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

 
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            }
 +
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    /*-----------------------------------------------------------------------------------*/
 
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−
    ul{
 
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−
    /*---------------------------------------------------------------------------------*/
 
−
    /*expert interview*/
 
−
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−
        width:100%
 
−
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−
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    .member_info blockquote {
 
−
        margin: 0px 0px 0px 0px;
 
−
        padding: 0px;
 
−
        font-size: 18px;
 
−
        line-height: 1.5em;
 
−
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−
 
−
    #FeiTao{
 
−
        height:350px;
 
−
    }
 
−
    #FeiTao .member_info{
 
−
        margin-top: 50px;
 
−
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−
 
−
    #DanielFigeys{
 
−
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−
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−
</style>
 
 
<body>
 
<body>
 
     <div class="wrapper">
 
     <div class="wrapper">
−
        <!-- HEADER -->
 
−
      <header class="cf">
 
−
          <div id="logo"><a href="https://2018.igem.org/Team:SJTU-software"> <img src="https://raw.githubusercontent.com/sjtusoftware2018/2018iGEM_wiki/master/images/teamlogo.png"  height="90"/></a></div>
 
−
          <div id="title">SJTU-software</div>
 
−
          <div id="subtitle">Metlab: a metabolic network alignment tool</div>
 
−
        </header>
 
−
 
−
        <!-- NAV -->
 
−
        <nav class="cf">
 
−
            <ul id="nav" class="sf-menu">
 
−
                <li class="current-menu-item"><a href="https://2018.igem.org/Team:SJTU-software">HOME</a></li>
 
−
                <li><a href="">TEAM</a>
 
−
                    <ul>
 
−
                        <li><a href="https://2018.igem.org/Team:SJTU-software/Team">TEAM</a></li>
 
−
                        <li><a href="https://2018.igem.org/Team:SJTU-software/Collaborations">COLLABRATIONS</a></li>>
 
−
                    </ul>
 
−
                </li>
 
−
                <li><a href="">PROJECT</a>
 
−
                    <ul>
 
−
                        <li><a href="https://2018.igem.org/Team:SJTU-software/Description">DESCRIPTION</a></li>
 
−
                        <li><a href="https://2018.igem.org/Team:SJTU-software/Design">DESIGN</a></li>
 
−
                        <li><a href="https://2018.igem.org/Team:SJTU-software/Notebook">NOTEBOOK</a></li>
 
−
                        <li><a href="https://2018.igem.org/Team:SJTU-software/Contribution">CONTRIBUTION</a></li>
 
−
                        <li><a href="https://2018.igem.org/Team:SJTU-software/Demonstrate">DEMONSTRATE</a></li>
 
−
                        <li><a href="https://2018.igem.org/Team:SJTU-software/Improve">IMPROVE</a></li>
 
−
                        <li><a href="https://2018.igem.org/Team:SJTU-software/Attributions">ATTRIBUTIONS</a></li>
 
−
                    </ul>
 
−
                </li>
 
−
                <li><a href="">HUMAN PRACTICE</a>
 
−
                    <ul>
 
−
                        <li><a href="https://2018.igem.org/Team:SJTU-software/HP/Silver">SILVER HP</a></li>
 
−
                        <li><a href="https://2018.igem.org/Team:SJTU-software/HP/Gold_Intergrated">INTERCRATED AND COLD</a></li>
 
−
                        <li><a href="https://2018.igem.org/Team:SJTU-software/Engagement">PUBLIC ENGAGEMENT</a></li>
 
−
                    </ul>
 
−
                </li>
 
−
            </ul>
 
−
        </nav>
 
−
        <!-- ENDS NAV-->
 
  
 
         <!-- MAIN-->
 
         <!-- MAIN-->
−
<div id="main" class="cf">
+
                <div id="main" class="cf">
−
<div class="headline">
+
<div class="headline">
−
            HUMAN PRACTICE —— INTERCRATED AND GOLD       
+
                     Collaboration 
−
        </div>
+
−
            <!-- posts list -->
+
−
            <div id="posts-list" class="cf">
+
−
               
+
−
                <article class="cf">
+
−
                     <div class="entry-title">
+
−
                        <!-- <div class="meta">April 7 2018</div> -->
+
−
                        <div class="post-heading" id="ExpertInterview">Expert Interview</div>
+
−
                    </div>
+
−
                    <div class="excerpt">
+
−
                        We discussed with different disciplines and fields scholars, their views inspired us a lot. Interviewing experts greatly advanced our project.
+
−
                    </div>
+
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                    <div class="expert_name" id="FT">Prof. Fei Tao</div>
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                    <div class="subtitle">School of Life Sciences & Biotechnology</div>
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                    <div class="subtitle">Shanghai Jiao Tong University</div>
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                                Dr. Tao is now an associate professor of SJTU. He has been engaged in the research of microbial synthetic biology since he got the doctoral degree. He mainly focuses on developing efficient cell factories and advanced biocatalytic technology based on the concept of synthetic biology.
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                        Our interview concentrated on the topic “Application of metabolic network alignment tool in the laboratory”. Dr. Tao told us design of metabolic networks in synthetic biology focus on these aspects: 1.Yield; 2. Efficiency(in A -> B, concentration of B/A); 3. Period. Then we briefly introduced the idea of our software (a metabolic network alignment tool). Dr. Tao was greatly interest in the tool. He also analyzed a number of factors that lead to the difficulty of metabolic network alignment. How to evaluate similarity of two metabolic networks? How to grade the result of alignment? How to evaluate similarity of different compound…… His opinion made us have a deeper understanding of how make our software more practical and functional in the laboratory.
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                    <div class="expert_name" id="DF">Prof. Daniel Figeys</div>
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                    <div class="subtitle">Department of Biochemistry, Microbiology and Immunology</div>
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                    <div class="subtitle">University of Ottawa</div>
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                                Daniel Figeys is a Professor and the Chair of the Department of Biochemistry, Microbiology and Immunology (BMI) and cross-appointed in the Department of Chemistry and Biomolecular Sciences at the University of Ottawa.  He is also a Canada Research Chair in Proteomics and Systems Biology.  His expertise is in the development of proteomics and systems biology and more recently in metaproteomics for microbial community analysis.
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                        In Prof. Daniel Figeys’s Lab, they have developed a advanced bioinformatics software “iMetaLab”. Their project is originally designed for human/mouse gut metaproteomics protein identification and quantification, rooted from the MetaProIQ workflow. Upon the rising request, they wrap up the workflow into a desktop standalone version, with taxon analysis module built in. In the meantime, they have been working on some meta-function annotation and enrichment analysis, as well as some data visualization modules. Then they realize that it would be good to wrap up all related functions and share them to the community. They aim to make iMetaLab a free and one-stop toolset for gut metaproteomics, with increasing amount of tools under development. This interview inspired us how to make our software “Metlab: a metabolic network alignment tool” more user-friendly and complete. The process of their software development enlightened us to make “Metlab” a functional toolset with many tools related metabolic network.
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                        <div class="meta">Jan 23 by <a href="#" class="author">Ansimuz</a></div>
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                        <a href="single.html" class="post-heading" >LOREM IPSUM DOLOR</a>
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                            <li class="cat-item"><a href="#FT" >Prof. Fei Tao</a></li>
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                            <li class="cat-item"><a href="#" >February 2012</a></li>
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                                 <div class="post-heading" >Tongji-software team </div>
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                              In the process of our project, we had some difficulty in network visualization. Just then Tongji-software team got in touch with us. They had some problem in the COBRA toolbox, hoping to get some help from us. Since they had completed the visualization work, they could help us with front-end visualization. So we decided to communicate face to face.
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                                    <a href="#">Pellentesque habitant morbi senectus </a><span class="meta"> Mar 12 <a href="#" >By ansimuz</a></span>
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                                        <img src="https://static.igem.org/mediawiki/2018/b/b7/T--SJTU-software--tongji_Communication2.jpg" alt="Thumbnail" />
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                            <div class="excerpt">
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                              On September 23rd, we met each other in our lab. Tongji-software gave us some suggestions on network visualization and showed us how D3.js package was used. They helped us to deploy the package with an example. And we taught them the FVA function in COBRA toolbox and some methods to do gene knockout analysis on the result of flux balance analysis as well. They added this function into their software later.
 
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                                    <a href="#">Pellentesque habitant morbi senectus </a><span class="meta"> Mar 12 <a href="#" >By ansimuz</a></span>
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                                 </div>
 
                                 </div>
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                            <div class="excerpt">
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                                Besides the communication on projects, our team leader Yangzhen Wei shared some experience in Giant Jamboree as an old iGEMer. What’s more, he shared some tips about transportation, climate, sightseeing in Boston.
 
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                                    <div class="post-heading" >USTC-software team</div>
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                                    <a href="#">Pellentesque habitant morbi senectus </a><span class="meta"> Mar 12 <a href="#" >By ansimuz</a></span>
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                                    After completing our tool box, we invited USTC-software to run our β test. And they gave us some feedbacks. They pointed out problems on user guiding, and gave us their opinions. Then we improved our software in the way they recommended, making our software more user-friendly.
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                                    We also participated in their test. Their software, Biohub was an experiment process recording tool. It was convenient for process-experiment recording. Creating process module and sharing them in the community facilitated the communication between researchers. We gave them advices on visualization and multithreading experiment recording. In the end, we exchanged some of the visualization methods.
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Latest revision as of 08:09, 17 October 2018

SJTU-software
Metlab: a metabolic network research tool box
Collaboration
Tongji-software team
In the process of our project, we had some difficulty in network visualization. Just then Tongji-software team got in touch with us. They had some problem in the COBRA toolbox, hoping to get some help from us. Since they had completed the visualization work, they could help us with front-end visualization. So we decided to communicate face to face.
Thumbnail
On September 23rd, we met each other in our lab. Tongji-software gave us some suggestions on network visualization and showed us how D3.js package was used. They helped us to deploy the package with an example. And we taught them the FVA function in COBRA toolbox and some methods to do gene knockout analysis on the result of flux balance analysis as well. They added this function into their software later.
Thumbnail
Besides the communication on projects, our team leader Yangzhen Wei shared some experience in Giant Jamboree as an old iGEMer. What’s more, he shared some tips about transportation, climate, sightseeing in Boston.
USTC-software team
After completing our tool box, we invited USTC-software to run our β test. And they gave us some feedbacks. They pointed out problems on user guiding, and gave us their opinions. Then we improved our software in the way they recommended, making our software more user-friendly.
We also participated in their test. Their software, Biohub was an experiment process recording tool. It was convenient for process-experiment recording. Creating process module and sharing them in the community facilitated the communication between researchers. We gave them advices on visualization and multithreading experiment recording. In the end, we exchanged some of the visualization methods.

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

    Contact Us

    rockywei@sjtu.edu.cn

    SJTU-software