Talk:CH391L/S13/BioBricksAndRegistry - Revision history

Dwight Tyler Fields: Knight's latest biobrick standard

Dwight Tyler Fields — Mon, 04 Feb 2013 19:32:41 GMT

Knight's latest biobrick standard

←Older revision		Revision as of 19:32, 4 February 2013
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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.		*'''[[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.
		+
		+	**'''[[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.

	'''[[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?		'''[[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?

Dwight Tyler Fields: "Synthetic Biology Explained" video link

Dwight Tyler Fields — Mon, 04 Feb 2013 19:21:43 GMT

"Synthetic Biology Explained" video link

←Older revision		Revision as of 19:21, 4 February 2013
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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.

-	**'''[[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: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.'
		+
		+	**'''[[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]

	*'''[[User:Dwight Tyler Fields\|Dwight Tyler Fields]] 15:48, 1 February 2013 (EST)''': I'm on it!		*'''[[User:Dwight Tyler Fields\|Dwight Tyler Fields]] 15:48, 1 February 2013 (EST)''': I'm on it!

Dwight Tyler Fields: Response to Gabe Wu

Dwight Tyler Fields — Mon, 04 Feb 2013 19:16:46 GMT

Response to Gabe Wu

←Older revision		Revision as of 19:16, 4 February 2013
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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.
		+
		+	**'''[[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.'

Dwight Tyler Fields at 20:48, 1 February 2013

Dwight Tyler Fields — Fri, 01 Feb 2013 20:48:07 GMT

←Older revision		Revision as of 20:48, 1 February 2013
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	'''[[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.'
		+
		+	*'''[[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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	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.		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.
		+
		+	'''[[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.

Jeffrey E. Barrick at 16:06, 1 February 2013

Jeffrey E. Barrick — Fri, 01 Feb 2013 16:06:27 GMT

←Older revision		Revision as of 16:06, 1 February 2013
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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...

-	*'''[[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 ~~fewer~~ positive comments than negative ones!	+	*'''[[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?

Thomas Wall at 04:08, 1 February 2013

Thomas Wall — Fri, 01 Feb 2013 04:08:16 GMT

←Older revision		Revision as of 04:08, 1 February 2013
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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?		'''[[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?
		+	*'''[[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

	'''[[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:		'''[[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:

Gabriel Wu at 22:36, 31 January 2013

Gabriel Wu — Thu, 31 Jan 2013 22:36:29 GMT

←Older revision		Revision as of 22:36, 31 January 2013
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	*that provided complete digestion, with few required bases outside of their recognition site.		*that provided complete digestion, with few required bases outside of their recognition site.
	*that exhibited low star (nonspecific) activity		*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.

Gabriel Wu at 22:35, 31 January 2013

Gabriel Wu — Thu, 31 Jan 2013 22:35:11 GMT

←Older revision		Revision as of 22:35, 31 January 2013
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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?		'''[[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?

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

Gabriel Wu at 22:33, 31 January 2013

Gabriel Wu — Thu, 31 Jan 2013 22:33:49 GMT

←Older revision		Revision as of 22:33, 31 January 2013
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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?		'''[[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?
		+
		+	'''[[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:
		+	*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

Max E. Rubinson at 03:13, 31 January 2013

Max E. Rubinson — Thu, 31 Jan 2013 03:13:47 GMT

←Older revision		Revision as of 03:13, 31 January 2013
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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.		*'''[[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.
		+
		+	'''[[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?

←Older revision		Revision as of 19:32, 4 February 2013
Line 22:		Line 22:

	*'''[[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.		*'''[[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.
		+
		+	**'''[[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.

	'''[[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?		'''[[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?

←Older revision		Revision as of 19:21, 4 February 2013
Line 1:		Line 1:
	'''[[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.

-	**'''[[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: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.'
		+
		+	**'''[[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]

	*'''[[User:Dwight Tyler Fields\|Dwight Tyler Fields]] 15:48, 1 February 2013 (EST)''': I'm on it!		*'''[[User:Dwight Tyler Fields\|Dwight Tyler Fields]] 15:48, 1 February 2013 (EST)''': I'm on it!

←Older revision		Revision as of 19:16, 4 February 2013
Line 1:		Line 1:
	'''[[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.
		+
		+	**'''[[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.'

←Older revision		Revision as of 16:06, 1 February 2013
Line 9:		Line 9:
	'''[[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...

-	*'''[[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 ~~fewer~~ positive comments than negative ones!	+	*'''[[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?

←Older revision		Revision as of 04:08, 1 February 2013
Line 18:		Line 18:

	'''[[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?		'''[[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?
		+	*'''[[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

	'''[[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:		'''[[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: