Talk:CH391L/S13/BioBricksAndRegistry

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Revision as of 17:33, 31 January 2013 by Gabriel Wu (Talk | contribs)
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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.

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Kevin Baldridge 17:49, 28 January 2013 (EST):The registry seems to be a bit outdated.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 fewer 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?

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:

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