Difference between revisions of "Team:SJTU-software/Design"

Line 195: Line 195:
 
             <div id="main" class="cf">
 
             <div id="main" class="cf">
 
                 <div class="headline">
 
                 <div class="headline">
−
                     Project —— Design  
+
                     Project —— Design & Contribution
 
                 </div>
 
                 </div>
 
                     <!-- posts list -->
 
                     <!-- posts list -->
Line 201: Line 201:
 
                          
 
                          
 
                         <article class="cf">
 
                         <article class="cf">
−
                         
+
                            <div class="entry-title">
 +
                                <div class="post-heading" id="Design" >Design</div>
 +
                            </div>
 
                             <div class="excerpt">
 
                             <div class="excerpt">
 
                                 Since the birth of synthetic biology in 2000, metabolic engineering has made increasingly huge progress on high value-added natural products. The synthesis and construction of metabolic pathways play a fundamental role in microbiology, biochemistry, and many other relevant fields. In 2003, Jay Keasling’s team reconstructed the biological synthesis pathway of arteannuinic acid in E. coli, providing functional confirmation for this metabolic process. In recent years, researchers have engineered yeast to produce a variety of plant-based natural products. These pathways are likely to involve the introduction of many heterologous genes and numerous genetic modifications to increase productivity. In the biosynthesis of opioids in yeast, 17 enzymes from different plants, animals, and yeasts were encoded through synthetic biological way. Although there are several tools for scientists to analyze and select the potential genes of the designed pathway, these tools all focus on the one or two specific gene instead of the whole metabolic system. Therefore, what our team’s trying to do is making comparisons between the designed pathway we want to synthesize and the natural-existing pathways to make sure that the researchers can get the whole picture. In this way, scientists can learn more about molecular functions and biological process from an innovating aspect.
 
                                 Since the birth of synthetic biology in 2000, metabolic engineering has made increasingly huge progress on high value-added natural products. The synthesis and construction of metabolic pathways play a fundamental role in microbiology, biochemistry, and many other relevant fields. In 2003, Jay Keasling’s team reconstructed the biological synthesis pathway of arteannuinic acid in E. coli, providing functional confirmation for this metabolic process. In recent years, researchers have engineered yeast to produce a variety of plant-based natural products. These pathways are likely to involve the introduction of many heterologous genes and numerous genetic modifications to increase productivity. In the biosynthesis of opioids in yeast, 17 enzymes from different plants, animals, and yeasts were encoded through synthetic biological way. Although there are several tools for scientists to analyze and select the potential genes of the designed pathway, these tools all focus on the one or two specific gene instead of the whole metabolic system. Therefore, what our team’s trying to do is making comparisons between the designed pathway we want to synthesize and the natural-existing pathways to make sure that the researchers can get the whole picture. In this way, scientists can learn more about molecular functions and biological process from an innovating aspect.
Line 211: Line 213:
  
 
                           <div class="excerpt">
 
                           <div class="excerpt">
−
                                Then, we took a survey among students in the biology department in our school, and selected another two commonly-needed functions to combine into the toolkit, including <strong>SMILES Drawer</strong> and <strong>Gene Editor</strong>. People taking our survey were reported of having the need to compare the similarities between metabolites. <strong>SMILES Drawer</strong> enables people to calculate the similarity coefficient between metabolites, and preview their molecular structures. At the same time, <strong>Gene Editor</strong> was created to help researchers simulate the process of enzyme digestion, DNA translation and manage Genbank features of genomes they study.
+
                              During the project, we had the pleasure to interview a PhD student. From his experiences working on biological metabolism, he has a great demand of comparing similarities between metabolites. Therefore, we created SMILES Drawer. SMILES Drawer enables people to calculate the similarity coefficient between metabolites, and preview their molecular structures.
 
                             </div>
 
                             </div>
 +
                             
 +
                        </article>
  
 +
                        <article class="cf">
 +
                            <div class="entry-title">
 +
                                <div class="post-heading" id="Contribution" >Contribution</div>
 +
                            </div>
 
                             <div class="excerpt">
 
                             <div class="excerpt">
−
                              Finally, from some feedbacks on our project, we made <strong>SBML Differ</strong>. After comparison of two networks, <strong>SBML Differ</strong> aims to visualize the difference between biological models, providing users with a clearer picture about network similarity apart from their similarity coefficient.
+
                                The aim of our project has always been designing and developing useful programs for Synthetic Biology and iGEM community. Comparative analysis of biological network is very useful and indicative in synthetic biology and other related studies. Specially, it enables people to handle unknown organisms starting from known ones with alike networks. However, most current tools are only for a specific problem or application, and the existing algorithm is inefficient. In order to solve these problems, we launch METLAB, a general purpose alignment software.
−
                             </div>            
+
                            </div>
−
                         </article>                  
+
                       
 +
                            <div class="excerpt">
 +
                              Metlab is a suite of synthetic biology aided tools and mainly functions as BLAST for networks. Besides network alignment, users may visualize networks, compare and draw metabolites and design their wet-lab experiments.
 +
                            </div>
 +
 
 +
                          <div class="excerpt">
 +
                              Combining various commonly-used functions into the toolkit, our project will definitely come in handy to people studying synthetic biology and related fields.
 +
                             </div>
 +
                           
 +
                         </article>                                    
 
             </div>
 
             </div>
  
Line 225: Line 242:
 
                         <ul>
 
                         <ul>
 
                             <li class="block">
 
                             <li class="block">
−
                                 <h4 class="heading" align="center">Description</h4>
+
                                 <h4 class="heading" align="center">Design & Contribution</h4>
 
                                 <ul>
 
                                 <ul>
−
                                     <li class="cat-item"><a href="#Background" >BACKGROUND</a></li>
+
                                     <li class="cat-item"><a href="#Design" >Design</a></li>
−
                                     <li class="cat-item"><a href="#What" >WHAT IS METLAB?</a></li>
+
                                     <li class="cat-item"><a href="#Contribution" >Contribution</a></li>
−
                                    <li class="cat-item"><a href="#How" >HOW TO USE IT?</a></li>
+
                                 
 
                                 </ul>
 
                                 </ul>
 
                             </li>
 
                             </li>

Revision as of 11:21, 16 October 2018

SJTU-software
Metlab: a metabolic network research tool box
Project —— Design & Contribution
Design
Since the birth of synthetic biology in 2000, metabolic engineering has made increasingly huge progress on high value-added natural products. The synthesis and construction of metabolic pathways play a fundamental role in microbiology, biochemistry, and many other relevant fields. In 2003, Jay Keasling’s team reconstructed the biological synthesis pathway of arteannuinic acid in E. coli, providing functional confirmation for this metabolic process. In recent years, researchers have engineered yeast to produce a variety of plant-based natural products. These pathways are likely to involve the introduction of many heterologous genes and numerous genetic modifications to increase productivity. In the biosynthesis of opioids in yeast, 17 enzymes from different plants, animals, and yeasts were encoded through synthetic biological way. Although there are several tools for scientists to analyze and select the potential genes of the designed pathway, these tools all focus on the one or two specific gene instead of the whole metabolic system. Therefore, what our team’s trying to do is making comparisons between the designed pathway we want to synthesize and the natural-existing pathways to make sure that the researchers can get the whole picture. In this way, scientists can learn more about molecular functions and biological process from an innovating aspect.
During the project, we had the pleasure to interview a PhD student in the university of Toronto. Based on his experiences working on biological metabolism, changing from several different software to visualize the network, do simulations or other studies, is quite inconvenient. Therefore, he suggested us to make our tool more handful for researches by integrating a few frequently-used functions together. Thanks to his advice, we added a new function into our project – SBML Drawer. SBML Drawer can visualize networks by taking xml files as input.
During the project, we had the pleasure to interview a PhD student. From his experiences working on biological metabolism, he has a great demand of comparing similarities between metabolites. Therefore, we created SMILES Drawer. SMILES Drawer enables people to calculate the similarity coefficient between metabolites, and preview their molecular structures.
Contribution
The aim of our project has always been designing and developing useful programs for Synthetic Biology and iGEM community. Comparative analysis of biological network is very useful and indicative in synthetic biology and other related studies. Specially, it enables people to handle unknown organisms starting from known ones with alike networks. However, most current tools are only for a specific problem or application, and the existing algorithm is inefficient. In order to solve these problems, we launch METLAB, a general purpose alignment software.
Metlab is a suite of synthetic biology aided tools and mainly functions as BLAST for networks. Besides network alignment, users may visualize networks, compare and draw metabolites and design their wet-lab experiments.
Combining various commonly-used functions into the toolkit, our project will definitely come in handy to people studying synthetic biology and related fields.

    Address

    NO. 800 Dongchuan Road, Minhang District, Shanghai, China

    Contact Us

    rockywei@sjtu.edu.cn

    SJTU-software