Difference between revisions of "User:Randy/Test8"
 
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===Welcome to the Registry of Standard Biological Parts.===
 
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'''The Registry is a [https://parts.igem.org/cgi/partsdb/Statistics.cgi continuously growing] collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems.  Founded in 2003 at MIT, the Registry is part of the Synthetic Biology community's efforts to make biology easier to engineer.  It provides a resource of available genetic parts to [https://igem.org iGEM] teams and academic labs. You can [https://igem.org register a new lab here].'''
 
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The Registry is based on the principle of "get some, give some".  Registry users benefit from using the parts and information available from the Registry in designing their engineered biological systems.  In exchange, the expectation is that Registry users will, in turn, contribute back information and data on existing parts and new parts that they make to grow and improve this community resource.
 
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|align='center' | '''[https://parts.igem.org/cgi/assembly/libraries.cgi DNA repositories]'''
 
|align='center' | '''[https://parts.igem.org/cgi/assembly/libraries.cgi DNA repositories]'''
 
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|valign='top' border="1" style="border:#c9c9c9 0px solid; margin: 1em 1em 1em 0; border-collapse: collapse;" |
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|valign='top' border="1" style="border:#c9c9c9 0px solid; margin: 1em 1em 0 0; border-collapse: collapse;" |
 
=== Registry tools===  
 
=== Registry tools===  
 
*'''[https://parts.igem.org/cgi/partsdb/search.cgi Search parts]''' '''[[Help:Search|(?)]]'''
 
*'''[https://parts.igem.org/cgi/partsdb/search.cgi Search parts]''' '''[[Help:Search|(?)]]'''
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| [[Image:NewG.jpg|100px]]
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|You'll notice some significant changes to the Registry recently.  In particular, the Registry [[Catalog|catalog of parts]] has been entirely redesigned to allow for easier browsing of the available parts and devices.  You can now browse parts and devices by type, by function, by chassis and by standard.  You'll also notice that the documentation and help pages for each class of parts have been greatly enhanced. 
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The Registry of Standard Biological Parts is *always* a work in progress. Please browse the new catalog and let us know what you think, or feel free to edit and improve the pages further.
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===Registry changes===
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<html>
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This year (2013) iGEM Headquarters is making some major changes to the Registry. Here are some of the changes you should expect:
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<style>.class li {margin-top: 1em} </style>
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<ul class='changes' style='line-height:1.2em'>
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<li>We are going to dramatically prune the collection of parts so that the excellent parts are
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not lost among the weeds. As a community collection, the Registry contains every part entered by anyone. This includes parts with no sequence, no description, and even parts with a description such as ''Delete me''. Many of the parts are old, poorly documented, and unused; these are the weeds. However, many parts have excellent documentation, proper sequences and matching DNA samples. Many of them are valuable and have been used by many teams; these are the roses.
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<p>We are going to "Discontinue" thousands of parts.</p></li>
  
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<li>iGEMers have sent us ''samples'' that contain ''parts''. In the past, we took a passive approach to quality control. We sent out a distribution
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and filled part requests without concern to the quality of the sample. In the case of the distribution, we sequenced each sample and
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tested the plasmid backbone by cutting and running on a gel as well as testing growth in several antibiotics. We published this quality information in the Registry but left it to the iGEMer to evaluate the QC information themselves.
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<p>This year's distribution will consist of parts that are sequence verified. We will eliminate samples that are incorrect and do more thorough curation of all the samples.</p></li>
  
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===Registry news===
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<li>For a couple years, we have been requiring samples to be sent to us in pSB1C3 but have sent old samples in whatever plasmid backbone we had. This year, we are following our own requirements and are transfering parts into pSB1C3.</li>
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This year (2013) iGEM Headquarters is making some major changes to the Registry. We would like to let you know what to expect.
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First, we are going to dramatically prune the collection of parts so that the excellent parts in the collection can be found and are
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<li>We are changing the way we think about the status of a part and a sample. The term ''Available'' was always misleading. Was the part released by the team (was its documentation and measurement complete?), was a sample of the the DNA available, was it correct? We used the fact that a team sent a part to indicate that it was an important part and should be included in tables and widely considered.</li>
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not lost in the weeds that are also in the collection. As a community collection, the Registry contains every part entered by anyone.
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This includes parts with no sequence, no description, and even parts with a description such as ''delete me''. Many of the parts are
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old, poorly documented, and unused.
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We are going to discontinue thousands of these parts.
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<li>We are introducing the concept of ''Releasing a Part''. This means that the author of the part says it is ready and important. Separately, we are introducing the concept of the status of a sample. Is it in a distribution, can you order it, or not. Perhaps it is of questionable quality or is unsequenced. Along with this, we are introducing a new sample analysis page with better information about the sample.</li>
  
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Second, iGEMers have sent us ''samples'' that contain ''parts''. In the past, we took a passive approach to quality control. We sent out a distribution
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<li>We are upgrading the web site. The new site will be more modern and easier to use. We will improve the search capability and introduce a new category browser to make it easier to find the part you want.</li>
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and sent parts on request without concern to the quality of the sample. In the case of the distribution, we sequenced each sample and
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tested the plasmid backbone by cutting and running on a gel as well as testing growth in several antibiotics. However, we sent the sample
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without regard for this information, trusting the iGEMer to evaluate the QC information themselves.
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This year's distribution will consist of parts that are sequence verified. In addition, we are transferring parts as needed to pSB1C3.
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<li>Teams are now using a great variety of assembly systems and software tools. We are changing the Registry to support external tools more easily and to accept different assembly systems more easily.</li>
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</ul>
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<BR>
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</html>
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The first of these changes will be ready when the DNA distributions ship. Many other changes will take place throughout the year. We hope you like the new Registry.
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-- Randy
  
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Third, we are changing the way we think about the status of a part (and sample). The term ''Available'' was always misleading. Was the part
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released by the team (was it complete), was the DNA available, was it correct? We used the fact that a team sent a part to indicate that it was an important part and should be included in tables and widely considered
+
  
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We are introducing the concept of ''Releasing a Part''. This means that the author of the part says it is ready and important. Separately, we are introducing the concept of the status of a sample. Is it in a distribution, can you order it, or not. Perhaps it is of questionable quality or is unsequenced.
 
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Along with this, we are introducing a new Sample page with better information about the sample.
 
  
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Fourth, we are upgrading the web site. The new site will be more modern and easier to use. We will improve the search capability and introduce a new category browser to make it easier to find the part you want.  
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'''The Registry is a [https://parts.igem.org/cgi/partsdb/Statistics.cgi continuously growing] collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems. Founded in 2003 at MIT, the Registry is part of the Synthetic Biology community's efforts to make biology easier to engineer.  It provides a resource of available genetic parts to [https://igem.org iGEM] teams and academic labs. You can [https://igem.org register a new lab here].'''
  
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These and many other changes are taking place now and will continue through the year. We hope you like the new Registry.
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The Registry is based on the principle of "get some, give some".  Registry users benefit from using the parts and information available from the Registry in designing their engineered biological systems. In exchange, the expectation is that Registry users will, in turn, contribute back information and data on existing parts and new parts that they make to grow and improve this community resource.
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-- Randy
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===Related resources & links===
 
===Related resources & links===

Latest revision as of 20:55, 12 April 2013

Montage_70.png DNArepositories70.png
Catalog of parts & devices Help Users & groups DNA repositories

 Registry tools

Registry changes

This year (2013) iGEM Headquarters is making some major changes to the Registry. Here are some of the changes you should expect:

  • We are going to dramatically prune the collection of parts so that the excellent parts are not lost among the weeds. As a community collection, the Registry contains every part entered by anyone. This includes parts with no sequence, no description, and even parts with a description such as ''Delete me''. Many of the parts are old, poorly documented, and unused; these are the weeds. However, many parts have excellent documentation, proper sequences and matching DNA samples. Many of them are valuable and have been used by many teams; these are the roses.

    We are going to "Discontinue" thousands of parts.

  • iGEMers have sent us ''samples'' that contain ''parts''. In the past, we took a passive approach to quality control. We sent out a distribution and filled part requests without concern to the quality of the sample. In the case of the distribution, we sequenced each sample and tested the plasmid backbone by cutting and running on a gel as well as testing growth in several antibiotics. We published this quality information in the Registry but left it to the iGEMer to evaluate the QC information themselves.

    This year's distribution will consist of parts that are sequence verified. We will eliminate samples that are incorrect and do more thorough curation of all the samples.

  • For a couple years, we have been requiring samples to be sent to us in pSB1C3 but have sent old samples in whatever plasmid backbone we had. This year, we are following our own requirements and are transfering parts into pSB1C3.
  • We are changing the way we think about the status of a part and a sample. The term ''Available'' was always misleading. Was the part released by the team (was its documentation and measurement complete?), was a sample of the the DNA available, was it correct? We used the fact that a team sent a part to indicate that it was an important part and should be included in tables and widely considered.
  • We are introducing the concept of ''Releasing a Part''. This means that the author of the part says it is ready and important. Separately, we are introducing the concept of the status of a sample. Is it in a distribution, can you order it, or not. Perhaps it is of questionable quality or is unsequenced. Along with this, we are introducing a new sample analysis page with better information about the sample.
  • We are upgrading the web site. The new site will be more modern and easier to use. We will improve the search capability and introduce a new category browser to make it easier to find the part you want.
  • Teams are now using a great variety of assembly systems and software tools. We are changing the Registry to support external tools more easily and to accept different assembly systems more easily.

The first of these changes will be ready when the DNA distributions ship. Many other changes will take place throughout the year. We hope you like the new Registry. -- Randy


The Registry is a continuously growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems. Founded in 2003 at MIT, the Registry is part of the Synthetic Biology community's efforts to make biology easier to engineer. It provides a resource of available genetic parts to iGEM teams and academic labs. You can register a new lab here.

The Registry is based on the principle of "get some, give some". Registry users benefit from using the parts and information available from the Registry in designing their engineered biological systems. In exchange, the expectation is that Registry users will, in turn, contribute back information and data on existing parts and new parts that they make to grow and improve this community resource.

Related resources & links

  • iGEM
  • [http://biobricks.org The BioBricks Foundation]
  • [http://openwetware.org OpenWetWare]
  • [http://www.neb.com/nebecomm/products/productE0546.asp BioBrick Assembly Kit] and [http://ginkgobioworks.com/support/ online step-by-step assembly manual].

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