Talk:CH391L/S13/BioBricksAndRegistry

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Current revision (14:32, 4 February 2013) (view source)
(Knight's latest biobrick standard)
 
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'''[[User:Gabriel Wu|Gabriel Wu]] 23:14, 27 January 2013 (EST)'''There's no way there's only 700 parts in the registry.  If you check the history on that page you've referenced the last time it was updated was in 2006.
'''[[User:Gabriel Wu|Gabriel Wu]] 23:14, 27 January 2013 (EST)'''There's no way there's only 700 parts in the registry.  If you check the history on that page you've referenced the last time it was updated was in 2006.
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**'''[[User:Dwight Tyler Fields|Dwight Tyler Fields]] 14:16, 4 February 2013 (EST)''': Unfortunately I haven't been able to find a better reference for the total number of parts in the registry. Most papers today still reference that page, and the only variation I've seen is the Wikipedia article for the registry, which says "over 3400 parts", however there is no reference for that number. To be honest, in light of the outdated nature of the registry in general, I doubt an accurate and current figure is even known or kept track of, especially since it's difficult to determine how many parts actually work.
'''[[User:Gabriel Wu|Gabriel Wu]]''': Please post the video you played in class on this website. I need a place to reference 'klivers.'
'''[[User:Gabriel Wu|Gabriel Wu]]''': Please post the video you played in class on this website. I need a place to reference 'klivers.'
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**'''[[User:Dwight Tyler Fields|Dwight Tyler Fields]] 14:21, 4 February 2013 (EST)''': Here's the link to the video: [http://youtu.be/rD5uNAMbDaQ "Synthetic Biology Explained" by James Hutson, Bridge8]
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*'''[[User:Dwight Tyler Fields|Dwight Tyler Fields]] 15:48, 1 February 2013 (EST)''': I'm on it!
'''[[User:Gabriel Wu|Gabriel Wu]] 17:42, 28 January 2013 (EST)''': What was the first BioBrick?
'''[[User:Gabriel Wu|Gabriel Wu]] 17:42, 28 January 2013 (EST)''': What was the first BioBrick?
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'''[[User:Catherine I. Mortensen|Catherine I. Mortensen]] 16:31, 30 January 2013 (EST)''': Are there any known labs that have had success with the something like AddGene or the registry? It seems users have had little success according to their reviews...
'''[[User:Catherine I. Mortensen|Catherine I. Mortensen]] 16:31, 30 January 2013 (EST)''': Are there any known labs that have had success with the something like AddGene or the registry? It seems users have had little success according to their reviews...
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*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 21:06, 30 January 2013 (EST)''':I think there are people out there who dip into these resources occasionally to get parts or set up a new technique in lab, especially at institutions or in countries where funding is tight. Like a lot of places, fewer people leave positive comments than negative ones!
'''[[User:Benjamin Gilman|Benjamin Gilman]] 18:36, 30 January 2013 (EST)''': The page says that there's no real way to measure PoPS ''in vivo.''  Where do the PoPS numbers for different BioBricks come from then?
'''[[User:Benjamin Gilman|Benjamin Gilman]] 18:36, 30 January 2013 (EST)''': The page says that there's no real way to measure PoPS ''in vivo.''  Where do the PoPS numbers for different BioBricks come from then?
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*'''[[User:Neil R Gottel|Neil R Gottel]] 19:03, 30 January 2013 (EST)''':Biobricks should really switch to some sort of standard where if you haven't proven that a part works as advertised, then it shouldn't be on the registry. Also the current standard is behind the current technology, as noted in the "legacy" section. Does Knight et al. still stand by the biobrick standard/concept? Is there a movement to have a real, usable registry that doesn't make me want to scream after using it for five seconds? A good start would be a "premium" section, where only parts that were demonstrated to work (or at least were presented as working at the regionals and finals) would be listed.
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'''[[User:Neil R Gottel|Neil R Gottel]] 19:03, 30 January 2013 (EST)''':Biobricks should really switch to some sort of standard where if you haven't proven that a part works as advertised, then it shouldn't be on the registry. Also the current standard is behind the current technology, as noted in the "legacy" section. Does Knight et al. still stand by the biobrick standard/concept? Is there a movement to have a real, usable registry that doesn't make me want to scream after using it for five seconds? A good start would be a "premium" section, where only parts that were demonstrated to work (or at least were presented as working at the regionals and finals) would be listed.
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*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 20:58, 30 January 2013 (EST)''':One of the activities that iGEM teams can do to earn medals is to test and improve the documentation of a part from previous years. Eventually, you would hope that the most-used parts just came to the top. It would be great if you could do a "cited ref" search on a part to see how much it is being used (by iGEM teams and in scientific publications). It would provide a way to sort parts that were never used again to the bottom (and have an all-time ranking of the best parts ever). These would be interesting human-practices exercises for an iGEM team, and we would probably find that the Coliroid is the most used part ever.
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**'''[[User:Dwight Tyler Fields|Dwight Tyler Fields]] 14:32, 4 February 2013 (EST)''': Tom Knight has updated the standard several times. Here is the latest draft from 2008, called BB2: [http://hdl.handle.net/1721.1/45139 Draft Standard for Biobrick BB-2 Biological Parts]. He otherwise hasn't expounded much philosophically about the place of BioBricks since that original "Idempotent Vector Design" paper.
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'''[[User:Max E. Rubinson|Max E. Rubinson]] 22:13, 30 January 2013 (EST)''': Did anyone find out what the first part added to the registry was?
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*'''[[User:Thomas Wall|Thomas Wall]] 22:13, 31 January 2013 (EST)''': I'm not 100 percent certain, but my 10 minutes of research leads me to believe it is the plasmid Knight wanted people to use for assembly of biobricks
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'''[[User:Gabriel Wu|Gabriel Wu]] 17:33, 31 January 2013 (EST)''': It was asked in class why were the original BioBrick enzymes chosen.  From Tom Knight's [http://dspace.mit.edu/bitstream/handle/1721.1/21168/biobricks.pdf?sequence=1 paper] (section 0.8), he explicitly states that he wanted enzymes:
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*that were easy to use and reliable
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*worked in compatible buffer systems
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*worked at compatible temperatures
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*that could be heat killed
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*that provided complete digestion, with few required bases outside of their recognition site.
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*that exhibited low star (nonspecific) activity
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It might be interesting to debate the merits of these criteria both from a historical viewpoint (in 2007) versus today in the age of Gibson cloning.
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'''[[User:Dwight Tyler Fields|Dwight Tyler Fields]] 15:48, 1 February 2013 (EST)''': Great comments and questions, I'll get back to you guys shortly.

Current revision

Gabriel Wu 23:14, 27 January 2013 (EST)There's no way there's only 700 parts in the registry. If you check the history on that page you've referenced the last time it was updated was in 2006.

    • Dwight Tyler Fields 14:16, 4 February 2013 (EST): Unfortunately I haven't been able to find a better reference for the total number of parts in the registry. Most papers today still reference that page, and the only variation I've seen is the Wikipedia article for the registry, which says "over 3400 parts", however there is no reference for that number. To be honest, in light of the outdated nature of the registry in general, I doubt an accurate and current figure is even known or kept track of, especially since it's difficult to determine how many parts actually work.

Gabriel Wu: Please post the video you played in class on this website. I need a place to reference 'klivers.'

Gabriel Wu 17:42, 28 January 2013 (EST): What was the first BioBrick?

Kevin Baldridge 17:49, 28 January 2013 (EST):The registry seems to be a bit outdated. It needs some serious work with user interface and curation by experienced scientists to remove duplicates, etc. Is the AddGene database similar concept with a better implementation?

Catherine I. Mortensen 16:31, 30 January 2013 (EST): Are there any known labs that have had success with the something like AddGene or the registry? It seems users have had little success according to their reviews...

  • Jeffrey E. Barrick 21:06, 30 January 2013 (EST):I think there are people out there who dip into these resources occasionally to get parts or set up a new technique in lab, especially at institutions or in countries where funding is tight. Like a lot of places, fewer people leave positive comments than negative ones!

Benjamin Gilman 18:36, 30 January 2013 (EST): The page says that there's no real way to measure PoPS in vivo. Where do the PoPS numbers for different BioBricks come from then?

Neil R Gottel 19:03, 30 January 2013 (EST):Biobricks should really switch to some sort of standard where if you haven't proven that a part works as advertised, then it shouldn't be on the registry. Also the current standard is behind the current technology, as noted in the "legacy" section. Does Knight et al. still stand by the biobrick standard/concept? Is there a movement to have a real, usable registry that doesn't make me want to scream after using it for five seconds? A good start would be a "premium" section, where only parts that were demonstrated to work (or at least were presented as working at the regionals and finals) would be listed.

  • Jeffrey E. Barrick 20:58, 30 January 2013 (EST):One of the activities that iGEM teams can do to earn medals is to test and improve the documentation of a part from previous years. Eventually, you would hope that the most-used parts just came to the top. It would be great if you could do a "cited ref" search on a part to see how much it is being used (by iGEM teams and in scientific publications). It would provide a way to sort parts that were never used again to the bottom (and have an all-time ranking of the best parts ever). These would be interesting human-practices exercises for an iGEM team, and we would probably find that the Coliroid is the most used part ever.

Max E. Rubinson 22:13, 30 January 2013 (EST): Did anyone find out what the first part added to the registry was?

  • Thomas Wall 22:13, 31 January 2013 (EST): I'm not 100 percent certain, but my 10 minutes of research leads me to believe it is the plasmid Knight wanted people to use for assembly of biobricks

Gabriel Wu 17:33, 31 January 2013 (EST): It was asked in class why were the original BioBrick enzymes chosen. From Tom Knight's paper (section 0.8), he explicitly states that he wanted enzymes:

  • that were easy to use and reliable
  • worked in compatible buffer systems
  • worked at compatible temperatures
  • that could be heat killed
  • that provided complete digestion, with few required bases outside of their recognition site.
  • that exhibited low star (nonspecific) activity

It might be interesting to debate the merits of these criteria both from a historical viewpoint (in 2007) versus today in the age of Gibson cloning.

Dwight Tyler Fields 15:48, 1 February 2013 (EST): Great comments and questions, I'll get back to you guys shortly.

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