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.logger:hover{
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<li> Read Python Wiki </li>
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    background-color: gold;
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}
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#registration{
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</ol>
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    padding: 10px;
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    margin: 15px;
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}
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#registration input{
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    margin: 5px;
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    border-radius: 15px;
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}
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    </style>
 
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    </head>
 
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    <body>
 
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        <!--navbar -->
 
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        <div class="container-fluid">
 
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            <!--navbar -->
 
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            <nav class="navbar navbar-header nav-justified" role="navigation" id='nav'>
 
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                <div class="btn-group  btn-group">
 
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                    <div class="btn btn-lg " id="home">Home</div>
 
-
                    <div class="btn btn-lg " id="about">About</div>
 
-
                    <div class="btn btn-lg " id="documentation">Documentation</div>
 
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                    <div class="btn btn-lg" id="wiki">Wiki</div>
 
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                    <div class="btn btn-lg" id="app">Application</div>
 
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                  <div class="btn btn-lg" id="contact">Contact</div>
 
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                    <div class="btn btn-lg"  data-toggle="modal" data-target="#loginModal">Register</div>
 
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              </div>
 
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                <div class="btn btn-lg pull-right " id="log" data-toggle="modal" data-target="#loginModal" ><span class="glyphicon glyphicon-log-in" id="userInfo"> LOGIN</span></div>
 
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            </nav>
 
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        </div>   
 
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    <!--navbar ends-->
 
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        <!--profiles-->
 
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        <div class="container">
 
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            <div class="row" id="groupInfo">
 
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                <div class="thumbnail" id="mainPic">
 
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                    <div class="page-header text-center">
 
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                        <h1 >UCSD iGEM SBiDer</h1>
 
-
                    </div>
 
-
                    <img class="img-responsive" src="ProfilePics/Team.JPG">
 
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                    <div class="caption">
 
-
                       
 
-
                            Genetic circuits are often difficult to engineer, requiring months to design, build, and test each individual genetic device involved in the circuit. SBiDer, a web tool developed by the UCSD Software iGEM team, will leverage existing devices to construct a database with consideration for the function of each device interpreted as boolean logic. The data can be queried by the user through SBiDer's visual interface to explore circuit designs. The displayed circuit's literature reference, characterization data, and images of included devices can be viewed through the built-in table. Basic validation of the circuit performance is also provided within in the interface. SBiDer's web of information can be expanded through user-generated additions to the database to improve the efficiency of the application and the accuracy of the models.
 
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                    </div>
 
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                </div>
 
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            </div>
 
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-
            <!--undergrads-->
 
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            <div class="row text-center" id="undergraduates">
 
-
                <div class="page-header"><h1 class="text-primary">The Team </h1></div>
 
-
                <div class="col-md-4">
 
-
                    <div class="thumbnail" id="underPic">
 
-
                        <img class="img-circle" src="ProfilePics/Huwate.jpg">
 
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                        <h2>Huwate Yeerna</h2>
 
-
                        <ul>
 
-
                            <li>Bioinformatics, 2015</li>
 
-
                            <li><a href="https://www.linkedin.com/in/hyeerna">LinkedIn</a></li>
 
-
                            <li></li>
 
-
                        </ul>
 
-
                    </div>
 
-
                </div>
 
-
                <div class="col-md-4">
 
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                    <div class="thumbnail" id="underPic">
 
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                        <img class="img-circle" src="ProfilePics/Joaquin.jpg">
 
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                        <h2>Joaquin Reyna</h2>
 
-
                        <ul>
 
-
                            <li>Bioinformatics, 2015</li>
 
-
                            <li><a href="">LinkedIn</a></li>
 
-
                            <li></li>
 
-
                        </ul>
 
-
                    </div>
 
-
                </div>
 
-
                    <div class="col-md-4">
 
-
                    <div class="thumbnail" id="underPic">
 
-
                        <img class="img-circle" src="http://3.images.spike.com/images/shows/blue-mountain-state/articles/thad_jail_blog2.jpg?quality=0.91">
 
-
                        <h2>Valeriy Sosnovskiy </h2>
 
-
                        <ul>
 
-
                            <li>Biochemistry, Computer Science, 2015</li>
 
-
                            <li><a href="https://www.linkedin.com/profile/view?id=306167421&trk=nav_responsive_tab_profile">LinkedIn</a></li>
 
-
                            <li></li>
 
-
                        </ul>
 
-
                    </div>
 
-
                </div>
 
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                </div>
 
-
            <div class="row text-center" id="undergraduates">
 
-
                <div class="col-md-4">
 
-
                    <div class="thumbnail" id="underPic">
 
-
                        <img class="img-circle" src="ProfilePics/Lauren.jpg">
 
-
                        <h2>Lauren Crudup </h2>
 
-
                        <ul>
 
-
                            <li>Bioengineering, 2015</li>
 
-
                            <li><a href="https://www.linkedin.com/profile/view?id=210400159&trk=nav_responsive_tab_profile_pic">LinkedIn</a></li>
 
-
                            <li></li>
 
-
                        </ul>
 
-
                    </div>
 
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                </div>
 
-
                <div class="col-md-4">
 
-
                    <div class="thumbnail" id="underPic">
 
-
                        <img class="img-circle" src="ProfilePics/Gary.JPG">
 
-
                        <h2>Gary Le</h2>
 
-
                        <ul>
 
-
                            <li>Human Biology, Business, 2017</li>
 
-
                            <li><a href="https://www.linkedin.com/pub/gary-le/a3/720/639">LinkedIn</a></li>
 
-
                            <li></li>
 
-
                        </ul>
 
-
                    </div>
 
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                </div>
 
-
                    <div class="col-md-4">
 
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                    <div class="thumbnail" id="underPic">
 
-
                        <img class="img-circle" src="ProfilePics/KP.jpg">
 
-
                        <h2>Kartikeya Puri</h2>
 
-
                        <ul>
 
-
                            <li>Computer Science, 2016</li>
 
-
                            <li><a href="https://www.linkedin.com/pub/kartikeya-puri/73/557/a09">LinkedIn</a></li>
 
-
                            <li></li>
 
-
                        </ul>
 
-
                    </div>
 
-
                </div>
 
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-
                </div>
 
-
            <div class="row text-center" id="undergraduates">
 
-
                <div class="col-md-4">
 
-
                    <div class="thumbnail" id="underPic">
 
-
                        <img class="img-circle" src="ProfilePics/Fred.jpg">
 
-
                        <h2>Luyao Zhou</h2>
 
-
                        <ul>
 
-
                            <li></li>
 
-
                            <li><a href="https://www.linkedin.com/profile/view?id=240077984&authType=NAME_SEARCH&authToken=k-dM&locale=en_US&trk=tyah&trkInfo=tarId%3A1411758557752%2Ctas%3Aluyao%20zhou%2Cidx%3A1-4-4">LinkedIn</a></li>
 
-
                            <li></li>
 
-
                        </ul>
 
-
                    </div>
 
-
                </div>
 
-
                <div class="col-md-4">
 
-
                    <div class="thumbnail" id="underPic">
 
-
                        <img class="img-circle" src="ProfilePics/Fernando.jpg">
 
-
                        <h2>Fernando Contreras</h2>
 
-
                        <ul>
 
-
                            <li>Biosystems, 2017</li>
 
-
                            <li><a href="https://www.linkedin.com/profile/view?id=372964518&trk=nav_responsive_tab_profile">LinkedIn</a></li>
 
-
                            <li></li>
 
-
                        </ul>
 
-
                    </div>
 
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                </div>
 
-
                    <div class="col-md-4">
 
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                    <div class="thumbnail" id="underPic">
 
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                        <img class="img-circle" src="">
 
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                        <h2>Rohit</h2>
 
-
                        <ul>
 
-
                            <li></li>
 
-
                            <li><a href="">LinkedIn</a></li>
 
-
                            <li></li>
 
-
                        </ul>
 
-
                    </div>
 
-
                </div>
 
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-
                </div>
 
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            <!--end of undergrads-->
 
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            <!--graduates-->
 
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            <div class="row text-center " id="graduates">
 
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-
                <div class="page-header"><h1 class="">Advisors</h1></div>
 
-
                <div class="col-md-6">
 
-
                    <div class="thumbnail text-center" id="gradPic">
 
-
                        <img class="img-circle" src="ProfilePics/Jenhan.jpg">
 
-
                        <h2>Jenhan Tao</h2>
 
-
                        <ul>
 
-
                            <li>Bioinformatics PhD, 2018<br>
 
-
                            Bioengineering, UC Berkeley, 2012
 
-
                            </li>
 
-
                            <li><a href="https://www.linkedin.com/pub/jenhan-tao/1a/763/83b">LinkedIn</a></li>
 
-
                                   
 
-
                        </ul>
 
-
                    </div>
 
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                </div>
 
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                <div class="col-md-6">
 
-
                    <p class="pull-left">
 
-
                                Jenhan is a PhD student in the Bioinformatics and Systems Biology program at UCSD. He's interested in utilizing computational technqiues to increase our capacity to understand complex biological problems such as cell signalling. This is Jenhan's second year working as an iGEM mentor. Previously Jenhan was involved in synthetic biology research as an iGEM team member at Boston University and as a research assistant at UC Berkeley, the BioFAB, and Boston University.
 
-
                                </p>
 
-
                </div>
 
-
                   
 
-
                   
 
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-
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-
                        <img class="img-circle" src="ProfilePics/Justin.jpg">
 
-
                        <h2>Justin Huang</h2>
 
-
                        <ul>
 
-
                            <li>Bioinformatics PhD, 2018<br>
 
-
                            Biology,Mathematics University of North Carolina-Chapel Hill, 2013
 
-
                            </li>
 
-
                            <li><a href="www.linkedin.com/in/justinkhuang">LinkedIn</a></li>
 
-
                                   
 
-
                        </ul>
 
-
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                <div class="col-md-6">
 
-
                    <p class="pull-left">
 
-
                      Justin Huang is a second year Bioinformatics PhD student at UC San Diego. Originally hailing from the great state of North Carolina, Justin completed his undergraduate studies with a BS in Biology and a BA in Mathematics from the University of North Carolina at Chapel Hill in 2013. Justin's research interests are in translational medicine, specifically in the role of translational medicine in cancer. Justin is also an avid sports fan, and an advocate for Asian American issues. You can follow him @huangger on Twitter. 
 
-
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-
                        <h2>Benjamin Kellman</h2>
 
-
                        <ul>
 
-
                            <li>Bioinformatics PhD, 2018<br>
 
-
                            Biology, University of Rochester, 2012
 
-
                            </li>
 
-
                            <li><a href="https://www.linkedin.com/profile/view?id=331388590&authType=NAME_SEARCH&authToken=3p2B&locale=en_US&trk=tyah2&trkInfo=tarId%3A1412133206770%2Ctas%3Aben%2Cidx%3A2-1-2">LinkedIn</a></li>
 
-
                                   
 
-
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                    </div>
 
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                        My name is Benjamin Kellman.  I am a PhD student at the University of California at San Diego studying Bioinformatics and Systems Biology.  My work uses existing formalisms in mathematics and computer science to consolidate the spurious information of experimental biology to a more codified rule set; many such reductions have already been made. I hope to apply fundamental biological axioms formalism to increase the power of my biological predictions.
 
-
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                        <h2>Andreas Dräger</h2>
 
-
                        <ul>
 
-
                            <li>Bioinformatics PhD, 2018<br>
 
-
                            Bioengineering, UC Berkeley, 2012
 
-
                            </li>
 
-
                            <li><a href="https://www.linkedin.com/in/andreasdraege">LinkedIn</a></li>
 
-
                                   
 
-
                        </ul>
 
-
                    </div>
 
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-
                <div class="col-md-6">
 
-
                    <p class="pull-left">
 
-
                        Andreas Dräger works as an independent research scholar in the Systems
 
-
Biology Research Group at UCSD. He studied bioinformatics at the Martin
 
-
Luther University in Halle and worked as an intern
 
-
at the Max Planck Institute for Molecular Genetics, Berlin, and at the
 
-
University of Illinois at Chicago. He did his PhD at the Center for
 
-
Bioinformatics in Tübingen and worked as visiting research student at
 
-
Keio University in Yokohama. The Faculty of Science (University of
 
-
Tuebingen) awarded his PhD thesis as the most outstanding work of 2011
 
-
and granted him a funding for an own graduate student.
 
-
                    </p>
 
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            <!--end of modal-->
+
 
-
    </body>
+
<hl> Gary </hl>
-
</html>
+
 
 +
<ol>
 +
 
 +
<li> Read Cytoscape.js API </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Joaquin </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Learnt Boolean Networks </li>
 +
 
 +
<li> Continued Petri Nets </li>
 +
 
 +
<li> Learnt Dynamic Programming and Path Traversal </li>
 +
 
 +
</ol>
 +
 
 +
<hl> Rohit </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Learnt Cytoscape </li>
 +
 
 +
<li> Learnt Python </li>
 +
 
 +
<li> Learnt Petri Nets </li>
 +
 
 +
</ol>
 +
 
 +
<hl> Fernando </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Finished command line interface </li>
 +
 
 +
<li> Acquired snippet of Linh's database </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<Div>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<Div class = "container-fluid" id = "two">
 +
 
 +
<hl> Kwat </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Learnt boolean networks </li>
 +
 
 +
<li> Continued learning Petri Nets</li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Lauren </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Learnt Boolean networks</li>
 +
 
 +
<li> Continued learning Petri nets </li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Gary </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Continued playing with Cytoscape.js add/remove nodes </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Joaquin </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Learnt Boolean Networks</li>
 +
 
 +
<li> Learnt reachability treees </li>
 +
 
 +
<li> Developed Entity Relationship Diagram </li>
 +
 
 +
</ol>
 +
 
 +
<hl> Rohit </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Learnt Boolean networks </li>
 +
 
 +
<li> Found SNAKES- a Python package that utilizes Petri nets </li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
<hl> Fernando </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Learnt Boolean networks </li>
 +
 
 +
<li> Disambiguated Linh's device composition</li>
 +
 
 +
<Div>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<Div>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<Div class = "container-fluid" id = "three">
 +
 
 +
<hl> Kwat </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Learnt SQL </li>
 +
 
 +
<li> Learnt traversal algorithms </li>
 +
 
 +
<li> Read assigned papers to populate database </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Lauren </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Petri net reading</li>
 +
 
 +
<li> CodeAcademy Python tutorials</li>
 +
 
 +
<li> BFS/DFS algorithms </li>
 +
 
 +
<li> Read papers to fill in database </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Gary </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Learnt basics of Angular.js </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Joaquin </hl>
 +
 
 +
<ol>
 +
 
 +
<li> SQl columns modification</li>
 +
 
 +
<li> Read papers to fill in database </li>
 +
 
 +
<li> </li>
 +
 
 +
</ol>
 +
 
 +
<hl> Rohit </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Learnt SQL </li>
 +
 
 +
<li> Conceptualized traversal algorithms </li>
 +
 
 +
<li> Read assigned papers to populate database </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Fernando </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Found possible approach to weigh our edges using "Quantitative Estimation of Activity and Quality for Collections of Functional Genetic Elements" and its database </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Valeriy </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Started relearning python to work with the traversal as suggested by Jenhan </li>
 +
 
 +
</ol>
 +
 
 +
<Div>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<Div class = "container-fluid" id = "four">
 +
 
 +
<hl> Kwat </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Learnt HTML </li>
 +
 
 +
<li> Went over everyone else's codes </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Lauren </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Wrote code for BFS and DFS </li>
 +
 
 +
<li> Learn Python the Hard Way </li>
 +
 
 +
<li> Prepared presentation for expanded BFS on Monday </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Gary </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Continued shifting through CyNetShare code </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Joaquin </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Learnt Bioservices for Miriam</li>
 +
 
 +
<li> Read papers to fill in database </li>
 +
 
 +
<li> scheme for UUID </li>
 +
 
 +
<li> add implicit output list to device table </li>
 +
 
 +
<li> promoter sequence database (biobrick registry) </li>
 +
 
 +
<li> insert_into_database fix </li>
 +
 
 +
<li> determine necessary data for device input </li>
 +
 
 +
</ol>
 +
 
 +
<hl> Rohit </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Worked on traversal algorithm</li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Fernando </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Continued debugging network</li>
 +
 
 +
<li> Updated database </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Valeriy </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Learnt Angular.js main functions to use for the website </li>
 +
 
 +
<li> Went over more CyNetShare code </li>
 +
 
 +
</ol>
 +
 
 +
<Div>
 +
 
 +
 
 +
 
 +
<Div class = "container-fluid" id = "five">
 +
 
 +
<hl> Kwat </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Created database structure </li>
 +
 
 +
<li> Normalization complete </li>
 +
 
 +
<li> Working on algorithm </li>
 +
 
 +
<li> Reading on petri nets </li>
 +
 
 +
<li> Learning about designing wiki </li>
 +
 
 +
<li> Populating new database </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Lauren </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Edited the Petri Net traversal to accept multiple inputs </li>
 +
 
 +
<li> Formatted integration of Bolean logic and multiple outputs </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Gary </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Busy with Final Exams </li>
 +
 
 +
<li> Began outlining Web part of presentation </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Joaquin </hl>
 +
 
 +
<ol>
 +
 
 +
<li>Designed a new structure for the database and the traversal</li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Rohit </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Improved BFS algorithm </li>
 +
 
 +
<li> Populated database </li>
 +
 
 +
<li> Kept journal clean </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Fernando </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Incorporated NetworkX into script</li>
 +
 
 +
<li> Began Boolean Satisfiability Problem </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Valeriy </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Worked on designing a specific JSON file to visualize database with CyNetShare
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> KP </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Enabled CyNetShare on his server </li>
 +
 
 +
<li> Cleaned up web dev part of master branch </li>
 +
 
 +
</ol>
 +
 
 +
<Div>
 +
 
 +
 
 +
 
 +
<Div class = "container-fluid" id = "six">
 +
 
 +
<hl> Kwat </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Cleaned the database and commented on everyone's data </li>
 +
 
 +
<li> Worked on search algorithm </li>
 +
 
 +
<li> Read about Petri nets </li>
 +
 
 +
<li> Tried to modify traverse algorithm to fit Petri Net model </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Lauren </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Edited the database </li>
 +
 
 +
<li> Fixed errors in traversal </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Gary </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Continued to clean up database </li>
 +
 
 +
<li> Added NOT gate entries to AND gates involving repressors </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Joaquin </hl>
 +
 
 +
<ol>
 +
 
 +
<li>Filled database PowerPoint presentation</li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Rohit </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Improved BFS algorithm </li>
 +
 
 +
<li> Populated database </li>
 +
 
 +
<li> Kept journal clean </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Fernando </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Incorporated NetworkX into script</li>
 +
 
 +
<li> Began Boolean Satisfiability Problem </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Valeriy </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Worked on designing a specific JSON file to visualize database with CyNetShare
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> KP </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Enabled CyNetShare on his server </li>
 +
 
 +
<li> Cleaned up web dev part of master branch </li>
 +
 
 +
</ol>
 +
 
 +
<Div>
 +
 
 +
 
 +
 
 +
<Div class = "container-fluid" id = "seven">
 +
 
 +
<hl> Kwat </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Made a script that parses a user input, searches graph and returns one more more linear searchable space </li>
 +
 
 +
<li> Learned SNAKES </li>
 +
 
 +
<li> Learned SQL stored function </li>
 +
 
 +
<li> Provided Fernando data for analysis </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Lauren </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Added traversal algorithm to presentation</li>
 +
 
 +
<li> Wrote project description </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Gary </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Continued to clean up database </li>
 +
 
 +
<li> Got CyNetShare running on NetBeans </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Joaquin </hl>
 +
 
 +
<ol>
 +
 
 +
<li>Worked on presentation</li>
 +
 
 +
<li> Started script to get JSON information </li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Rohit </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Added minimum spanning tree slides to presentation </li>
 +
 
 +
<li> Started learning JSON </li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Fernando </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Read Overpowering the Component Problem and Circuit Simulation of Genetic Networks</li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Valeriy </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Designed web app page </li>
 +
 
 +
<li> Worked on wiki </li>
 +
 
 +
<li> Added slides to presentation </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<Div>
 +
 
 +
 
 +
 
 +
<Div class = "container-fluid" id = "eight">
 +
 
 +
<hl> Kwat </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Finished parser </li>
 +
 
 +
<li> Finished database structure</li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> KP </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Changed size/shapes of nodes in CyNetShare</li>
 +
 
 +
<li> Began learning Angular UI Bootstrap </li>
 +
 
 +
<li> Began working on carousel within CyNetShare </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Gary </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Added dynamic labels to graph that enumerates lines as they are added</li>
 +
 
 +
<li> Got CyNetShare running on NetBeans </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Joaquin </hl>
 +
 
 +
<ol>
 +
 
 +
<li>Finished operon, plasmid I.D.s etc. In database</li>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Rohit </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Worked on JSON</li>
 +
 
 +
<li> Edited presentation</li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Tiffany</hl>
 +
 
 +
<ol>
 +
 
 +
<li> Modified pigeon command generator for plasmid to generate commands for each individual operon</li>
 +
 
 +
<li> Modified logo </li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Valeriy </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Designed web app page </li>
 +
 
 +
<li> Worked on wiki </li>
 +
 
 +
<li> Added slides to presentation </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<Div>
 +
 
 +
 
 +
 
 +
<Div class = "container-fluid" id = "nine">
 +
 
 +
<hl> Kwat </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Got inputs on parser working </li>
 +
 
 +
<li> Began working on outputs and verifying codes</li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> KP </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Remote </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Gary </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Finished adding line removal buttons to legend</li>
 +
 
 +
<li> Cleaned up Web Dev branch </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Joaquin </hl>
 +
 
 +
<ol>
 +
 
 +
<li>Populated working data</li>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Rohit </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Worked on JSON</li>
 +
 
 +
<li> Began learning NetworkX</li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<Div>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<Div class = "container-fluid" id = "ten”>
 +
 
 +
<hl> Kwat </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Patched codes together </li>
 +
 
 +
<li> Finished database with Joaquin</li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> KP </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Remote </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Gary </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Validated database</li>
 +
 
 +
<li> Drafted JSON format </li>
 +
 
 +
<li> Went remote </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Joaquin </hl>
 +
 
 +
<ol>
 +
 
 +
<li>Parsed excel file into database</li>
 +
 
 +
<li> Prepared for presentation </li>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Rohit </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Wrote Python script that takes SQL query and outputs JSON</li>
 +
 
 +
<li> Began learning Cytoscape.js</li>
 +
 
 +
<li> Began learning igraph </li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<Div class = "container-fluid" id = "eleven”>
 +
 
 +
<hl> Kwat </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Worked on poster </li>
 +
 
 +
<li> Worked on presentation outline</li>
 +
 
 +
<li> Updated traverse code </li>
 +
 
 +
<li> Updated Google Drive </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> KP </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Remote </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Gary </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Remote </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Joaquin </hl>
 +
 
 +
<ol>
 +
 
 +
<li>Designed master Python</li>
 +
 
 +
<li> Designed device insert page</li>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Rohit </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Read up on network motif algorithms (mfinder, color-coding, Kavosh)</li>
 +
 
 +
<li> Decided on Kavosh</li>
 +
 
 +
<li> Began learning CytoKavosh </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Fernando </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Almost finished JSON graph constructor </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Lauren </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Verified database code compatibility with network traversal </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<Div>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<Div class = "container-fluid" id = "twelve”>
 +
 
 +
<hl> Kwat </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Populated and finalized database </li>
 +
 
 +
<li> Combined visualization property with traverse code</li>
 +
 
 +
<li> Tested and debugged traversal algorithm </li>
 +
 
 +
<li> Started working on presentation </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> KP </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Remote </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Gary </hl>
 +
 
 +
<ol>
 +
 
 +
<li> No longer remote </li>
 +
 
 +
<li> Met with Ryan and Jenhan to refine modeling development directoin </li>
 +
 
 +
<li> Decided to use dictionaries of each operon's modeling information </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Joaquin </hl>
 +
 
 +
<ol>
 +
 
 +
<li>Populated new database structure</li>
 +
 
 +
<li> Implemented dictionaries necessary for traversal</li>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Rohit </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Continued network analysis with Kavosh</li>
 +
 
 +
<li> Began validating database</li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Fernando </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Remote </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Lauren </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Generated DOT file creator to retrieve node coordinates from GraphViz </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<Div>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<Div class = "container-fluid" id = "thirteen”>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<hl> KP </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Remote </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Gary </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Rendered full network JSON </li>
 +
 
 +
<li> Tweaked HTML and laid down function frameworks for search box </li>
 +
 
 +
<li> Reorganized app HTML for easier styling and positioning </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Joaquin </hl>
 +
 
 +
<ol>
 +
 
 +
<li>Fixed operon I.D.s in database creator</li>
 +
 
 +
<li> Fixed operon to output transition mapping</li>
 +
 
 +
<li> Connected positions to JSON creator </li>
 +
 
 +
<li> Worked on Pidgeon </li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Rohit </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Rendered full network on CytoScape</li>
 +
 
 +
<li> Attempted to run Linux VirtualBox on my machine to run CytoKavosh</li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Fernando </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Remote </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Lauren </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Debugged JSON file creator </li>
 +
 
 +
<li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<Div>
 +
 
 +
 
 +
 
 +
<Div class = "container-fluid" id = "fourteen”>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<hl> KP </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Remote </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Gary </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Connected algorithms and servlet between database and SBIDer</li>
 +
 
 +
<li> Modified GET requests to accept JSON strings instead of JSON files </li>
 +
 
 +
<li> Edited color scheme and style of nodes</li>
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Joaquin </hl>
 +
 
 +
<ol>
 +
 
 +
<li>Connected algorithms to servlet between database and SBIDer</li>
 +
 
 +
<li>Integrated database into file creator </li>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Rohit </hl>
 +
 
 +
<ol>
 +
 
 +
<li> VirtualBox did not work</li>
 +
 
 +
<li> Ran CytoKavosh on CSE lab Linux machines and found motifs</li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Fernando </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Worked on SBML modeling script </li>
 +
 
 +
<li> Finished QualitativeSpecies class and Modeling class </li>
 +
 
 +
</ol>
 +
 
 +
 
 +
 
 +
<hl> Lauren </hl>
 +
 
 +
<ol>
 +
 
 +
<li> Integrated database into file creator</li>
 +
 
 +
<li>
 +
 
 +
</ol>
 +
</div>

Revision as of 05:56, 13 October 2014

<hl> Name of person </hl>

  1. what they did




<hl> Kwat </hl>

  1. Generated Pydoc
  2. Learnt SQL
  3. Learnt Petri Nets


<hl> Lauren </hl>

  1. Did Learn Python the Hard Way
  2. Read Python Wiki


<hl> Gary </hl>

  1. Read Cytoscape.js API


<hl> Joaquin </hl>

  1. Learnt Boolean Networks
  2. Continued Petri Nets
  3. Learnt Dynamic Programming and Path Traversal

<hl> Rohit </hl>

  1. Learnt Cytoscape
  2. Learnt Python
  3. Learnt Petri Nets

<hl> Fernando </hl>

  1. Finished command line interface
  2. Acquired snippet of Linh's database







<hl> Kwat </hl>

  1. Learnt boolean networks
  2. Continued learning Petri Nets


<hl> Lauren </hl>

  1. Learnt Boolean networks
  2. Continued learning Petri nets



<hl> Gary </hl>

  1. Continued playing with Cytoscape.js add/remove nodes


<hl> Joaquin </hl>

  1. Learnt Boolean Networks
  2. Learnt reachability treees
  3. Developed Entity Relationship Diagram

<hl> Rohit </hl>

  1. Learnt Boolean networks
  2. Found SNAKES- a Python package that utilizes Petri nets


<hl> Fernando </hl>

  1. Learnt Boolean networks
  2. Disambiguated Linh's device composition

    3. </ol>




    <hl> Kwat </hl>

    1. Learnt SQL
    2. Learnt traversal algorithms
    3. Read assigned papers to populate database


    <hl> Lauren </hl>

    1. Petri net reading
    2. CodeAcademy Python tutorials
    3. BFS/DFS algorithms
    4. Read papers to fill in database


    <hl> Gary </hl>

    1. Learnt basics of Angular.js


    <hl> Joaquin </hl>

    1. SQl columns modification
    2. Read papers to fill in database

    <hl> Rohit </hl>

    1. Learnt SQL
    2. Conceptualized traversal algorithms
    3. Read assigned papers to populate database


    <hl> Fernando </hl>

    1. Found possible approach to weigh our edges using "Quantitative Estimation of Activity and Quality for Collections of Functional Genetic Elements" and its database


    <hl> Valeriy </hl>

    1. Started relearning python to work with the traversal as suggested by Jenhan



    <hl> Kwat </hl>

    1. Learnt HTML
    2. Went over everyone else's codes


    <hl> Lauren </hl>

    1. Wrote code for BFS and DFS
    2. Learn Python the Hard Way
    3. Prepared presentation for expanded BFS on Monday


    <hl> Gary </hl>

    1. Continued shifting through CyNetShare code


    <hl> Joaquin </hl>

    1. Learnt Bioservices for Miriam
    2. Read papers to fill in database
    3. scheme for UUID
    4. add implicit output list to device table
    5. promoter sequence database (biobrick registry)
    6. insert_into_database fix
    7. determine necessary data for device input

    <hl> Rohit </hl>

    1. Worked on traversal algorithm


    <hl> Fernando </hl>

    1. Continued debugging network
    2. Updated database


    <hl> Valeriy </hl>

    1. Learnt Angular.js main functions to use for the website
    2. Went over more CyNetShare code


    <hl> Kwat </hl>

    1. Created database structure
    2. Normalization complete
    3. Working on algorithm
    4. Reading on petri nets
    5. Learning about designing wiki
    6. Populating new database


    <hl> Lauren </hl>

    1. Edited the Petri Net traversal to accept multiple inputs
    2. Formatted integration of Bolean logic and multiple outputs


    <hl> Gary </hl>

    1. Busy with Final Exams
    2. Began outlining Web part of presentation


    <hl> Joaquin </hl>

    1. Designed a new structure for the database and the traversal


    <hl> Rohit </hl>

    1. Improved BFS algorithm
    2. Populated database
    3. Kept journal clean


    <hl> Fernando </hl>

    1. Incorporated NetworkX into script
    2. Began Boolean Satisfiability Problem


    <hl> Valeriy </hl>

    1. Worked on designing a specific JSON file to visualize database with CyNetShare


    <hl> KP </hl>

    1. Enabled CyNetShare on his server
    2. Cleaned up web dev part of master branch


    <hl> Kwat </hl>

    1. Cleaned the database and commented on everyone's data
    2. Worked on search algorithm
    3. Read about Petri nets
    4. Tried to modify traverse algorithm to fit Petri Net model


    <hl> Lauren </hl>

    1. Edited the database
    2. Fixed errors in traversal


    <hl> Gary </hl>

    1. Continued to clean up database
    2. Added NOT gate entries to AND gates involving repressors


    <hl> Joaquin </hl>

    1. Filled database PowerPoint presentation



    <hl> Rohit </hl>

    1. Improved BFS algorithm
    2. Populated database
    3. Kept journal clean


    <hl> Fernando </hl>

    1. Incorporated NetworkX into script
    2. Began Boolean Satisfiability Problem


    <hl> Valeriy </hl>

    1. Worked on designing a specific JSON file to visualize database with CyNetShare


    <hl> KP </hl>

    1. Enabled CyNetShare on his server
    2. Cleaned up web dev part of master branch


    <hl> Kwat </hl>

    1. Made a script that parses a user input, searches graph and returns one more more linear searchable space
    2. Learned SNAKES
    3. Learned SQL stored function
    4. Provided Fernando data for analysis


    <hl> Lauren </hl>

    1. Added traversal algorithm to presentation
    2. Wrote project description


    <hl> Gary </hl>

    1. Continued to clean up database
    2. Got CyNetShare running on NetBeans


    <hl> Joaquin </hl>

    1. Worked on presentation
    2. Started script to get JSON information



    <hl> Rohit </hl>

    1. Added minimum spanning tree slides to presentation
    2. Started learning JSON



    <hl> Fernando </hl>

    1. Read Overpowering the Component Problem and Circuit Simulation of Genetic Networks



    <hl> Valeriy </hl>

    1. Designed web app page
    2. Worked on wiki
    3. Added slides to presentation




    <hl> Kwat </hl>

    1. Finished parser
    2. Finished database structure



    <hl> KP </hl>

    1. Changed size/shapes of nodes in CyNetShare
    2. Began learning Angular UI Bootstrap
    3. Began working on carousel within CyNetShare


    <hl> Gary </hl>

    1. Added dynamic labels to graph that enumerates lines as they are added
    2. Got CyNetShare running on NetBeans


    <hl> Joaquin </hl>

    1. Finished operon, plasmid I.D.s etc. In database




    <hl> Rohit </hl>

    1. Worked on JSON
    2. Edited presentation



    <hl> Tiffany</hl>

    1. Modified pigeon command generator for plasmid to generate commands for each individual operon
    2. Modified logo



    <hl> Valeriy </hl>

    1. Designed web app page
    2. Worked on wiki
    3. Added slides to presentation




    <hl> Kwat </hl>

    1. Got inputs on parser working
    2. Began working on outputs and verifying codes



    <hl> KP </hl>

    1. Remote


    <hl> Gary </hl>

    1. Finished adding line removal buttons to legend
    2. Cleaned up Web Dev branch


    <hl> Joaquin </hl>

    1. Populated working data




    <hl> Rohit </hl>

    1. Worked on JSON
    2. Began learning NetworkX











    <hl> Kwat </hl>

    1. Patched codes together
    2. Finished database with Joaquin



    <hl> KP </hl>

    1. Remote


    <hl> Gary </hl>

    1. Validated database
    2. Drafted JSON format
    3. Went remote


    <hl> Joaquin </hl>

    1. Parsed excel file into database
    2. Prepared for presentation




    <hl> Rohit </hl>

    1. Wrote Python script that takes SQL query and outputs JSON
    2. Began learning Cytoscape.js
    3. Began learning igraph



    <hl> Kwat </hl>

    1. Worked on poster
    2. Worked on presentation outline
    3. Updated traverse code
    4. Updated Google Drive


    <hl> KP </hl>

    1. Remote


    <hl> Gary </hl>

    1. Remote


    <hl> Joaquin </hl>

    1. Designed master Python
    2. Designed device insert page




    <hl> Rohit </hl>

    1. Read up on network motif algorithms (mfinder, color-coding, Kavosh)
    2. Decided on Kavosh
    3. Began learning CytoKavosh


    <hl> Fernando </hl>

    1. Almost finished JSON graph constructor


    <hl> Lauren </hl>

    1. Verified database code compatibility with network traversal









    <hl> Kwat </hl>

    1. Populated and finalized database
    2. Combined visualization property with traverse code
    3. Tested and debugged traversal algorithm
    4. Started working on presentation


    <hl> KP </hl>

    1. Remote


    <hl> Gary </hl>

    1. No longer remote
    2. Met with Ryan and Jenhan to refine modeling development directoin
    3. Decided to use dictionaries of each operon's modeling information


    <hl> Joaquin </hl>

    1. Populated new database structure
    2. Implemented dictionaries necessary for traversal




    <hl> Rohit </hl>

    1. Continued network analysis with Kavosh
    2. Began validating database


    <hl> Fernando </hl>

    1. Remote


    <hl> Lauren </hl>

    1. Generated DOT file creator to retrieve node coordinates from GraphViz











    <hl> KP </hl>

    1. Remote


    <hl> Gary </hl>

    1. Rendered full network JSON
    2. Tweaked HTML and laid down function frameworks for search box
    3. Reorganized app HTML for easier styling and positioning


    <hl> Joaquin </hl>

    1. Fixed operon I.D.s in database creator
    2. Fixed operon to output transition mapping
    3. Connected positions to JSON creator
    4. Worked on Pidgeon



    <hl> Rohit </hl>

    1. Rendered full network on CytoScape
    2. Attempted to run Linux VirtualBox on my machine to run CytoKavosh


    <hl> Fernando </hl>

    1. Remote


    <hl> Lauren </hl>

    1. Debugged JSON file creator










    <hl> KP </hl>

    1. Remote


    <hl> Gary </hl>

    1. Connected algorithms and servlet between database and SBIDer
    2. Modified GET requests to accept JSON strings instead of JSON files
    3. Edited color scheme and style of nodes



    <hl> Joaquin </hl>

    1. Connected algorithms to servlet between database and SBIDer
    2. Integrated database into file creator




    <hl> Rohit </hl>

    1. VirtualBox did not work
    2. Ran CytoKavosh on CSE lab Linux machines and found motifs


    <hl> Fernando </hl>

    1. Worked on SBML modeling script
    2. Finished QualitativeSpecies class and Modeling class


    <hl> Lauren </hl>

    1. Integrated database into file creator
Retrieved from "http://2014.igem.org/Team:UCSD_Software/Teaml"