Team:SJTU-Software/Overview

From 2014.igem.org

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<p class="text"  style="margin:5% 60px auto"><font face="Microsoft YaHei" size="4px"  color="#242424">An EASY Biobrick Blueprint’s <br>pacKage
<p class="text"  style="margin:5% 60px auto"><font face="Microsoft YaHei" size="4px"  color="#242424">An EASY Biobrick Blueprint’s <br>pacKage
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                             <p class="text"  style="margin:3% 60px auto"><font face="Helvetica" size="3px"  color="#242424">Digging into the current biobrick database maintained by the iGEM foundation, we have found the current biobrick database is difficult for users to interpret and find biobricks of good quality. In addition, different types of biobricks which were presented in the previous biosystems varied from each other so greatly that even the most experienced synthetic biologists might find it difficult to interpret the biosystem the teams had created.<br>
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                             <p class="text"  style="margin:3% 60px auto"><font face="Helvetica" size="3px"  color="#242424">We have constructed an Easy Biobrick Blueprint’s pacKage (EASY BBK) to assist users to search biobricks of good quality, compare the quality of biobricks, present bio-systems with standardized icons and upload biobricks to Registry or Easy BBK database.
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Given the above reasons, we have constructed an Easy Biobrick Blueprint’s pacKage (EASY BBK) to solve the problems. Its functions are listed as follows.  
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                           <div  class="container2" style="margin:-4% 0 0 0;height:450px;width:75%;float:left; display:inline" >
                           <div  class="container2" style="margin:-4% 0 0 0;height:450px;width:75%;float:left; display:inline" >
                           <p class="text"  style="margin:5% 60px auto"><font face="Helvetica" size="5px"  color="#242424">Search</font></p>
                           <p class="text"  style="margin:5% 60px auto"><font face="Helvetica" size="5px"  color="#242424">Search</font></p>
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                             <p class="text"  style="margin:3% 60px auto"><font face="Helvetica" size="3px"  color="#242424">This function is provide to users to search and evaluate the candidate biobricks based on keywords or part names. It can help users to decide if an existing biobrick meets their requirements before they start their experiments.<br>
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                             <p class="text"  style="margin:3% 60px auto"><font face="Helvetica" size="3px"  color="#242424">This function enables users to search by keywords or by sequence against our database. Advanced search mode is also provided to refine or sort the search results. In default mode, search results are sorted by a score given by our assessment model.
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The searching engine is based on a database converted from the iGEM Registry (Up to 2014 August). More details on database: <a  href="https://2014.igem.org/Team:SJTU-Software/Database" target="blank">https://2014.igem.org/Team:SJTU-Software/Database</a>.
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The searching engine is based on a database converted from the iGEM biobrick database (Date, or version number). There are 27,093 biobricks in the database If the input are one or more keywords, the biobricks related to the keywords will be listed, sorted and displayed to the users. Advanced search mode is also provided to refine or sort the search results based.
 
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Besides, users can search the biobrick database based on sequence similarity. If users input a DNA sequence,  the hit sequences in the database by NCBI Blastn will be returned, sorted by their E-values and displayed.
 
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                           <div  class="container2" style="margin:-4% 0 0 0;height:200px;width:75%;float:left; display:inline" >
                           <div  class="container2" style="margin:-4% 0 0 0;height:200px;width:75%;float:left; display:inline" >
                           <p class="text"  style="margin:5% 60px auto"><font face="Helvetica" size="5px"  color="#242424">Compare</font></p>
                           <p class="text"  style="margin:5% 60px auto"><font face="Helvetica" size="5px"  color="#242424">Compare</font></p>
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                             <p class="text"  style="margin:3% 60px auto"><font face="Helvetica" size="3px"  color="#242424">Multiple biobricks can be selected and compared. You can search and get multiple (up to three) biobricks, and compare them side by side. </font></p>
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                             <p class="text"  style="margin:3% 60px auto"><font face="Helvetica" size="3px"  color="#242424">Multiple biobricks can be added from search engine and then compared. You can search and get multiple (up to three) biobricks, and compare them side by side. </font></p>
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                           <div  class="container2" style="margin:-4% 0 0 0;height:250px;width:75%;float:left; display:inline" >
                           <p class="text"  style="margin:5% 60px auto"><font face="Helvetica" size="5px"  color="#242424">Present</font></p>
                           <p class="text"  style="margin:5% 60px auto"><font face="Helvetica" size="5px"  color="#242424">Present</font></p>
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                             <p class="text"  style="margin:3% 60px auto"><font face="Helvetica" size="3px"  color="#242424">Users could draw their biobrick system diagram using EASY BBK. With standardized biobrick icons according to the iGEM Registry, a standardized picture of a biosystem could be plotted using our tool. The result can be exported to a picture file in jpeg, bmp and png format, which could be used for the presentation in the publication, presentation or later design.</font></p>
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                             <p class="text"  style="margin:3% 60px auto"><font face="Helvetica" size="3px"  color="#242424">In this function, a standardized picture of a biosystem could be plotted with standardized biobrick icons according to the iGEM Registry. The result can be exported, which could be used for the presentation in the publication, presentation or later design. Additionally, with presented biobricks connected with database, the upload form could be directly filled out in "upload".</font></p>
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                           <p class="text"  style="margin:5% 60px auto"><font face="Helvetica" size="5px"  color="#242424">Upload</font></p>
                           <p class="text"  style="margin:5% 60px auto"><font face="Helvetica" size="5px"  color="#242424">Upload</font></p>
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                             <p class="text"  style="margin:3% 60px auto"><font face="Helvetica" size="3px"  color="#242424">Here, users could not only upload their self-created biobricks to our database, but also submit their form filled out in our software to the Registry to upload their self-created biobricks.</font></p>
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                             <p class="text"  style="margin:3% 60px auto"><font face="Helvetica" size="3px"  color="#242424">Here, users could not only upload their biobricks to our database, but also submit their form filled out in our software to the Registry to upload their self-created biobricks..</font></p>
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Revision as of 01:01, 17 October 2014




EASY BBK:

An EASY Biobrick Blueprint’s
pacKage

We have constructed an Easy Biobrick Blueprint’s pacKage (EASY BBK) to assist users to search biobricks of good quality, compare the quality of biobricks, present bio-systems with standardized icons and upload biobricks to Registry or Easy BBK database.



Search

This function enables users to search by keywords or by sequence against our database. Advanced search mode is also provided to refine or sort the search results. In default mode, search results are sorted by a score given by our assessment model.
The searching engine is based on a database converted from the iGEM Registry (Up to 2014 August). More details on database: https://2014.igem.org/Team:SJTU-Software/Database.



Compare

Multiple biobricks can be added from search engine and then compared. You can search and get multiple (up to three) biobricks, and compare them side by side.



Present

In this function, a standardized picture of a biosystem could be plotted with standardized biobrick icons according to the iGEM Registry. The result can be exported, which could be used for the presentation in the publication, presentation or later design. Additionally, with presented biobricks connected with database, the upload form could be directly filled out in "upload".



Upload

Here, users could not only upload their biobricks to our database, but also submit their form filled out in our software to the Registry to upload their self-created biobricks..



iGemdry2014@163.com

SJTU-Software,Shanghai,China

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