Team:USTC-Software/project

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Team:USTC-Software - 2011.igem.org

Contents:

Introduction

What is Lachesis?
Available Features for Now

Documents parsers
Models
Views
Technology & Algorithms

Future Plans

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.

Welcome to University of Science and Technology of China !

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-            <h1><img src="https://static.igem.org/mediawiki/2011/b/b8/USTC_Software_iGEM_logo.jpg" alt="iGEM" width="173" height="150" /> </br> </br> USTC-Software </h1>
-        </div>
- <!-- navigation -->
-	<ul id="nav">
-		<li><a href="https://2011.igem.org/Team:USTC-Software">Home</a></li>
-    		<li><a class="on" href="#">Project</a>
-			<ul>
-				<li><a href="https://2011.igem.org/Team:USTC-Software/documents">Documents Parser</a></li>
-				<li><a href="https://2011.igem.org/Team:USTC-Software/models">Models</a></li>
-			    	<li><a href="#">Views</a>
-                            <ul>
-                                <li><a href="https://2011.igem.org/Team:USTC-Software/aview">Assembly View</a></li>
-                                <li><a href="https://2011.igem.org/Team:USTC-Software/bview">Behavior View</a></li>
-                                <li><a href="https://2011.igem.org/Team:USTC-Software/nview">Network View</a></li>
-                            </ul>
-                                <li><a href="https://2011.igem.org/Team:USTC-Software/tech&algo">Technology & Algorithm</a></li>
-                                <li><a href="https://2011.igem.org/Team:USTC-Software/tutorial">Tutorial & Demo</a></li>
-			</ul>
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-                <li><a href="https://2011.igem.org/Team:USTC-Software/notebook">Notebook</a></li>
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-                        <ul>
-                            <li><a href="https://2011.igem.org/Team:USTC-Software/members">members</a></li>
-                            <li><a href="https://2011.igem.org/Team:USTC-Software/collaboration">collaboration</a></li>
-                            <li><a href="https://2011.igem.org/Team:USTC-Software/attribution">attribution & contributions</a></li>
-                            <li><a href="https://2011.igem.org/Team:USTC-Software/acknowledgements">acknowledgements</a></li>
-                        </ul>
-                 </li>
-  		<li><a class="last"href="https://2011.igem.org/Team:USTC-Software/human practice">Human practice</a>
-			<ul>
-			    <li><a href="https://2011.igem.org/Team:USTC-Software/safety">safety</a></li>
-			    <li><a href="https://2011.igem.org/Team:USTC-Software/meetup">meetup</a></li>
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-		<li><a href="https://2011.igem.org/Team:USTC-Software/download">Download</a></li>
-	</ul>
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-    </div> <!-- end of header -->
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 <div id="content_wrapper">
@@ Line 362: / Line 12: @@
            <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>
@@ Line 369: / Line 20: @@
                      <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>
               </ul>
@@ Line 376: / Line 29: @@
 </div>
+<!--
-<h2><a name="Introduction" id="Introduction"></a>Motivation</h2>
+<h2><a name="Motivation" id="Motivation"></a><strong>Motivation</strong></h2>-->
+<!--<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>
+  <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>
-<p>The project Lachesis aims at providing and integrated, easy-using and extensible CAD environment for the general purpose of Synthetic Biology.</p>
+<p>The project Lachesis aims at providing an integrated, easy-using and extensible CAD environment for the general purpose of Synthetic Biology.</p>
-<p>To achieve this goal, Lachesis adopts an plug-in based structure. We provide the following three kinds of plug-ins:
+<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>
@@ Line 396: / Line 57: @@
 <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>
-<p><a name="Documents parsers" id="Documents parsers"></a><a href="https://2011.igem.org/Team:USTC-Software/documents"><strong>Documents parsers</strong></a></p>
+<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>
-<p><a name="Models" id="Models"></a><a href="https://2011.igem.org/Team:USTC-Software/models"><strong>Models</strong></a></p>
+<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>
@@ Line 405: / Line 66: @@
 </ul>
-<p><a name="Views" id="Views"></a><a href="https://2011.igem.org/Team:USTC-Software/views"><strong>Views</strong></a></p>
+<p><a name="Views" id="Views"></a><strong>Views</strong></p>
 <ul type="square" class="ul_p">
 <li>Assembly View provides an easy-using graphical interface for working with MoDeL,</li>
@@ Line 412: / Line 73: @@
 </ul>
-<p><a name="Technology & Algorithms" id="Technology & Algorithms"></a><a href="https://2011.igem.org/Team:USTC-Software/tech&algo"><strong>Technology & Algorithms</strong></a></p>
+<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>
+<h3><a name="Future Plans" id="Future Plans"></a>Future Plans</h3>
+<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>
+<p> • 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.
+<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.
-<h2>Continue reading:</h2>
-                        <ul>
-				<li><a href="https://2011.igem.org/Team:USTC-Software/documents">Documents</a></li>
-				<li><a href="https://2011.igem.org/Team:USTC-Software/models">Models</a></li>
-				<li><a href="https://2011.igem.org/Team:USTC-Software/views">Views</a></li>
-                                <li><a href="https://2011.igem.org/Team:USTC-Software/tech&algo">Technology & Algorithm</a></li>
-                                <li><a href="https://2011.igem.org/Team:USTC-Software/tutorial">Tutorial</a></li>
-			</ul>
 </div>