Team:SJTU-Software

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Revision as of 07:43, 14 August 2014

An EASY Biobrick Blueprint’s pacKage

Digging into the current biobrick database maintained by the iGEM foundation, we have found the database is organized in a confusing manner, which made it difficult for all the teams to interpret and find the high-rated biobricks. In addition, different types of biobricks which were presented in the previously-designed biosystems varied from each other so greatly that even the most experienced synthetic biologists might find it troublesome to interpret the biosystem the teams had created.
Given the above-mentioned reasons, we have worked on an EASY Biobrick Blueprint’s pacKage with an entrenched relationship with the current biobrick database to solve the problems, the functions of which are listed as follows:

WHAT DO YOU WANT? (An EASY Search Engine)

The searching engine is based on a database covering more than 20000 biobricks, the information of which were collected from Registry of Biological Parts. With an input of the keywords you are interested in, the biobricks related to this keyword will be listed, sorted by a score given by our assessment model. After picking out the user-interested types and status, users will attain more precise results only satisfying their requirements. The results can also be sorted by the score of popularity and user reviews.
Besides, users can search for the biobricks containing similar sequences on the basis of the given sequence. The output will be sorted by the score calculated by our BLAST algorithm.

HOW IS YOUR BIOBRICK? (An EASY Uploader)

Here, users could not only upload their self-created biobricks to our database, but also an evaluation will be conducted to examine the quality of the uploading biobricks. The sequence of the self-created biobrick will be aligned with the sequences of the existing biobricks to find a similar biobrick, if exist, and a reference score for the quality of the self-created biobrick will be given according to the score given to the similar biobrick judging by our assessment model.

WHAT IS YOUR BIOSYSTEM? (An EASY tool for presentation)

Users could draw their biosystem and look into the detailed information about the biobricks in the biosystem. With standardized biobrick icons according to the iGEM Registry, a standardized picture of a biosystem could be plotted using our tool. The tool can automatically check the basic reliability of the system based on the property of the biobricks. The result can be exported to a picture file or an SBOL file, which could be used for the presentation in the publications or later design.

See the Video

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 			<div class="jumbotron">
 				<h2>
-					Motivation
+					An EASY Biobrick Blueprint’s pacKage
 				</h2>
 				<p>
-					In our research of the previous projects in previous competitions, every team had their own way to present their systems which made the later researchers difficult to understand the different ways of presentation. So we put forward a user-friendly tool to output standardized and uniform biobricks and their relationships in your designed system.
+					Digging into the current biobrick database maintained by the iGEM foundation, we have found the database is organized in a confusing manner, which made it difficult for all the teams to interpret and find the high-rated biobricks. In addition, different types of biobricks which were presented in the previously-designed biosystems varied from each other so greatly that even the most experienced synthetic biologists might find it troublesome to interpret the biosystem the teams had created.</br>
+Given the above-mentioned reasons, we have worked on an EASY Biobrick Blueprint’s pacKage with an entrenched relationship with the current biobrick database to solve the problems, the functions of which are listed as follows:
 				</p>
 <h2>
-					Function
+					WHAT DO YOU WANT? (An EASY Search Engine)
 				</h2>
 				<p>
-					<font color="blue">Search</font>:You can search in the biobricks database which was established by us to find the ideal model in your mind.</br>
+					The searching engine is based on a database covering more than 20000 biobricks, the information of which were collected from Registry of Biological Parts. With an input of the keywords you are interested in, the biobricks related to this keyword will be listed, sorted by a score given by our assessment model. After picking out the user-interested types and status, users will attain more precise results only satisfying their requirements. The results can also be sorted by the score of popularity and user reviews. </br>
-                                        <font color="blue">Upload</font>:You can upload your  new discovery into the database to build a vaster biobrick world.</br>
+Besides, users can search for the biobricks containing similar sequences on the basis of the given sequence. The output will be sorted by the score calculated by our BLAST algorithm.
-                                        <font color="blue">Detail</font>:You can see all the details of a biobrick and the quantity evaluation according to our evaluation algorithm.</br>
-                                        <font color="blue">Organization</font>:You can design and organize a sketch map of your wetlab by the basic elements of the biobrick.</br>
+				</p>
+<h2>
+					HOW IS YOUR BIOBRICK? (An EASY Uploader)
+				</h2>
+				<p>
+					Here, users could not only upload their self-created biobricks to our database, but also an evaluation will be conducted to examine the quality of the uploading biobricks. The sequence of the self-created biobrick will be aligned with the sequences of the existing biobricks to find a similar biobrick, if exist, and a reference score for the quality of the self-created biobrick will be given according to the score given to the similar biobrick judging by our assessment model.
+				</p>
+<h2>
+					WHAT IS YOUR BIOSYSTEM? (An EASY tool for presentation)
+				</h2>
+				<p>
+					Users could draw their biosystem and look into the detailed information about the biobricks in the biosystem. With standardized biobrick icons according to the iGEM Registry, a standardized picture of a biosystem could be plotted using our tool. The tool can automatically check the basic reliability of the system based on the property of the biobricks. The result can be exported to a picture file or an SBOL file, which could be used for the presentation in the publications or later design.
 				</p>
 <p>