Difference between revisions of "Team:Tongji-Software/Requirements"

 
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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="35%" ></li></a>
 
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     <a href="https://2018.igem.org/Team:Tongji-Software/Human_Practice" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/c/cc/T--Tongji-Software--Hum.svg" width="35%" ></li></a>
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<div class="left"  id = "sidebar-wrapper">
 
     <ul>
 
     <ul>
 
       <li><a href="#Contribution">Contribution</a></li>
 
       <li><a href="#Contribution">Contribution</a></li>
−
      <li><a href="#Demonstration">Demonstration</a></li>
 
 
       <li><a href="#Safety">Safety</a></li>
 
       <li><a href="#Safety">Safety</a></li>
 
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<span class="h1" id="Contribution">  
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<span class="h1" name='con' id="Contribution">  
 
             Contribution</br>  
 
             Contribution</br>  
 
           </span>
 
           </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>  
+
<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/Project#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>  
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(这里放我们软件的截图)
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<img src="https://static.igem.org/mediawiki/2018/f/f2/T--Tongji-Software--alpha1.png" width="70%"></br>
 +
<span class="fig">Fig. 1. Home page of Alpha Ant.</span></br>
 +
 
 +
 
 +
 
 
<span class="detail">There are three main contribution to synthetic biology:</span></br>  
 
<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"> 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/Project#Demonstrate">Demonstrate</a>.</span></br>
 +
 
 +
<img src="https://static.igem.org/mediawiki/2018/f/f5/T--Tongji-Software--alpha3.png" width="70%"></br>
 +
<span class="fig">Fig. 2. Search page of Alpha Ant.</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">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>
 +
 +
<img src="https://static.igem.org/mediawiki/2018/2/2f/T--Tongji-Software--alpha2.png" width="70%"></br>
 +
<span class="fig">Fig. 3. Result page of Alpha Ant.</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="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="detail"></span></br>
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<img src="https://static.igem.org/mediawiki/2018/0/00/T--Tongji-Software--alpha4.png" width="70%"></br>
 +
<span class="fig">Fig. 4. SMILES comparison page in Alpha Ant.</span></br>
 +
<img src="https://static.igem.org/mediawiki/2018/3/3a/T--Tongji-Software--alpha5.png" width="70%"></br>
 +
<span class="fig">Fig. 5. Organism recommendation page in Alpha Ant.</span></br>
 +
<img src="https://static.igem.org/mediawiki/2018/9/9c/T--Tongji-Software--project-p22.png" width="70%"></br>
 +
<span class="fig">Fig. 6. Example of FBA results in Alpha Ant.</span></br>
  
  
−
<span class="detail"></span></br>
+
<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"></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>
 +
 +
<img src="https://static.igem.org/mediawiki/2018/7/75/T--Tongji-Software--requirement-1.png" width="70%">
 +
<span class="fig">Fig. 7. Data comparison among Alpha Ant, Gil and KEGG.</span></br>
 +
 +
<span class="detail">As data shows above, we have more data than Gil and almost cover all KEGG reaction,compound data. Besides, we have 630275 gene data, same as KEGG while Gil only have 1950 E.coli K12 gene information.</span></br>
 +
 +
</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>
 +
 +
</br></br>
 +
<span class="question">Statement</span></br>
 +
 +
<span class="detail">We provide Alpha Ant as a public service. We do not collect any personally identifiable information (PII) about you when you visit our Web site. Alpha Ant is only for academic research and will be not for any commercial uses. The sources of data we obtained from other databases are as follows.</span></br>
 +
<span class="detail"><b>Copyright:</b></span></br>
 +
<span class="detail">KEGG:</span></br> 
 +
<span class="detail">Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima; KEGG: new perspectives on genomes, pathways, diseases and drugs, Nucleic Acids Research, Volume 45, Issue D1, 4 January 2017, Pages D353–D361</br>
 +
<a href="https://doi.org/10.1093/nar/gkw1092">https://doi.org/10.1093/nar/gkw1092</a></span></br>
 +
 +
<span class="detail">Metacyc:</span></br> 
 +
<span class="detail">Ron Caspi, Richard Billington, Carol A Fulcher, Ingrid M Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Peter E Midford, Quang Ong, Wai Kit Ong, Suzanne Paley, Pallavi Subhraveti, Peter D Karp; The MetaCyc database of metabolic pathways and enzymes, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D633–D639</br>
 +
<a href="https://doi.org/10.1093/nar/gkx935">https://doi.org/10.1093/nar/gkx935</a></span></br>
 +
 +
<span class="detail">BRENDA:</span></br>
 +
<span class="detail">Sandra Placzek, Ida Schomburg, Antje Chang, Lisa Jeske, Marcus Ulbrich, Jana Tillack, Dietmar Schomburg; BRENDA in 2017: new perspectives and new tools in BRENDA, Nucleic Acids Research, Volume 45, Issue D1, 4 January 2017, Pages D380–D388</br>
 +
<a href="https://doi.org/10.1093/nar/gkw952">https://doi.org/10.1093/nar/gkw952</a></br>
 +
BRENDA is available at <a href="www.brenda-enzymes.org">www.brenda-enzymes.org</a></span></br>
 +
 +
<span class="detail">eQuilibrator:</span></br> 
 +
<span class="detail">Flamholz, A., Noor, E., Bar-Even, A., & Milo, R. (2012). eQuilibrator—the biochemical thermodynamics calculator. Nucleic Acids Research, 40(Database issue), D770–D775.</br>
 +
<a href="http://doi.org/10.1093/nar/gkr874">http://doi.org/10.1093/nar/gkr874</a></span></br>
 +
 +
<span class="detail">ChEBI:</span></br> 
 +
<span class="detail">Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res. 2016 Jan;44(D1) D1214-9. PMID: 26467479; PMCID: PMC4702775.</br>
 +
<a href="http://doi:10.1093/nar/gkv1031">http://doi:10.1093/nar/gkv1031</a></span></br>
 +
 +
<span class="detail">Drugbank:</span></br> 
 +
<span class="detail">David S. Wishart, Craig Knox, An Chi Guo, Savita Shrivastava, Murtaza Hassanali, Paul Stothard, Zhan Chang, Jennifer Woolsey; DrugBank: a comprehensive resource for in silico drug discovery and exploration, Nucleic Acids Research, Volume 34, Issue suppl_1, 1 January 2006, Pages D668–D672</br>
 +
<a href="https://doi.org/10.1093/nar/gkj067">https://doi.org/10.1093/nar/gkj067</a></span></br>
 +
 +
<div id="contact">
 +
<h3>CONTACT</h3>
 +
<span>annecao@tongji.edu.cn</span><hr/>
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<h3>ADDRESS</h3>
 +
<span>1239# Siping Road</br>Tongji University,Shanghai China</span><hr/>
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<h3>GET IN TOUCH</h3>
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Latest revision as of 16:25, 17 October 2018

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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.

Fig. 1. Home page of Alpha Ant.
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 Demonstrate.

Fig. 2. Search page of Alpha Ant.
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.

Fig. 3. Result page of Alpha Ant.
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.

Fig. 4. SMILES comparison page in Alpha Ant.

Fig. 5. Organism recommendation page in Alpha Ant.

Fig. 6. Example of FBA results in Alpha Ant.
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?
Fig. 7. Data comparison among Alpha Ant, Gil and KEGG.
As data shows above, we have more data than Gil and almost cover all KEGG reaction,compound data. Besides, we have 630275 gene data, same as KEGG while Gil only have 1950 E.coli K12 gene information.

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).


Statement
We provide Alpha Ant as a public service. We do not collect any personally identifiable information (PII) about you when you visit our Web site. Alpha Ant is only for academic research and will be not for any commercial uses. The sources of data we obtained from other databases are as follows.
Copyright:
KEGG:
Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima; KEGG: new perspectives on genomes, pathways, diseases and drugs, Nucleic Acids Research, Volume 45, Issue D1, 4 January 2017, Pages D353–D361
https://doi.org/10.1093/nar/gkw1092
Metacyc:
Ron Caspi, Richard Billington, Carol A Fulcher, Ingrid M Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Peter E Midford, Quang Ong, Wai Kit Ong, Suzanne Paley, Pallavi Subhraveti, Peter D Karp; The MetaCyc database of metabolic pathways and enzymes, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D633–D639
https://doi.org/10.1093/nar/gkx935
BRENDA:
Sandra Placzek, Ida Schomburg, Antje Chang, Lisa Jeske, Marcus Ulbrich, Jana Tillack, Dietmar Schomburg; BRENDA in 2017: new perspectives and new tools in BRENDA, Nucleic Acids Research, Volume 45, Issue D1, 4 January 2017, Pages D380–D388
https://doi.org/10.1093/nar/gkw952
BRENDA is available at www.brenda-enzymes.org
eQuilibrator:
Flamholz, A., Noor, E., Bar-Even, A., & Milo, R. (2012). eQuilibrator—the biochemical thermodynamics calculator. Nucleic Acids Research, 40(Database issue), D770–D775.
http://doi.org/10.1093/nar/gkr874
ChEBI:
Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C. ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res. 2016 Jan;44(D1) D1214-9. PMID: 26467479; PMCID: PMC4702775.
http://doi:10.1093/nar/gkv1031
Drugbank:
David S. Wishart, Craig Knox, An Chi Guo, Savita Shrivastava, Murtaza Hassanali, Paul Stothard, Zhan Chang, Jennifer Woolsey; DrugBank: a comprehensive resource for in silico drug discovery and exploration, Nucleic Acids Research, Volume 34, Issue suppl_1, 1 January 2006, Pages D668–D672
https://doi.org/10.1093/nar/gkj067

CONTACT

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Tongji University,Shanghai China

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