Team:SUSTC-Shenzhen-B/SBOL

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<p>We believe our project qualify for the reward “Best SBOL Based Tool” since we fulfill all requirement of this reward</p>
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<p>Requirement 1: Adopt SBOL in your software to enable synthetic biology information sharing.</p>
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<p>Both our PC offline software and web support SBOL document of terminators. Users can input terminator xml file,
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then our software will analyze the sequence and output the results.
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</p>
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<p>Requirement 2: Document your use of SBOL by describing how it was used to perform information exchange.
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</p>
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<p>Our software can take SBOL format biobrick as input. From the SBOL xml file, we extract the nucleotide sequence. The nucleotide sequence is analyzed by our software to predict terminator efficiency. Then, we can write back to the SBOL file and add efficiency information in documentation of this biobrick part.</p>
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<p>Requirement 3: Describe any challenges you faced in conforming to the SBOL standard.
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</p>
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<p>During our developing process of our software, we found that one major issue of SBOL format is that it does not clearly identify the type of the biobrick parts. We would suggest further SBOL format to include the “type” of parts, whether it is a terminator, or promoter, or RBS. And the type should be clearly defined.</p>
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Latest revision as of 04:02, 27 October 2012

Title

SBOL in Software

Synthetic Biology Open Language (SBOL) is a data exchange standard for descriptions of genetic parts, devices, modules, and systems. SBOL is neutral with respect to programming languages and software encoding. By supporting SBOL for reading and writing synthetic biology designs, different software tools can directly communicate and store the same representation of these designs. This removes an impediment to sharing engineered systems and permits other researchers and commercial enterprises to start with an unambiguous representation of the design.


Both our PC offline software and web support SBOL document of terminators. Users can input terminator xml file, then our software will analyze the sequence and output the results.

Web SBOL Interface

PC software SBOL Interface




We believe our project qualify for the reward “Best SBOL Based Tool” since we fulfill all requirement of this reward

Requirement 1: Adopt SBOL in your software to enable synthetic biology information sharing.

Both our PC offline software and web support SBOL document of terminators. Users can input terminator xml file, then our software will analyze the sequence and output the results.

Requirement 2: Document your use of SBOL by describing how it was used to perform information exchange.

Our software can take SBOL format biobrick as input. From the SBOL xml file, we extract the nucleotide sequence. The nucleotide sequence is analyzed by our software to predict terminator efficiency. Then, we can write back to the SBOL file and add efficiency information in documentation of this biobrick part.

Requirement 3: Describe any challenges you faced in conforming to the SBOL standard.

During our developing process of our software, we found that one major issue of SBOL format is that it does not clearly identify the type of the biobrick parts. We would suggest further SBOL format to include the “type” of parts, whether it is a terminator, or promoter, or RBS. And the type should be clearly defined.