Team:USTC-Software/project

From 2011.igem.org

(Difference between revisions)
(conflict)
 
(84 intermediate revisions not shown)
Line 1: Line 1:
__NOTOC__
__NOTOC__
-
{{:Team:USTC-Software/banner hidden}}
+
{{:Team:USTC-Software/header}}
-
 
+
<html xmlns="http://www.w3.org/1999/xhtml">
<html xmlns="http://www.w3.org/1999/xhtml">
-
<head>
+
<body>
-
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
-
<meta name="author" content="Ao Xu">
+
<div id="content_wrapper">
-
<meta name="revised" content="2011/07/10"/>
+
-
<meta name="description" content="project description"/>
+
-
<meta name="keywords" content="USTC_Software iGEM lachesis project"/>
+
 +
<div id="intro">
 +
<p> Contents:
 +
<ul type="square">
-
<title>Project</title>
+
          <li><a href="#Introduction">Introduction</a></li>
 +
            <ul type="circle">
 +
            <!-- <li><a href="#Motivation">Motivation</a></li>-->
 +
              <li><a href="#What is Lachesis?">What is Lachesis?</a></li>
 +
              <li><a href="#Available Features for Now">Available Features for Now</a></li>
 +
                <ul type="disc">
 +
                    <li><a href="#Documents parsers">Documents parsers</a></li>
 +
                    <li><a href="#Models">Models</a></li>
 +
                    <li><a href="#Views">Views</a></li>
 +
                    <li><a href="#Technology & Algorithms">Technology & Algorithms</a></li>
 +
                  </ul>     
 +
              <li><a href="#Future Plans">Future Plans</a></li>
-
<style type="text/css">
+
            </ul>
-
body {
+
      </ul>
-
margin: 0;
+
</p>
-
padding: 0;
+
             
-
line-height: 1.5em;
+
</div> 
-
font-family: Georgia, "Times New Roman", Times, serif;
+
<!--
-
font-size: 12px;
+
<h2><a name="Motivation" id="Motivation"></a><strong>Motivation</strong></h2>-->
-
color: #555a4a;
+
<!--<p>CAD tools in the field of electronic engineering has become a necessity, it saves the engineer a lot of time from simple trial and error.</p>
-
        background: #a0c73f;
+
  <p>Design in silicon is flexible, and one can manage the complexity of a framework, and analyze the result easily.</p>
-
}
+
  <p>But in silicon design of gene circuit is far from mature. Pursuant to the goal of a user friendly tool, which can really give synthetic biologist some aids in designing gene circuit, the USTC SOFTWARE oriented in the following points:</p>
 +
<p>• Free user from the chores of blind trial and error.</p>
 +
<p>• Software prediction attests to model validity at the current state of synthetic biology development.</p>
 +
<p>• Predictive behavior in silicon</p>
 +
<p>• Combine rational design and directed evolution with an assessment tool of the robustness of the circuit.</p>
 +
<p>• Various criteria to access a design: robustness to parameter variation and stochastic noise.</p>
 +
-->
 +
<h3><a name="What is Lachesis?" id="What is Lachesis?"></a>What is Lachesis?</h3>
-
a:link, a:visited { color: #0683ab; text-decoration: none; font-weight: normal; }
+
<p>The project Lachesis aims at providing an integrated, easy-using and extensible CAD environment for the general purpose of Synthetic Biology.</p>
-
a:active, a:hover { color: #0683ab; text-decoration: underline; }
+
 +
<p>To achieve this goal, Lachesis adopts plug-ins based structure. We provide the following three kinds of plug-ins:
 +
  <ul type="square" class="ul_p">
 +
      <li>Document parsers that handles various types of files, such as SBML and MoDeL.</li>
 +
      <li>Models that each represents a specific kind of synthetic biological model.</li>
 +
      <li>Views that present graphical user interface for users to work with biological models.</li>
 +
  </ul>
 +
</p>
 +
<br/>
 +
<h3><a name="Available Features for Now" id="Available Features for Now"></a>Available Features for Now</h3>
-
p { margin: 0px; padding: 0px; }
+
<p>We have developed several useful plug-ins to justify our motivation as well as make Lachesis a powerful tool for designing and simulating Synthetic Biology models. Lachesis is coded with C++ and Qt. We welcome everyone to develop more helpful plug-ins for Lachesis.</p>
-
img { margin: 0px; padding: 0px; border: none; }
+
<p><a name="Documents parsers" id="Documents parsers"></a><strong>Documents parsers</strong></p>
 +
<p>Currently, we provide support for .sbml file, .model file and various kinds of other file types.</p>
-
.cleaner { clear: both; width: 100%; height: 0px; font-size: 0px;  }
+
<p><a name="Models" id="Models"></a><strong>Models</strong></p>
 +
<ul type="square" class="ul_p">
 +
<li>Reaction Network Model represents an biological reaction network,e.g. read from an .sbml file,</li>
 +
<li>MoDeL model represents an model for the software MoDeL, which is an refactored and superior version of our last year's project iGaME.</li>
 +
</ul>
-
.cleaner_h30 { clear: both; width:100%; height: 30px; }
+
<p><a name="Views" id="Views"></a><strong>Views</strong></p>
-
.cleaner_h40 { clear: both; width:100%; height: 40px; }
+
<ul type="square" class="ul_p">
 +
<li>Assembly View provides an easy-using graphical interface for working with MoDeL,</li>
 +
<li>Network View provides an graphical interface for editing biological reaction network,</li>
 +
<li>Parameter fitting view(still under construction) can analysis synthetic biology models' behavior with respect to parameter changing, and tune parameters to give the desired behavior.</li>
 +
</ul>
-
.margin_r10 { margin-right: 10px; }
+
<p><a name="Technology & Algorithms" id="Technology & Algorithms"></a><strong>Technology & Algorithms</strong></p>
 +
<p>Chen Liao refactored iGaME to form the new software package MoDeL, which is a rule-based modeling approach for synthetic biology.</p>
 +
<p>Xudong Sun designed an algorithm for parameter analyzing for biological reaction network. We currently working on re-implementing
 +
the algorithm to provide an efficient graphical interface and free users from mathematical details.</p>
-
.float_l { float: left; }
+
<h3><a name="Future Plans" id="Future Plans"></a>Future Plans</h3>
-
.float_r { float:  right; }
+
-
#header_wrapper {
+
<p>In the future version of our software, we plan to combine the reverse and forward engineering approach more closely, hoping to give users more guide to achieve better performance of the gene circuit. Probably from the following prospect:</p>
-
width: 100%;
+
<p> • Find a good algorithm to mutate the design automatically.
-
height: 265px;
+
Keep the backbone of the biobrick assembly, and change the “connections” of the parts, discover various combinations or connectivities of parts to get new behaviors of the circuit.
-
background: url(https://static.igem.org/mediawiki/2011/0/04/USTC_Software_header.jpg) no-repeat top center;
+
<em>For example</em>, change the assembly Promoter1(gene1 repressed)-rbs-gene1-term1-promoter2(gene1 repressed)-rbs-gene2-term2  to Promoter1(gene2 activate)-rbs-gene1-term1-promoter2(gene1 repressed)-rbs-gene2-term2 would get a new behavior.
-
}
+
We are inspired by many literatures and find this interesting. A fast such algorithm would help speed up the evolutionary process in silicon.</p>
 +
We are even thinking that we already have an rule based modeling approach, why can’t we have a rule based evolutionary design approach?  Devise a good set of rules to decide how to mutate the network?
 +
<p> •Integrate more Synthetic biology network analysis approachs into our software. For example, introduce more sensitivity and robustness analysis algorithms into our software.</p>
 +
<p> •Make a dynamic network view which can show the process of rule based modelling approch.  
 +
<p> •Provide a graphics view to the structure of species.
 +
<p> •Provide a 3d view to show the dose response curve of a circuit.
-
#header {
+
</div>
-
position: relative;
+
 
-
width: 980px;
+
<div id="content_wrapper_bottom"> </div>
-
height: 265px;
+
-
padding: 0 10px;
+
-
margin: 0 auto;
+
-
background: url(https://static.igem.org/mediawiki/2011/0/04/USTC_Software_header.jpg) no-repeat top center;
+
-
}
+
-
/* site title */
+
<!-- end of content_wrapper -->
 +
   
 +
<div id="mfooter">
-
#header  #site_title {
+
  <ul class="mfooter_menu">
-
float: left;
+
                 <li><a href="https://2011.igem.org/Team:USTC-Software" target="_parent">Home</a></li>
-
width: 220px;
+
-
padding: 50px 0 10px 10px;
+
-
}
+
-
 
+
-
#site_title h1 {
+
-
margin: 0;
+
-
padding: 0;
+
-
}
+
-
 
+
-
#site_title h1 a {
+
-
margin: 0px;
+
-
padding: 0px;
+
-
font-size: 30px;
+
-
color: #ffffff;
+
-
font-weight: bold;
+
-
text-decoration: none;
+
-
}
+
-
 
+
-
#site_title h1 a:hover {
+
-
font-weight: bold;
+
-
text-decoration: none;
+
-
}
+
-
 
+
-
#site_title h1 a span {
+
-
display: block;
+
-
margin-left: 2px;
+
-
font-size: 14px;
+
-
color: #416902;
+
-
font-weight: bold;
+
-
letter-spacing: 2px;
+
-
}
+
-
 
+
-
/* end of site title */
+
-
 
+
-
/* menu */
+
-
 
+
-
#menu {
+
-
float: right;
+
-
padding-top: 70px;
+
-
height: 43px;
+
-
}
+
-
 
+
-
#menu ul {
+
-
margin: 0;
+
-
padding: 0;
+
-
list-style: none;
+
-
}
+
-
 
+
-
#menu ul li {
+
-
padding: 0;
+
-
margin: 0;
+
-
display: inline;
+
-
}
+
-
 
+
-
#menu ul li a {
+
-
float: left;
+
-
display: block;
+
-
height: 35px;
+
-
width: 125px;
+
-
margin: 0;
+
-
padding: 8px 0 0 0;
+
-
text-align: center;
+
-
font-size: 12px;
+
-
text-decoration: none;
+
-
color: #333333;
+
-
font-weight: bold;
+
-
outline: none;
+
-
}
+
-
 
+
-
#menu li a:hover, #menu li .current {
+
-
color: #333333;
+
-
background: url(https://static.igem.org/mediawiki/2011/6/69/USTC_Software_menu_hover.png) no-repeat top;
+
-
}
+
-
 
+
-
/* end of menu */
+
-
 
+
-
/* back to igem.org*/
+
-
#header #to_org_box {
+
-
position:fixed;
+
-
width: 73px;
+
-
height: 75px;
+
-
bottom: 210px;
+
-
right: 18px;
+
-
}
+
-
 
+
-
 
+
-
#to_org_box form {
+
-
width: 280px;
+
-
height: 27px;
+
-
margin: 0;
+
-
padding: 25px 0 0 0;
+
-
}
+
-
/* end of back to igem.org*/
+
-
/* mcontent */
+
-
 
+
-
#mcontent_wrapper {
+
-
width: 920px;
+
-
margin: 0 auto;
+
-
padding: 30px 40px;
+
-
background: url(https://static.igem.org/mediawiki/2011/b/bc/USTC_Software_content.jpg) repeat-y;
+
-
}
+
-
 
+
-
#mcontent_wrapper_bottom {
+
-
width: 1000px;
+
-
height: 15px;
+
-
margin: 0 auto;
+
-
background: url(https://static.igem.org/mediawiki/2011/a/a5/USTC_Software_content_bottom.jpg) no-repeat;
+
-
}
+
-
 
+
-
#mcontent {
+
-
 
+
-
width:auto;
+
-
}
+
-
 
+
-
#mcontent p {
+
-
text-align: justify;
+
-
margin-bottom: 10px;
+
-
}
+
-
 
+
-
.mcontent_section {
+
-
clear: both;
+
-
width: 100%;
+
-
}
+
-
 
+
-
#mcontent h2 {
+
-
color: #3a5909;
+
-
font-size: 24px;
+
-
padding: 0 0 60px 20px;
+
-
background: url(https://static.igem.org/mediawiki/2011/4/4d/USTC_Software_header_bg.png) no-repeat bottom left;
+
-
}
+
-
 
+
-
 
+
-
#mcontent .em_text {
+
-
color: #537c11;
+
-
}
+
-
 
+
-
 
+
-
/* end of mcontent */
+
-
 
+
-
/* mfooter */
+
-
 
+
-
#mfooter {
+
-
width: 980px;
+
-
margin: 0 auto;
+
-
padding: 30px 10px;
+
-
text-align: center;
+
-
color: #333333;
+
-
}
+
-
 
+
-
#mfooter a {
+
-
color: #000000;
+
-
}
+
-
 
+
-
#mfooter .mfooter_menu {
+
-
margin: 0 0 10px 0;
+
-
padding: 0px;
+
-
list-style: none;
+
-
}
+
-
 
+
-
.mfooter_menu li {
+
-
margin: 0px;
+
-
padding: 0 20px;
+
-
display: inline;
+
-
border-right: 1px solid #000000;
+
-
}
+
-
 
+
-
.mfooter_menu .last_menu {
+
-
border: none;
+
-
}
+
-
 
+
-
#mfooter #totop_box {
+
-
position:fixed;
+
-
width: 73px;
+
-
height: 75px;
+
-
bottom: 21px;
+
-
right: 18px;
+
-
}
+
-
 
+
-
 
+
-
#totop_box form {
+
-
width: 280px;
+
-
height: 27px;
+
-
margin: 0;
+
-
padding: 25px 0 0 0;
+
-
}
+
-
 
+
-
 
+
-
/* end of mfooter */
+
-
 
+
-
</style>
+
-
 
+
-
 
+
-
</head>
+
-
 
+
-
 
+
-
 
+
-
 
+
-
<body>
+
-
<div id="header_wrapper">
+
-
 
+
-
    <div id="header">
+
-
   
+
-
  <div id="site_title">
+
-
            <h1><img src="https://static.igem.org/mediawiki/2011/b/b8/USTC_Software_iGEM_logo.jpg" alt="iGEM" width="128" height="92" />
+
-
            </br></br></br>
+
-
            <span>USTC_Software</span>
+
-
            </h1>
+
-
        </div>
+
-
       
+
-
        <div id="menu">
+
-
            <ul>
+
-
                 <li><a href="https://2011.igem.org/Team:USTC-Software">Home</a></li>
+
                 <li><a href="#" class="current">Project</a></li>
                 <li><a href="#" class="current">Project</a></li>
-
                <li><a href="https://2011.igem.org/Team:USTC-Software/model" target="_parent">MoDeL</a></li>
 
                 <li><a href="https://2011.igem.org/Team:USTC-Software/notebook" target="_parent">Notebook</a></li>
                 <li><a href="https://2011.igem.org/Team:USTC-Software/notebook" target="_parent">Notebook</a></li>
-
                 <li><a href="https://2011.igem.org/Team:USTC-Software/human_practice" target="_parent">Human Practice</a></li>
+
                 <li><a href="https://2011.igem.org/Team:USTC-Software/team" target="_parent">Team</a></li>
-
                 <li class="last_menu" target="_parent"><a href="https://2011.igem.org/Team:USTC-Software/team">Team</a></li>
+
                 <li><a href="https://2011.igem.org/Team:USTC-Software/team" target="_parent">Human Practice</a></li>
-
            </ul>  
+
                <li class="last_menu"><a href="https://2011.igem.org/Team:USTC-Software/download" target="_parent">Download</a></li>
-
        </div> <!-- end of menu -->
+
  </ul>
-
     
+
  <b> Welcome to &#160;&#160;<a href="http://en.ustc.edu.cn/" target="_blank">University of Science and Technology of China</a>&#160;! </b>
-
      <div class="cleaner"></div>
+
-
    </div> <!-- end of header -->
+
-
</div>  
+
  <div id="to_org_box"><a href="https://2011.igem.org/Main_Page"><img class="logo" src="https://static.igem.org/mediawiki/2011/8/88/USTC_Software_back_to_igem.png" width="69" height="70"alt="Go back to igem.org"  style="right:auto"/></a>
-
<!-- end of header_wrapper -->
+
  </div>
-
<div id="mcontent_wrapper">
 
-
 
-
<div id="mcontent">
 
-
   
 
-
        <div class="mcontent_section">
 
-
       
 
-
            <h2>Sorry,this is an unfinished feature...</h2>
 
-
           
 
-
            <div class="cleaner"> </div>
 
-
       
 
-
        </div>
 
-
       
 
-
        <div class="cleaner_h40"> </div>
 
-
       
 
-
   
 
-
    </div> <!-- end of mcontent -->
 
-
   
 
-
    <div class="cleaner"> </div>   
 
-
   
 
-
</div> 
 
-
 
 
-
<div id="mcontent_wrapper_bottom"> </div>
 
-
<!-- end of mcontent_wrapper -->
 
-
   
 
-
 
-
 
-
<div id="mfooter">
 
-
 
-
  <ul class="mfooter_menu">
 
-
                <li><a href="https://2011.igem.org/Team:USTC-Software">Home</a></li>
 
-
                <li><a href="#" target="_parent">Project</a></li>
 
-
                <li><a href="https://2011.igem.org/Team:USTC-Software/model" target="_parent">MoDeL</a></li>
 
-
                <li><a href="https://2011.igem.org/Team:USTC-Software/notebook" target="_parent">Notebook</a></li>
 
-
                <li><a href="https://2011.igem.org/Team:USTC-Software/human_practice" target="_parent">Human Practice</a></li>
 
-
                <li class="last_menu" target="_parent"><a href="https://2011.igem.org/Team:USTC-Software/team">Team</a></li>
 
-
            </ul>
 
-
  Welcome to &#160;&#160;<a href="http://en.ustc.edu.cn/" target="_blank">University of Science and Technology of China</a>&#160;!
 
-
 
 
-
  <div id="to_org_box"><a href="https://2011.igem.org/Main_Page"><img class="logo" src="https://static.igem.org/mediawiki/2011/8/88/USTC_Software_back_to_igem.png" width="87" height="73"alt="to igem.org"  style="right:auto"/></a></div>
 
-
 
   <div id="totop_box">
   <div id="totop_box">
-
       <a href="#top"><img class="logo" src="https://static.igem.org/mediawiki/2011/e/eb/USTC_Software_top_icon.gif" width="73" height="75"alt="go back to top"  style="right:auto"/></a>  
+
       <a href="#top"><img class="logo" src="https://static.igem.org/mediawiki/2011/e/eb/USTC_Software_top_icon.gif" width="76" height="72"alt="Go back to Top"  style="right:auto"/></a>  
   </div>
   </div>

Latest revision as of 13:59, 28 October 2011


Team:USTC-Software - 2011.igem.org

What is Lachesis?

The project Lachesis aims at providing an integrated, easy-using and extensible CAD environment for the general purpose of Synthetic Biology.

To achieve this goal, Lachesis adopts plug-ins based structure. We provide the following three kinds of plug-ins:

  • Document parsers that handles various types of files, such as SBML and MoDeL.
  • Models that each represents a specific kind of synthetic biological model.
  • Views that present graphical user interface for users to work with biological models.


Available Features for Now

We have developed several useful plug-ins to justify our motivation as well as make Lachesis a powerful tool for designing and simulating Synthetic Biology models. Lachesis is coded with C++ and Qt. We welcome everyone to develop more helpful plug-ins for Lachesis.

Documents parsers

Currently, we provide support for .sbml file, .model file and various kinds of other file types.

Models

  • Reaction Network Model represents an biological reaction network,e.g. read from an .sbml file,
  • MoDeL model represents an model for the software MoDeL, which is an refactored and superior version of our last year's project iGaME.

Views

  • Assembly View provides an easy-using graphical interface for working with MoDeL,
  • Network View provides an graphical interface for editing biological reaction network,
  • Parameter fitting view(still under construction) can analysis synthetic biology models' behavior with respect to parameter changing, and tune parameters to give the desired behavior.

Technology & Algorithms

Chen Liao refactored iGaME to form the new software package MoDeL, which is a rule-based modeling approach for synthetic biology.

Xudong Sun designed an algorithm for parameter analyzing for biological reaction network. We currently working on re-implementing the algorithm to provide an efficient graphical interface and free users from mathematical details.

Future Plans

In the future version of our software, we plan to combine the reverse and forward engineering approach more closely, hoping to give users more guide to achieve better performance of the gene circuit. Probably from the following prospect:

• Find a good algorithm to mutate the design automatically. Keep the backbone of the biobrick assembly, and change the “connections” of the parts, discover various combinations or connectivities of parts to get new behaviors of the circuit. For example, change the assembly Promoter1(gene1 repressed)-rbs-gene1-term1-promoter2(gene1 repressed)-rbs-gene2-term2 to Promoter1(gene2 activate)-rbs-gene1-term1-promoter2(gene1 repressed)-rbs-gene2-term2 would get a new behavior. We are inspired by many literatures and find this interesting. A fast such algorithm would help speed up the evolutionary process in silicon.

We are even thinking that we already have an rule based modeling approach, why can’t we have a rule based evolutionary design approach? Devise a good set of rules to decide how to mutate the network?

•Integrate more Synthetic biology network analysis approachs into our software. For example, introduce more sensitivity and robustness analysis algorithms into our software.

•Make a dynamic network view which can show the process of rule based modelling approch.

•Provide a graphics view to the structure of species.

•Provide a 3d view to show the dose response curve of a circuit.

Retrieved from "http://2011.igem.org/Team:USTC-Software/project"