Team:SUSTC-Shenzhen-A/RFC

From 2012.igem.org

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=Ways leading to a standardized bio-engineered-world=
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  <p>In 2003, the first attempt to make a synthetic biology a discipline that everyone can share about it was made. After the appearance of the first BioBrick(tm), the concept about standardization had been widely accepted. And it is a trend in synthetic biology now. </p>
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<head>
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  <p>Thanks to the standardization, biologists have developed many useful tools with the help of the standardized parts, the BioBricks. These BioBricks really contribute a lot to the research field. And they make easier for researchers to communicate with each other under the same technical standards. Due to the convenience of BioBricks, thousands of BioBricks have been created and introduced during these years. Thus the database containing these BioBricks is getting larger and larger.</p>
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  <p>But here comes the problem. Since every one can share their BioBricks, sometimes the information of the BioBricks are incomplet when they submit. So it becomes hard for users to search for a BioBrick that they want. Although there is an RFC, RFC 52 already, but we are not satisfied. Because of the generl description of it, the database of the BioBricks is still a mess. So we want to create a new RFC to replace RFC 52.</p>
+
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  <p>We want to establish an RFC to describe the minimum information for a qualified BioBrick. We listed the minimum information a BioBrick should have, and gave a short description for each of them. Especially, we want to qualify the classification of BioBricks. All the BioBricks should be organized, so that users can search for it easily.</p>
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=The current problem=
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==Informations are not complete in partsregistry.org==
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<p>When the partsregistry.org was established at first, it is worth to be called the authority of the BioBricks. But as time goes by, more and more BioBricks are added in, now partsregistry.org becomes less satisfy. Information of many BioBricks are incomplete, some even wrong. Because every one can submit one's BioBrick as long as one logs in, many information is informal since the website doesn't examine the information users submit. This would waste resource as well as mess up the database.</p>
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<p>Moreover, the layout of the website becomes more unclear as the database becomes larger and larger. For example, the Catlog. In this page, BioBricks are classified according to many different criteria. But the interface style in one section is far different from it in another section. Sometimes it is the description of a project, sometimes it becomes BioBrick list. A large list will be prsented in front of users with hundreds of BioBricks, but no search tool is available for users to search for the BioBrick that they really want. All of these would increase the difficulty for users to find the information that they want. For example, in the following figure, no list for Translational units can be found while others have long lists.</p>
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<h1 class="title"><strong>Introduction</strong></h1>
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<p>&nbsp;&nbsp;</p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;In 2003, the first attempt to make a synthetic biology a discipline that everyone can share about it was made. After the appearance of the first BioBrick(tm), the concept about standardization had been widely accepted. And it is a trend in synthetic biology now. </p>
 +
  <p>&nbsp;&nbsp;&nbsp;&nbsp;Thanks to the standardization, biologists have developed many useful tools with the help of the standardized parts, the BioBricks. These BioBricks really contribute a lot to the research field. And they make it easier for researchers to communicate with each other under the same technical standards. Due to the convenience of BioBricks, thousands of BioBricks have been created and introduced during these years. Thus the database containing these BioBricks is getting larger and larger.</p>
 +
  <p>&nbsp;&nbsp;&nbsp;&nbsp;But here comes the problem. Since every one can share their BioBricks, sometimes the information of the BioBricks are incomplet when they submit. So it becomes hard for users to search for a BioBrick that they want. Although there is an RFC, RFC 52 already, but we are not satisfied. Because the description of it is too general, the database of the BioBricks is still a mess. So we want to create a new RFC to replace RFC 52.</p>
 +
  <p>&nbsp;&nbsp;&nbsp;&nbsp;We want to establish an RFC to describe the minimum information for a qualified BioBrick. We listed the minimum information a BioBrick should have, and gave a short description for each of them. Especially, we want to qualify the classification of BioBricks. All the BioBricks should be organized, so that users can search for it easily.</p>
 +
<p>&nbsp;&nbsp;</p>
 +
<p>&nbsp;&nbsp;</p>
 +
<h1 class="title"><strong>The current problem</strong></h1>
 +
<p>&nbsp;&nbsp;</p>
 +
<p class="title1">&nbsp;&nbsp;Information is not complete in partsregistry.org</p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;When the <a href="http://partsregistry.org/Main_Page">partsregistry.org</a> was established at first, it is worth to be called the authority of the BioBricks. But as time goes by, more and more BioBricks are added in, now <a href="http://partsregistry.org/Main_Page">partsregistry.org</a> becomes less satisfy. Information of many BioBricks are incomplete, some even wrong. Because every one can submit one's BioBrick as long as one logs in, many information is informal since the website doesn't examine the information users submit. This would waste resource as well as mess up the database.</p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;Moreover, the layout of the website becomes more unclear as the database becomes larger and larger. For example, the Catalog. In this page, BioBricks are classified according to many different criteria. But the interface style in one section is far different from it in another section. Sometimes it is the description of a project, sometimes it becomes BioBrick list. A large list will be prsented in front of users with hundreds of BioBricks, but no search tool is available for users to search for the BioBrick that they really want. All of these would increase the difficulty for users to find the information that they want. For example, in the following figure, no list for Translational units can be found while others have long lists.</p>
 +
<p>&nbsp;&nbsp;</p>
 +
<p align="center">&nbsp;&nbsp;&nbsp;&nbsp;<img src="https://static.igem.org/mediawiki/2012/b/b5/Problem1.jpg"></p>
 +
<p>&nbsp;&nbsp;</p>
<p>This BioBrick is totally useless but it is still on the BioBrick list. This shows that the uploading of BioBricks should be standardized.</p>
<p>This BioBrick is totally useless but it is still on the BioBrick list. This shows that the uploading of BioBricks should be standardized.</p>
 +
<p>&nbsp;&nbsp;</p>
 +
<p align="center">&nbsp;&nbsp;&nbsp;&nbsp;<img src="https://static.igem.org/mediawiki/2012/e/e0/Problem2.jpg"></p>
 +
<p>&nbsp;&nbsp;</p>
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<p class="title1">&nbsp;&nbsp;Information is not useful in database</p>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;We got a database that contains all the information about all the BioBricks. In this database, every BioBrick has 40 properties, they are:</p>
 +
<p>&nbsp;&nbsp;</p>
 +
<p align="center"><img src="https://static.igem.org/mediawiki/2012/6/6d/Properties_list.png"></p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;With these long list, nobody has the patience to look through them all. Indeed many properties are rubbish. Look at the property No.34-No.37, they are completely useless because they are apparently not a part of information of a BioBrick. Another example is property No.14, specified_scar_u_list. This property is NULL, which means it contains no information, for nearly all the BioBricks. We draw a histogram to demonstrate the percentage of unqualified and qualified BioBricks.</p>
 +
<p>&nbsp;&nbsp;</p>
 +
<p align="center">&nbsp;&nbsp;<img src="https://static.igem.org/mediawiki/2012/2/22/Histogram_for_database.png"></p>
 +
<p>&nbsp;&nbsp;</p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;Explanation of the above histogram:</p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;x-axis:&nbsp;&nbsp;&nbsp; 1 - number o properties whose information is NULL for more 3000 BioBricks (our database contains 13442 BioBricks).</p>  <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2 - number of properties whose information for most BioBrick is a number '0'.</p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3 - number of properties whose information for most BioBrick is some random number.</p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;4 - number of properties with valid information.</p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;y-axis:&nbsp;&nbsp;&nbsp; number of corresponding properties</p>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;We can conclude from the above histogram that only one fourth of the properties are valid properties. So most information in the database is trash. Because of the mess in the database, it is essential to standardize the minimum information for a qualified BioBrick.</p>
 +
<p>&nbsp;&nbsp;</p>
 +
<p class="title"><strong>Our BBF RFC 89:</strong></p><h1 class="title"><strong>The minimum information for a qualified BioBrick</strong></h1>
 +
<h3>Motivation to write this BBF RFC</h3>
 +
<p>&nbsp;&nbsp;Since the information of many existing BioBricks is incomplete, thus the usage of the BioBricks will be affected. It is necessary to standardize the minimum information required for a qualified BioBrick. Furthermore this standardization will reduce the time to locate and find a BioBrick. So it is essential to create a default template for storing the information of BioBricks.</p>
 +
<br/>
 +
<p><big>&nbsp;&nbsp;To see the complete version of this BBF RFC, please click <a href="https://2012.igem.org/Team:SUSTC-Shenzhen-A/RFC_draft">here!</a></big></p>
 +
<br/>
 +
<p><big>&nbsp;&nbsp;To download this BBF RFC, please click <a href="http://dspace.mit.edu/handle/1721.1/73910">here!</a></big></p>
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[[File:problem2.jpg]]
 
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==Informations are not useful in database==
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<!-- end of header -->
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<div>
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  <p>We got a database that contains all the information about all the BioBricks. In this database, every BioBrick has 40 properties, they are:</p>
+
-
  <p>[[File:properties_list.png]]</p>
+
-
  <p>With these long list, no nobody has the patience to look through them all. Indeed many properties are rubbish. Look at the property No.34-No.37, they are completely useless because they are apparently not a part of information of a BioBrick. Another example is property No.14, specified_scar_u_list. This property is NULL, which means it contains no information, for nearly all the BioBricks. We draw a histogram to demonstrate the percentage of unqualified and qualified BioBricks.</p>
+
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  <p>[[File: histogram_for_database.png]]</p>
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-
  <p>Explanation of the above histogram:&nbsp;&nbsp;&nbsp; x-axis:&nbsp;&nbsp;&nbsp; 1 - number o properties whose information is NULL for more 3000 BioBricks (our database contains 13442 BioBricks).       
+
-
  </p>  <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2 - number of properties whose information for most BioBrick is a number '0'.</p>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3 - number of properties whose information for most BioBrick is some random number.</p>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;4 - number of properties with valid information.</p>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;y-axis: number of corresponding properties</p>
+
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<p>We can conclude from the above histogram that only one fourth of the properties are valid properties. So most information in the database is trash. Because of the mess in the database, it is essential to standardize the minimum information for a qualified BioBrick.</p>
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=Our brand new RFC#:The minimum information for a qualified BioBrick=
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[[file:footbar.jpg|center]]

Latest revision as of 14:50, 26 October 2012

Introduction

  

    In 2003, the first attempt to make a synthetic biology a discipline that everyone can share about it was made. After the appearance of the first BioBrick(tm), the concept about standardization had been widely accepted. And it is a trend in synthetic biology now.

    Thanks to the standardization, biologists have developed many useful tools with the help of the standardized parts, the BioBricks. These BioBricks really contribute a lot to the research field. And they make it easier for researchers to communicate with each other under the same technical standards. Due to the convenience of BioBricks, thousands of BioBricks have been created and introduced during these years. Thus the database containing these BioBricks is getting larger and larger.

    But here comes the problem. Since every one can share their BioBricks, sometimes the information of the BioBricks are incomplet when they submit. So it becomes hard for users to search for a BioBrick that they want. Although there is an RFC, RFC 52 already, but we are not satisfied. Because the description of it is too general, the database of the BioBricks is still a mess. So we want to create a new RFC to replace RFC 52.

    We want to establish an RFC to describe the minimum information for a qualified BioBrick. We listed the minimum information a BioBrick should have, and gave a short description for each of them. Especially, we want to qualify the classification of BioBricks. All the BioBricks should be organized, so that users can search for it easily.

  

  

The current problem

  

  Information is not complete in partsregistry.org

    When the partsregistry.org was established at first, it is worth to be called the authority of the BioBricks. But as time goes by, more and more BioBricks are added in, now partsregistry.org becomes less satisfy. Information of many BioBricks are incomplete, some even wrong. Because every one can submit one's BioBrick as long as one logs in, many information is informal since the website doesn't examine the information users submit. This would waste resource as well as mess up the database.

    Moreover, the layout of the website becomes more unclear as the database becomes larger and larger. For example, the Catalog. In this page, BioBricks are classified according to many different criteria. But the interface style in one section is far different from it in another section. Sometimes it is the description of a project, sometimes it becomes BioBrick list. A large list will be prsented in front of users with hundreds of BioBricks, but no search tool is available for users to search for the BioBrick that they really want. All of these would increase the difficulty for users to find the information that they want. For example, in the following figure, no list for Translational units can be found while others have long lists.

  

    

  

This BioBrick is totally useless but it is still on the BioBrick list. This shows that the uploading of BioBricks should be standardized.

  

    

  

  Information is not useful in database

    We got a database that contains all the information about all the BioBricks. In this database, every BioBrick has 40 properties, they are:

  

    With these long list, nobody has the patience to look through them all. Indeed many properties are rubbish. Look at the property No.34-No.37, they are completely useless because they are apparently not a part of information of a BioBrick. Another example is property No.14, specified_scar_u_list. This property is NULL, which means it contains no information, for nearly all the BioBricks. We draw a histogram to demonstrate the percentage of unqualified and qualified BioBricks.

  

  

  

    Explanation of the above histogram:

                               x-axis:    1 - number o properties whose information is NULL for more 3000 BioBricks (our database contains 13442 BioBricks).

                                             2 - number of properties whose information for most BioBrick is a number '0'.

                                             3 - number of properties whose information for most BioBrick is some random number.

                                             4 - number of properties with valid information.

                               y-axis:    number of corresponding properties

    We can conclude from the above histogram that only one fourth of the properties are valid properties. So most information in the database is trash. Because of the mess in the database, it is essential to standardize the minimum information for a qualified BioBrick.

  

Our BBF RFC 89:

The minimum information for a qualified BioBrick

Motivation to write this BBF RFC

  Since the information of many existing BioBricks is incomplete, thus the usage of the BioBricks will be affected. It is necessary to standardize the minimum information required for a qualified BioBrick. Furthermore this standardization will reduce the time to locate and find a BioBrick. So it is essential to create a default template for storing the information of BioBricks.


  To see the complete version of this BBF RFC, please click here!


  To download this BBF RFC, please click here!

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