Difference between revisions of "Template:Tongji-software"

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<body>
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<div class="icon">
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    <ul>
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    <a href="https://2018.igem.org/Team:Tongji-Software" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/f/fa/T--Tongji-Software--logo.svg" width="55%"  ></li></a>
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    <a href="https://2018.igem.org/Team:Tongji-Software/Project" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/e/ed/T--Tongji-Software--Pro.svg" width="30%" ></li></a>
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    <a href="https://2018.igem.org/Team:Tongji-Software/Team" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/1/1f/T--Tongji-Software--Tea.svg" width="30%" ></li></a>
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    <a href="https://2018.igem.org/Team:Tongji-Software/Attributions" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/8/86/T--Tongji-Software--Att.svg" width="30%" ></li></a>
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    <a href="https://2018.igem.org/Team:Tongji-Software/Model" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/7/77/T--Tongji-Software--Mod.svg" width="30%" ></li></a>
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    <a href="https://2018.igem.org/Team:Tongji-Software/Collaborations" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/d/d3/T--Tongji-Software--Col.svg" width="30%" ></li></a>
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    <a href="https://2018.igem.org/Team:Tongji-Software/Requirements" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/5/5f/T--Tongji-Software--Req.svg" width="30%" ></li></a>
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    <a href="https://2018.igem.org/Team:Tongji-Software/Human_Practices" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/c/cc/T--Tongji-Software--Hum.svg" width="30%" ></li></a>
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    <a href="https://2018.igem.org/Team:Tongji-Software/Measurement" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/8/8b/T--Tongji-Software--Med.svg" width="30%" ></li></a>
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<div class="left"  id = "sidebar-wrapper">
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    <ul>
 +
      <li><a href="#Contribution">Contribution</a></li>
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      <li><a href="#Demonstration">Demonstration</a></li>
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      <li><a href="#Safety">Safety</a></li>
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    </ul>
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</div>
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<div class="picture">
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  <div class="title">
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    <span>Requirements</span>
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  </div>
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<div class="content" id="con">
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<span class="h1" name='con' id="Contribution">
 +
            Contribution</br>
 +
          </span>
 +
 +
<span class="detail">Alpha Ant is a convenient and efficient pathway design tool. More importantly, it is reliable. Check it in <a href="https://2018.igem.org/Team:Tongji-Software/Validation">Validation</a>. We provide users with enzyme gene information of Biobricks, including sequence information and physiochemical characteristics. The core idea is to design proper and efficient pathway and recommend Biobricks (mainly enzyme gene) for users’ need.</span></br>
 +
(这里放我们软件的截图)
 +
<span class="detail">There are three main contribution to synthetic biology:</span></br>
 +
 +
<span class="detail"> First one is that we offer more possibilities. We collect 7 reliable online databases and create our own data structure, including KEGG, MetaCyc, BRENDA and so on. Users can find several possible pathways consist of different enzyme-encoding genes. Those genes could be from any organism in nature. Consequently, many possible options are given to the user. Check users’ guide in <a href ="https://2018.igem.org/Team:Tongji-Software/Requirements#Demonstration">Demonstration</a>.</span></br>
 +
 +
<span class="detail">Second one is that more information is provided including Physiochemical characteristics of compounds and enzymes, gene information and FBA data. Especially the physiochemical data, changes in each one of the chassis cell system could contribute to inefficiency or failure of a pathway. So we want to provide information as much as possible. What we are doing right now is for everyone who is engaged in synthetic biology and for their consideration.</span></br>
 +
 +
<span class="detail">Third one is that we offer some very useful functions other than pathway design, which are microorganism recommendation, SMILES comparison and FBA. Actually, we are trying to meet every experimenters need as much as possible. Details can be found in <a href="https://2018.igem.org/Team:Tongji-Software/Project">Project</a> and <a href = "https://2018.igem.org/Team:Tongji-Software/Model">model</a>.</span></br>
 +
 +
 +
<span class="h1" id="Demonstration">
 +
            Demonstration</br>
 +
          </span>
 +
 +
<span class="h1" id="Safety">
 +
            Safety</br>
 +
          </span>
 +
<span class="question">Q1: Who will use your software? What will the user concern about?</span></br>
 +
<b>Alpha Ant:</b></br>
 +
<span class="detail">1. For synthetic biologist</span></br>
 +
<span class="detail">Pathway engineering: design proper metabolic pathways while taking into account several criteria such as thermodynamic feasibility, material competition of heterologous reactions, atom conservation, toxicity of intermediates. </span></br>
 +
 +
<span class="detail">2. For environmentalist</span></br>
 +
<span class="detail">Find proper Microorganism to make some harmful substances degrade. The purpose is to be helpful to improve the environment.</span></br>
 +
 +
<span class="detail">3. For chemist</span></br>
 +
<span class="detail">Find more reliable and convenient path to synthesis target compound (cell-free synthetic biology)</span></br>
 +
 +
<span class="detail">4. For drug researcher</span></br>
 +
<span class="detail">By using our software, researchers can study the small molecular drug and explore new pathway to synthesize it</span></br>
 +
 +
To be continued ...</br></br>
 +
<span class="question">Q2: Are there any safety problem of biobricks in Alpha Ant we need to concern about?</span></br>
 +
Alpha Ant:
 +
<span class="detail">We provide users with enzyme gene information of Biobricks, including sequence information and physiochemical characteristics. The core idea is to design proper and efficient pathway and recommend mainly enzyme gene for users’ need. Consequently, users can get gene information. After that, they can design new biobricks or search existing one by their own. </span></br>
 +
 +
 +
</br>
 +
<span class="question">Q3:  What about chassis cell? Since your software can recommend chassis cell for users, have you ever think about safety of your chassis cell?</span></br>
 +
Alpha Ant: 
 +
<span class="detail">In our microorganism recommendation system, we only recommend common used organism in iGEM and organisms in iGEM white list(link). We want ensure the biosafety of our project and people who use our software.</span></br></br>
 +
 +
<span class="question">Q4:  How many compounds and enzyme genes do you have in your software project?</span></br>
 +
Alpha Ant:  7689 compounds  10865 reactions  6385 gibbs  630275 genes
 +
KEGG: 21831          10865 reaction
 +
Gil:  6160 compounds    7164 reactions
 +
 +
</br>
 +
<span class="question">Q5: Do users have any way to access your data, or change data without any limitations?</span></br>
 +
Alpha Ant: 
 +
<span class="detail">Our data has a very neat format, mostly dictionary format. They are all stored in excel files. Users can simply search metabolic pathway in the browser and don’t need to download any files to use our software. So it’s quite convenient for them. Generally, users can not change our data in web client. But they can contact us and exchange suggestions. By the way, full data can be downloaded in github(link).</span></br>
 +
 +
 +
 +
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Revision as of 08:08, 15 October 2018

    •
Requirements
Contribution
 Alpha Ant is a convenient and efficient pathway design tool. More importantly, it is reliable. Check it in Validation. We provide users with enzyme gene information of Biobricks, including sequence information and physiochemical characteristics. The core idea is to design proper and efficient pathway and recommend Biobricks (mainly enzyme gene) for users’ need.
(这里放我们软件的截图) There are three main contribution to synthetic biology:
First one is that we offer more possibilities. We collect 7 reliable online databases and create our own data structure, including KEGG, MetaCyc, BRENDA and so on. Users can find several possible pathways consist of different enzyme-encoding genes. Those genes could be from any organism in nature. Consequently, many possible options are given to the user. Check users’ guide in Demonstration.
Second one is that more information is provided including Physiochemical characteristics of compounds and enzymes, gene information and FBA data. Especially the physiochemical data, changes in each one of the chassis cell system could contribute to inefficiency or failure of a pathway. So we want to provide information as much as possible. What we are doing right now is for everyone who is engaged in synthetic biology and for their consideration.
Third one is that we offer some very useful functions other than pathway design, which are microorganism recommendation, SMILES comparison and FBA. Actually, we are trying to meet every experimenters need as much as possible. Details can be found in Project and model.
Demonstration
 Safety
 Q1: Who will use your software? What will the user concern about?
Alpha Ant:
1. For synthetic biologist
Pathway engineering: design proper metabolic pathways while taking into account several criteria such as thermodynamic feasibility, material competition of heterologous reactions, atom conservation, toxicity of intermediates.
2. For environmentalist
Find proper Microorganism to make some harmful substances degrade. The purpose is to be helpful to improve the environment.
3. For chemist
Find more reliable and convenient path to synthesis target compound (cell-free synthetic biology)
4. For drug researcher
By using our software, researchers can study the small molecular drug and explore new pathway to synthesize it
To be continued ...

Q2: Are there any safety problem of biobricks in Alpha Ant we need to concern about?
Alpha Ant: We provide users with enzyme gene information of Biobricks, including sequence information and physiochemical characteristics. The core idea is to design proper and efficient pathway and recommend mainly enzyme gene for users’ need. Consequently, users can get gene information. After that, they can design new biobricks or search existing one by their own.

Q3: What about chassis cell? Since your software can recommend chassis cell for users, have you ever think about safety of your chassis cell?
Alpha Ant: In our microorganism recommendation system, we only recommend common used organism in iGEM and organisms in iGEM white list(link). We want ensure the biosafety of our project and people who use our software.

Q4: How many compounds and enzyme genes do you have in your software project?
Alpha Ant: 7689 compounds 10865 reactions 6385 gibbs 630275 genes KEGG: 21831 10865 reaction Gil: 6160 compounds 7164 reactions
Q5: Do users have any way to access your data, or change data without any limitations?
Alpha Ant: Our data has a very neat format, mostly dictionary format. They are all stored in excel files. Users can simply search metabolic pathway in the browser and don’t need to download any files to use our software. So it’s quite convenient for them. Generally, users can not change our data in web client. But they can contact us and exchange suggestions. By the way, full data can be downloaded in github(link).