Difference between revisions of "Add a Part to the Registry"

(Undo revision 229662 by Unsw2012 (talk))
m
 
(48 intermediate revisions by 2 users not shown)
Line 1: Line 1:
−
__notoc__
+
{{HelpPage/MainLinks}}
−
<small>Just starting? Need [[Help:Contents|help]]?  Check out our documentation on [[Help:How to make a BioBrick| How to make a Biobrick]]! <br>
+
__NOTOC__
−
Or maybe you're looking for how to [[Help:Standardization|standardize a non-Biobrick sequence]] before you add it?</small>
+
Members of iGEM teams and labs can add two kinds of parts to the Registry: '''Basic Parts''' and '''Composite Parts'''.
  
−
Members of Registry groups may add three kinds of parts to the registry:
 
−
Basic Parts, Composite Parts, and Construction Intermediates.
 
−
<br>
 
−
<hr>
 
−
==='''Basic Parts'''  [https://parts.igem.org/cgi/partsdb/add_part_b.cgi Add a Basic Part Now...]===
 
  
−
Basic Parts are discrete functional units of DNA.  They cannot be subdivided into smaller component parts.  DNA for a basic part may be obtained by ''de novo'' synthesis, by total synthesis based on a sequence from GenBank, by primer extension and PCR, or via other techniques.  Like all parts, a Basic Part is stored in a plasmid, flanked by restriction-enzyme cloning regions ("BioBrick ends").  These cloning region are ''not'' included in the sequence of the part as defined by the Registry. They can be provided by the Registry software.  Here is an [[Part:BBa_B0010:Design|example]] of a Basic Part.  New users:  check out these[[Help:An Introduction to BioBricks| important notes regarding BioBricks&trade; and basic part standardization.]]<br>
+
'''The most important feature of a standard biological part should be that a user of the part does not have to talk to the part's designer. This is achieved by completely documenting the part.'''
  
−
==='''Composite Parts''' [https://parts.igem.org/cgi/partsdb/add_part_c.cgi Add a Composite Part Now...]===
 
  
−
Composite Parts are functional units made from an ordered series of basic parts or other composite parts. ''Explicit base pairs of DNA cannot be entered in as sequence for these parts'' (parts which do require you to manually enter sequence are Basic Parts). The Registry's software provides information and sequence for all the basic parts that you list as components of your composite part. While the Registry provides the sequence from the component parts specified, the function and design issues of the composite part should be documented in detail.  Here is an [[Part:BBa_B0015:Design|example]] of a Composite Part.
+
Parts '''must''' have a DNA sequence. Registry users should [[Help:Document_Parts|document]], model, characterize, and measure their parts, and provide that information on their [[Help:Nav/Part_Main_Page|part pages]].  
  
−
==='''Construction Intermediates''' [https://parts.igem.org/cgi/partsdb/add_part_ci.cgi Add a Construction Intermediate Now...]===
+
A part can be identified by its DNA sequence, and may be compatible with several [[Help:Assembly_Compatibility|Assembly Standards]]. A <strong>sample</strong> of a part may be stored in a plasmid backbone that dictates assembly (ex. [[Part:pSB1C3|pSB1C3]]), and flanked by the [[Help:Prefix-Suffix|prefix and suffix]]. The prefix and suffix are ''never'' included in the sequence of the part when documented on the Registry, as they are a product of the plasmid backbone, and not the part itself. '''Sample submission of parts is no longer a requirement for the iGEM competition.'''
  
−
Construction Intermediates have no specific function and are just
+
 
 +
{{AssemblyStandards/Accepted}}
 +
<br />
 +
 
 +
 
 +
 
 +
<hr/>
 +
 
 +
 +
<html>
 +
<style>
 +
 
 +
.button {    margin: auto;
 +
    text-align: center;
 +
    font-size: 15px;
 +
 
 +
margin:30px 5px;
 +
}
 +
 
 +
.button.yellow a {
 +
    padding: 15px 20px;
 +
    text-decoration: none;
 +
    background-color: #ffd755;
 +
    color: #333333;
 +
}
 +
 
 +
.button.yellow a:hover { background-color: #333333;  color: #ffd755; }
 +
</style>
 +
 
 +
<div style="width:45%; margin:auto; float:left; padding:15px;">
 +
 
 +
<h3>Basic Parts</h3>
 +
<div class="button yellow">
 +
<a href="https://parts.igem.org/cgi/partsdb/add_part_b.cgi">Add a Basic Part </a>
 +
</div>
 +
 
 +
<p><a href="https://parts.igem.org/Help:Parts"> Basic Parts </a>  are discrete functional units of DNA: promoters, ribosome binding sites, protein coding regions, etc.  They cannot be subdivided into smaller component parts. DNA for a basic part may be obtained by ''de novo'' synthesis, by primer extension and PCR, or via other techniques. <a href="https://parts.igem.org/wiki/index.php/Part:BBa_K863006">BBa_K863006</a> is a good example of a well documented Basic Part. Read <a href="https://parts.igem.org/Help:Adding_Parts">our help page on adding a basic part.</a></p>
 +
</div>
 +
 
 +
<div style="width:45%; margin:auto; float:left; padding:15px;">
 +
 
 +
<h3> Composite Parts</h3>
 +
<div class="button yellow">
 +
<a href="https://parts.igem.org/cgi/partsdb/add_part_c.cgi"> Add a Composite Part  </a>
 +
</div>
 +
<p><a href="https://parts.igem.org/Help:Parts">Composite Parts</a> are functional units made from an ordered series of basic parts or other composite parts. <strong>Explicit base pairs of DNA cannot be entered in as sequence for these parts.</strong> The Registry's software provides information and sequence for all the basic parts that you list as components of your composite part. While the Registry provides the sequence from the component parts specified, the function and design issues of the composite part should be documented in detail. <a href="https://parts.igem.org/wiki/index.php/Part:BBa_K1150020">BBa_K1150020</a> is a good example of a well documented Composite Part. Read <a href="https://parts.igem.org/Help:Adding_Parts/Composite"> our help page on adding a composite part</a>.</p>
 +
 
 +
</div>
 +
 
 +
<!--
 +
<div style="width:30%; margin:auto; float:left; padding:15px;">
 +
<h3>Construction Intermediates </h3>
 +
 
 +
<div class="button yellow">
 +
<a href="https://parts.igem.org/cgi/partsdb/add_part_ci.cgi">Add a Construction Intermediate </a>
 +
</div>
 +
 
 +
<p> Construction Intermediates have no specific function and are just
 
the result of assembling two parts together. They require no further documentation.  Often they are unwanted byproducts of construction
 
the result of assembling two parts together. They require no further documentation.  Often they are unwanted byproducts of construction
 
They all have the type 'Intermediate' and part names of the form 'BBa_Snnnnn'. These part names are automatically assigned by the Registry software. Once you enter your intermediate part in the Registry, you will be able to use BioBrick Blast to check your assembly's sequence  
 
They all have the type 'Intermediate' and part names of the form 'BBa_Snnnnn'. These part names are automatically assigned by the Registry software. Once you enter your intermediate part in the Registry, you will be able to use BioBrick Blast to check your assembly's sequence  
 
and your part will show up in the subpart and superpart search functions. If you send us the DNA, we will be able to share your
 
and your part will show up in the subpart and superpart search functions. If you send us the DNA, we will be able to share your
−
work with others and include it in assemblies done by the Registry.  There are no examples of these parts available yet.
+
work with others and include it in assemblies done by the Registry.  </p>
 +
</div>
 +
-->
 +
 
 +
<div style="clear:both"></div>
 +
</html>
 +
 
  
−
==='''Deleting A Part'''===
 
−
You can ''try'' to delete a part by going to a part's "Hard Information" and setting the <b>DNA status</b> to "deleted".
 
 
<hr>
 
<hr>
  
−
<font color="purple">''The most important feature of a standard biological part should be that a user of the part does not have to talk to you, the designer of the part.  This is achieved by completely documenting the part.''</font>
+
 
 +
==='''Useful Help Pages'''===
 +
{{HelpPage/AddingParts}}
 +
 
 +
 
 +
==FAQ==
 +
{{FAQ/Adding_Parts}}

Latest revision as of 13:37, 16 July 2020

Members of iGEM teams and labs can add two kinds of parts to the Registry: Basic Parts and Composite Parts.


The most important feature of a standard biological part should be that a user of the part does not have to talk to the part's designer. This is achieved by completely documenting the part.


Parts must have a DNA sequence. Registry users should document, model, characterize, and measure their parts, and provide that information on their part pages.

A part can be identified by its DNA sequence, and may be compatible with several Assembly Standards. A sample of a part may be stored in a plasmid backbone that dictates assembly (ex. pSB1C3), and flanked by the prefix and suffix. The prefix and suffix are never included in the sequence of the part when documented on the Registry, as they are a product of the plasmid backbone, and not the part itself. Sample submission of parts is no longer a requirement for the iGEM competition.


Users can add parts to the Registry that adhere to other assembly standards, however BioBrick RFC[10] and Type IIS are the Registry's current de facto standards; all parts on the Registry that will be considered for the iGEM competition (medals, awards, etc.) must be assembly compatible for BioBrick or Type IIS.



Basic Parts

Add a Basic Part

Basic Parts are discrete functional units of DNA: promoters, ribosome binding sites, protein coding regions, etc. They cannot be subdivided into smaller component parts. DNA for a basic part may be obtained by ''de novo'' synthesis, by primer extension and PCR, or via other techniques. BBa_K863006 is a good example of a well documented Basic Part. Read our help page on adding a basic part.

Composite Parts

Add a Composite Part

Composite Parts are functional units made from an ordered series of basic parts or other composite parts. Explicit base pairs of DNA cannot be entered in as sequence for these parts. The Registry's software provides information and sequence for all the basic parts that you list as components of your composite part. While the Registry provides the sequence from the component parts specified, the function and design issues of the composite part should be documented in detail. BBa_K1150020 is a good example of a well documented Composite Part. Read our help page on adding a composite part.



Useful Help Pages

Add a Part to the Registry: Related Registry Help Pages
Ready to add your part? Go to the Add a Part page.
Have questions on adding a part to the Registry? Send an email to hq (at) igem . org.


FAQ

What's the difference between a basic and composite part?

  • Basic Parts are discrete functional units of DNA. They cannot be subdivided into smaller component parts.
  • Composite Parts are functional units made from an ordered series of basic parts or other composite parts.

In order to create a composite part, each basic part that composes it must already be added and documented to the Registry.


How do I delete a part?

You can delete a part by going to a part's "Hard Information" and setting the DNA status to "deleted".


I synthesized my entire device. Can I add it as a basic part and give it the correct part type?

No, this should be added as a composite part. You should make sure that the basic parts that compose these parts are on the Registry (already exist or you'll be adding them as new basic parts if necessary). You can can go to part tools > edit sequence and features and generate your composite part without BioBrick scars (Blunt Assembly). You can create a small basic part(s) with a part type of "Scar," and enter those in between the basic parts that constitute your composite part.


I want to add a part but do not know the sequence

All users should know their part's sequence before working with it. However, you can still add and document your part and add/edit the sequence later by going to part tools >> edit sequence and features. If you are submitting a sample of your part to the Registry, your part's sequence must be documented before submission per the Registry's submission requirements.


How do I document an improvement on an existing part on the Registry?

There are many different ways to improve an existing part, from adding measurement data to codon-optimization. Please see our help page on contributions. Note that the following page is on how to document different types of contributions or improvements. Make sure to read through the medal criteria for a given iGEM year to understand what the judges are looking for.


We have a part that we'd like to add, but it is not BioBrick RFC10 compatible or iGEM Type IIS compatible

Yes, please add and document it on the Registry. However, this part will not meet the Registry's sample submission requirements.


Should I include the BioBrick prefix and suffix or iGEM Type IIS prefix and suffix in my part's sequence?

No, your part's sequence should not include the prefix and suffix. While your parts should be assembly compatible, the prefix and suffix are an element of the plasmid backbone, not the part.