Team:Shenzhen BGIC 0101/NewStandard

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<h1>New Standard</h1>  
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<h2>Assembly Strategy Standard</h2>
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<p>Synthesized fragments to Biodevice Assembly<br/>
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Different from the traditional bottom-up strategy, <a href="http://parts.igem.org/Assembly:Standard_assembly?title=Assembly:Standard_assembly">biobrick</a> & <a href="http://openwetware.org/wiki/Synthetic_Biology:BioBricks/3A_assembly">3A</a> standard assembly, to assemble biobricks into a high-level biodevice, Genovo would assist users to directly design brand new chromosome denovo in silico and design its segmentation adding with adaptors, so that we can synthesize DNA fragments, and integrate them into megachunks by using <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Modules">"2k to 10k to 30k to whole" method and Gibson, Goldengate assembly, homologous recombination</a>.</p><br/>
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<div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Software">Overview</a></div>
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<div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Modules">Modules</a></div>
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<div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Next_version">Next version</a></div>
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<div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Compatibility">Compatibility</a></div>
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<div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/NewStandard#">New Standard</a></div>
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<nav class="menu-main-navigation-container"><a  href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Home"  class="menu-item-20 menu-item menu-item-type-post_type menu-item-object-page">Home</a> <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Team"  class="menu-item-19 menu-item menu-item-type-post_type menu-item-object-page">Team</a> <a  href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Software"  class="menu-item-18 menu-item menu-item-type-post_type menu-item-object-page current-menu-item">Software</a> <a  href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Requirements" class="menu-item-17 menu-item menu-item-type-post_type menu-item-object-page">Requirements</a> <a  href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Criteria"  class="menu-item-15 menu-item menu-item-type-post_type menu-item-object-page">Criteria</a> </nav>
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<h2 sytle="color:#83f">Develop New Standard</h2>
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<h1>Chromosome Design Standard </h1>
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<p>After grap the information of pathway of interest, we can rewire genes' relation, replace genes with ortholog scoring higher, add human control upon genes' expression and experimentally synthesize this chromosome-like biodevice directly.</p><br/>
<p>After grap the information of pathway of interest, we can rewire genes' relation, replace genes with ortholog scoring higher, add human control upon genes' expression and experimentally synthesize this chromosome-like biodevice directly.</p><br/>
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<h1>Design Operation Standard </h1>
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<h2>Design Operation Standard </h2>
<p>Drag & drop biodevice Design<br/>
<p>Drag & drop biodevice Design<br/>
We can change the position, strand of genes in neochromsome, in a user-friendly way.</p><br/>
We can change the position, strand of genes in neochromsome, in a user-friendly way.</p><br/>
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<h1>Assembly Stategy Standard</h1>
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<h2>Data Transmission Standard</h2>
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<p>Synthesized fragments to Biodevice Assembly
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Different from the traditional bottom-up strategy, <a href="http://parts.igem.org/Assembly:Standard_assembly?title=Assembly:Standard_assembly">biobrick</a> & <a href="http://openwetware.org/wiki/Synthetic_Biology:BioBricks/3A_assembly">3A</a> standard assembly, to assemble biobricks into a high-level biodevice, we directly design brand new chromosome denovo in silico and design its segmentation with adaptors, so that we can synthesize DNA fragments, and integrate them into megachunks, and use a special method to transform megachunks to whole Chromosome.</p><br/>
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<h1>Data Transmission Standard</h1>
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<p>KGML is an XML presentation of KEGG pathway database, and rewrite relationships between genes use JavaScript (JS) language. In order to transfer XML be more readable for JS, we convert XML into JSON and transform data in more convenience way. We only reserve genes’ relationships and three kinds of subtype attribution, activation, inhibition and link. Through this data transmission standard, computer and users can directly and clearly understand the information. The diagram below is the data structure of our transmitted JSON format.</p>
<p>KGML is an XML presentation of KEGG pathway database, and rewrite relationships between genes use JavaScript (JS) language. In order to transfer XML be more readable for JS, we convert XML into JSON and transform data in more convenience way. We only reserve genes’ relationships and three kinds of subtype attribution, activation, inhibition and link. Through this data transmission standard, computer and users can directly and clearly understand the information. The diagram below is the data structure of our transmitted JSON format.</p>
<img src="https://static.igem.org/mediawiki/igem.org/7/77/Data_trans.png" />
<img src="https://static.igem.org/mediawiki/igem.org/7/77/Data_trans.png" />
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<h3>contact us</h3>
 
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<p>BGI-Shenzhen, Beishan Industrial Zone<br />
 
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Yantian District, Shenzhen, 518083, China</p>
 
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<p> <span>email:</span><br />
 
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<a href="mailto:gongjianhui@genomics.com">gongjianhui@genomics.com</a></p>
 
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Latest revision as of 20:42, 28 October 2013




New Standard

Assembly Strategy Standard

Synthesized fragments to Biodevice Assembly
Different from the traditional bottom-up strategy, biobrick & 3A standard assembly, to assemble biobricks into a high-level biodevice, Genovo would assist users to directly design brand new chromosome denovo in silico and design its segmentation adding with adaptors, so that we can synthesize DNA fragments, and integrate them into megachunks by using "2k to 10k to 30k to whole" method and Gibson, Goldengate assembly, homologous recombination.


Chromosome Design Standard

After grap the information of pathway of interest, we can rewire genes' relation, replace genes with ortholog scoring higher, add human control upon genes' expression and experimentally synthesize this chromosome-like biodevice directly.


Design Operation Standard

Drag & drop biodevice Design
We can change the position, strand of genes in neochromsome, in a user-friendly way.


Data Transmission Standard

KGML is an XML presentation of KEGG pathway database, and rewrite relationships between genes use JavaScript (JS) language. In order to transfer XML be more readable for JS, we convert XML into JSON and transform data in more convenience way. We only reserve genes’ relationships and three kinds of subtype attribution, activation, inhibition and link. Through this data transmission standard, computer and users can directly and clearly understand the information. The diagram below is the data structure of our transmitted JSON format.


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