Team:USTC-Software/project

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Latest revision as of 13:59, 28 October 2011

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>
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-		<li><a href="https://2011.igem.org/Team:USTC-Software">Home</a></li>
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-                        </ul>
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-  		<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>
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@@ Line 353: / Line 9: @@
 <p> Contents:
 <ul type="square">
-          <li><a href="#Overview">Overview</a></li>
-            <ul type="circle">
-              <li><a href="#Design and automatic modeling">Design and automatic modeling</a></li>
-              <li><a href="#Visualization">Visualization</a></li>
-              <li><a href="#Visualization">Parameter tune and sensitivity analysis</a></li>
-              <li><a href="#Visualization">Assessment</a></li>
-             </ul>
-           <li><a href="#Algorithm">Introduction</a></li>
+           <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 370: / 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 377: / Line 29: @@
 </div>
+<!--
-<h1>Project Lachesis</h1>
+<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>
-<h2><a name="Overview" id="Overview"></a>Overview</h2>
+  <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>The endeavor to build a user’s friendly powerful software tool for synthetic biology has passed on to the2011USTC software team.</p>
+<p>•	Software prediction attests to model validity at the current state of synthetic biology development.</p>
+<p>•	Predictive behavior in silicon</p>
-<p>“The programming talents needed to make great software need nuturing”
+<p>•	Combine rational design and directed evolution with an assessment tool of the robustness of the circuit.</p>
-Over the past 3 three years, the USTC softwares hasformed series.And we are going to develop more in the future, hoping that the USTC software series, with rounds of refinement, could stand out in the world to do something for synthetic biologist.</p>
+<p>•	Various criteria to access a design: robustness to parameter variation and stochastic noise.</p>
+-->
-<p>Under the care of many elder IGEMers, instructors, faculty members, ustc2011 software team devote themselves to a more professional and committedpractice both in technique and biology reality.</p>
-<p>We named our project Lachesisand believe that our software will provide the user with a uniform platform to use their intelligence in synthetic biology as well as a coachfellow to novice.</p>
-<p>On this platform, users arefree to fetch parts they want from the registry, build their assembly and visualize the network, and look at the design from different aspects.</p>
-<h3><a name=Design and automatic modeling"" id="Design and automatic modeling"></a>Design and automatic modeling</h3>
-<p>We inherited the traditional way to demonstrate a design with an assembly view, which allow users to drag parts to form an assembly.The following step is to generate the network associated with the assembly.Here, we used an rule based modeling approachto build the network.On simulating the dynamics of the network, the ode modeling approach is adapted.</p>
-<p>The biological system is complex, and sometimes the mathematical models trying to describe that is far from accurate.How do you know which substance or which ode equation plays a more vital role in the total performance?And it’s hard for modeler to tell the software all the possible combinations by listing all the reactions, all the substances that make sense.Based on these considerations, we use rule based modeling approach to depict a more comprehensive and elaborate profile of the gene circuit.That is, we first list out almost all the possible species and then decide which is more important.Anetwork generated with such an approach is immune to incompetent or too simplified modeling of the system.And it’s the software’s duty to analyze which ode can be omitted, which parameter is crucial.</p>
-<h3><a name="Visualization" id="Visualization"></a>Visualization</h3>
-<p>Traditional synthetic biology software tools try to illustrate the outcome of a circuit with a time course demonstration. The method is not so intuitive. To help novice to understand how the circuit work. We provide a new way to visualize the network.Putting the species and reactions on one map as nodes and show their relationships with lines connecting each other.If we have time , we will also make it possible to show how a network is generated in a dynamic visualized way.</p>
-<h3><a name="Parameter tune and sensitivity analysis" id="Parameter tune and sensitivity analysis"></a>Parameter tune and sensitivity analysis</h3>
-<p>In order to establish a workable circuit, biologist has to spend a lot of time on fine tuning the network, balancing on increase one promoter’s strength or decreasing another activator’s  binding affinity. The process is a sweat, and sometimes there are just too much to consider and how can a novice know which parameter to tune to adjust to a better performance circuit? Our software will suggest the user a local direction of where to go when they are tracked in a plaetu, boggling what to do.</p>
-<h3><a name="Assessment" id="Assessment"></a>Assessment</h3>
-<p>Topology is more important than parameters, once you got a bad design, it’s hard to realize the anticipated behavior in a wide range of parameters, and our software can help to assess whether a designated network can work under parameter variations.</p>
-<h2><a name="Introduction" id="Introduction"></a>Introduction</h2>
 <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 categories 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 436: / 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 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 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>
 <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>
-<p><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 452: / Line 73: @@
 </ul>
-<p><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>
@@ Line 487: / Line 109: @@
     <b> Welcome to &#160;&#160;<a href="http://en.ustc.edu.cn/" target="_blank">University of Science and Technology of China</a>&#160;! </b>
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+   <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>
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