Difference between revisions of "Team:SJTU-software/Human Practices"

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    <div class="wrapper">
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        <!-- HEADER -->
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      <header class="cf">
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          <div id="logo"><a href="https://2018.igem.org/Team:SJTU-software/Home"> <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>
  
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<div class="column full_size">
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        <!-- NAV -->
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        <nav class="cf">
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            <ul id="nav" class="sf-menu">
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                <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>
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            </ul>
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        </nav>
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        <!-- ENDS NAV-->
  
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<h1>Human Practices</h1>
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        <!-- MAIN-->
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<p>
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<div id="main" class="cf">
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At iGEM we believe societal considerations should be upfront and integrated throughout the design and execution of synthetic biology projects. “Human Practices” refers to iGEM teams’ efforts to actively consider how the world affects their work and the work affects the world. Through your Human Practices activities, your team should demonstrate how you have thought carefully and creatively about whether your project is responsible and good for the world. We invite you to explore issues relating (but not limited) to the ethics, safety, security, and sustainability of your project, and to show how this exploration feeds back into your project purpose, design and execution.
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<div class="headline">
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</p>
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            HUMAN PRACTICE —— INTERCRATED AND GOLD       
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        </div>
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            <!-- posts list -->
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            <div id="posts-list" class="cf">
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                <article class="cf">
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                    <div class="entry-title">
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                        <!-- <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>
 +
                    <div class="expert_name" id="FT">Prof. Fei Tao</div>
 +
                    <div class="subtitle">School of Life Sciences & Biotechnology</div>
 +
                    <div class="subtitle">Shanghai Jiao Tong University</div>
  
 +
                    <div id="FeiTao">
 +
                        <div class="photo">
 +
                                <img src="https://raw.githubusercontent.com/sjtusoftware2018/2018iGEM_wiki/master/images/HP/FeiTao.jpg" style="display: inline;">
 +
                        </div>
 +
                        <div class="member_info">
 +
                            <blockquote>
 +
                                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.
 +
                            </blockquote>
 +
                        </div>
 +
                    </div>
 +
                    <div class="excerpt">
 +
                        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.
 +
                    </div>
  
 +
                    <div class="expert_name" id="DF">Prof. Daniel Figeys</div>
 +
                    <div class="subtitle">Department of Biochemistry, Microbiology and Immunology</div>
 +
                    <div class="subtitle">University of Ottawa</div>
  
−
<p>For more information, please see the <a href="https://2018.igem.org/Human_Practices">Human Practices Hub</a>. There you will find:</p>
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                    <div id="DanielFigeys">
−
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                        <div class="photo">
−
<ul>
+
                                <img src="https://raw.githubusercontent.com/sjtusoftware2018/2018iGEM_wiki/master/images/HP/DanielFigeys.jpg" style="display: inline;">
−
<li> an <a href="https://2018.igem.org/Human_Practices/Introduction">introduction</a> to Human Practices at iGEM </li>
+
                        </div>
−
<li>tips on <a href="https://2018.igem.org/Human_Practices/How_to_Succeed">how to succeed</a> including explanations of judging criteria and advice about how to conduct and document your Human Practices work</li>
+
                        <div class="member_info">
−
<li>descriptions of <a href="https://2018.igem.org/Human_Practices/Examples">exemplary work</a> to inspire you</li>
+
                            <blockquote>
−
<li>links to helpful <a href="https://2018.igem.org/Human_Practices/Resources">resources</a></li>
+
                                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.
−
<li>And more! </li>
+
                            </blockquote>
−
</ul>
+
                        </div>
−
+
                    </div>
 +
                    <div class="excerpt">
 +
                        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.
 +
                    </div>
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 +
                </article>
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                <article class="cf">
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                        <a href="single.html" ><img src="img/dummies/620x450-b.jpg" alt="Thumbnail" /></a>
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                    </div>
 +
                    <div class="entry-title">
 +
                        <div class="meta">Jan 23 by <a href="#" class="author">Ansimuz</a></div>
 +
                        <a href="single.html" class="post-heading" >LOREM IPSUM DOLOR</a>
 +
                    </div>
 +
                    <div class="excerpt">
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                        Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra.
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                    </div>
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                <article class="cf">
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                    <div class="feature-image">
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                        <a href="single.html" ><img src="https://raw.githubusercontent.com/sjtusoftware2018/2018iGEM_wiki/master/images/dummies/620x450-c.jpg" alt="Thumbnail" /></a>
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                    </div>
 +
                    <div class="entry-title">
 +
                        <div class="meta">Jan 23 by <a href="#" class="author">Ansimuz</a></div>
 +
                        <a href="single.html" class="post-heading" >LOREM IPSUM DOLOR</a>
 +
                    </div>
 +
                    <div class="excerpt">
 +
                        Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra.
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Revision as of 05:04, 12 October 2018

SJTU-software
Metlab: a metabolic network research tool box
SJTU-software
Metlab: a metabolic network alignment tool
HUMAN PRACTICE —— INTERCRATED AND GOLD
Expert Interview
We discussed with different disciplines and fields scholars, their views inspired us a lot. Interviewing experts greatly advanced our project.
Prof. Fei Tao
School of Life Sciences & Biotechnology
Shanghai Jiao Tong University
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.
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.
Prof. Daniel Figeys
Department of Biochemistry, Microbiology and Immunology
University of Ottawa
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.
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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Jan 23 by Ansimuz
LOREM IPSUM DOLOR
Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra.
Thumbnail
Jan 23 by Ansimuz
LOREM IPSUM DOLOR
Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra.
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Jan 23 by Ansimuz
LOREM IPSUM DOLOR
Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra.
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