Open Source Biotechnology - Revision history

Eric: Organizational Changes + Additions

2018-06-01T20:57:09Z

Organizational Changes + Additions

← Older revision		Revision as of 20:57, 1 June 2018
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	[[File:Bacteria-microbiology.jpg\|400px\|thumb\|right\|Bacterial culture]]		[[File:Bacteria-microbiology.jpg\|400px\|thumb\|right\|Bacterial culture]]

			=Basics=
	Open source biotechnology is in some ways more challenging than open source software, content or hardware. The unanswered question is: is there a place for an ecosystem based around free "software" running on biological processors ? Biological hacking has the potential to transform health care, address energy problems, mitigate climate change, and more. Or it could wreak environmental devastation and facilitate horrifying attacks by either individuals or governments.		Open source biotechnology is in some ways more challenging than open source software, content or hardware. The unanswered question is: is there a place for an ecosystem based around free "software" running on biological processors ? Biological hacking has the potential to transform health care, address energy problems, mitigate climate change, and more. Or it could wreak environmental devastation and facilitate horrifying attacks by either individuals or governments.

	=Open source ~~biotechnology projects~~=		=Existing Open source Biotechnology Projects=

	==IGEM==		==IGEM==
	The International Genetically Engineered Machine competition (iGEM) is the premiere undergraduate Synthetic Biology competition. Student teams are given a kit of biological parts at the beginning of the summer from the Registry of Standard Biological Parts. Working at their own schools over the summer, they use these parts and new parts of their own design to build biological systems and operate them in living cells. This project design and competition format is an exceptionally motivating and effective teaching method. iGEM began in January of 2003 with a month-long course at MIT during their Independent Activities Period (IAP). The students designed biological systems to make cells blink. This design course grew to a summer competition with 5 teams in 2004, 13 teams in 2005 - the first year that the competition grew internationally - 32 teams in 2006, 54 teams in 2007, 84 teams in 2008, and 112 teams in 2009. Projects ranged from a rainbow of pigmented bacteria, to banana and wintergreen smelling bacteria, an arsenic biosensor, Bactoblood, and buoyant bacteria.		The International Genetically Engineered Machine competition (iGEM) is the premiere undergraduate Synthetic Biology competition. Student teams are given a kit of biological parts at the beginning of the summer from the Registry of Standard Biological Parts. Working at their own schools over the summer, they use these parts and new parts of their own design to build biological systems and operate them in living cells. This project design and competition format is an exceptionally motivating and effective teaching method. iGEM began in January of 2003 with a month-long course at MIT during their Independent Activities Period (IAP). The students designed biological systems to make cells blink. This design course grew to a summer competition with 5 teams in 2004, 13 teams in 2005 - the first year that the competition grew internationally - 32 teams in 2006, 54 teams in 2007, 84 teams in 2008, and 112 teams in 2009. Projects ranged from a rainbow of pigmented bacteria, to banana and wintergreen smelling bacteria, an arsenic biosensor, Bactoblood, and buoyant bacteria.

	==Community labs==		==Community labs==
			*

	==DIYbio==		==DIYbio==
			*

	==Video==		=Video=
	<html>		<html>
	<iframe title="YouTube video player" width="480" height="390" src="https://www.youtube.com/embed//a6JpbIWej-E" frameborder="0" allowfullscreen></iframe></html>		<iframe title="YouTube video player" width="480" height="390" src="https://www.youtube.com/embed//a6JpbIWej-E" frameborder="0" allowfullscreen></iframe></html>

	==Implications of recent advances in DNA synthesis, assembly, and synthetic biology==		=Implications of recent advances in DNA synthesis, assembly, and synthetic biology=

	Traditionally, genetic engineering has relied on techniques such as gene cloning, restriction enzymes and ligation. Introduction of the desired gene into a cell (in a process known as transformation) usually requires an antibiotic resistance gene to select for positive transformants. The antibiotic corresponding to the resistance gene is included in the media and kills (or slows the growth of) bacteria that do not contain the antibiotic resistance gene. There are a variety of techniques that are used to distinguish bacteria containing the fused (ligated) target gene from bacteria containing the resistance gene without the target gene including blue/white screening, target PCR, or gene sequencing.		Traditionally, genetic engineering has relied on techniques such as gene cloning, restriction enzymes and ligation. Introduction of the desired gene into a cell (in a process known as transformation) usually requires an antibiotic resistance gene to select for positive transformants. The antibiotic corresponding to the resistance gene is included in the media and kills (or slows the growth of) bacteria that do not contain the antibiotic resistance gene. There are a variety of techniques that are used to distinguish bacteria containing the fused (ligated) target gene from bacteria containing the resistance gene without the target gene including blue/white screening, target PCR, or gene sequencing.

	More recently, progress has been made with alternative techniques such as [http://en.wikipedia.org/wiki/Recombineering recombineering], which is takes advantage of homologous recombination in cells undergoing meiosis. The resulting mutated sequence in the target organism may be indistinguishable from a naturally occurring mutation, for example when single-base substitutions are created. Therefore, it is becoming doubtful whether some patents that are based on this technique are actually enforceable. The user of the modified organism could claim that this is a natural, random mutation and there is no way to prove that it is not.		More recently, progress has been made with alternative techniques such as [http://en.wikipedia.org/wiki/Recombineering recombineering], which is takes advantage of homologous recombination in cells undergoing meiosis. The resulting mutated sequence in the target organism may be indistinguishable from a naturally occurring mutation, for example when single-base substitutions are created. Therefore, it is becoming doubtful whether some patents that are based on this technique are actually enforceable. The user of the modified organism could claim that this is a natural, random mutation and there is no way to prove that it is not.

	==~~Related pages on OSE Wiki~~==		=Areas Worth Exploring=
	*[[Microfluidics]], [[Biolab]], [[Fermentor]], [[Biorefinery]], [[Lignin]]		*Biosensors
			*Ethonol Production
			*Bio-Hydrogen Production
			*Bioluminescence Based Lighting
			*Bioplastics
			*Sensible GMO Crops
			*Bioremediation

			==See Also==
			*[https://wiki.opensourceecology.org/wiki/Construction_Sets#Lab_Stuff The "Lab Stuff" Subsection of the "Construction Sets" Page]
			*[[Microfluidics]]
			*[[Biolab]]
			*[[Fermentor]]
			*[[Biorefinery]]
			*[[Lignin]]

	==Linkfest==		==Linkfest==

Poli at 17:18, 1 June 2018

2018-06-01T17:18:57Z

← Older revision		Revision as of 17:18, 1 June 2018
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	==Implications of recent advances in DNA synthesis, assembly, and synthetic biology==		==Implications of recent advances in DNA synthesis, assembly, and synthetic biology==

	Traditionally, genetic engineering has relied on techniques such as gene cloning, restriction enzymes and ligation. ~~Low rates~~ of ~~recombination often required the use of selection markers, such as antibiotic resistance sequences. Antibiotic selection fuses antibiotic resistance genes with~~ the desired gene ~~which is then inserted~~ into a cell (in a process known as transformation). The antibiotic corresponding to the resistance gene is included in the media and kills (or slows the growth of) bacteria that do not contain the antibiotic resistance gene. There are a variety of techniques that are used to distinguish bacteria containing the fused (ligated) target gene from bacteria containing the resistance gene without the target gene including blue/white screening, target PCR, or gene sequencing.		Traditionally, genetic engineering has relied on techniques such as gene cloning, restriction enzymes and ligation. Introduction of the desired gene into a cell (in a process known as transformation) usually requires an antibiotic resistance gene to select for positive transformants. The antibiotic corresponding to the resistance gene is included in the media and kills (or slows the growth of) bacteria that do not contain the antibiotic resistance gene. There are a variety of techniques that are used to distinguish bacteria containing the fused (ligated) target gene from bacteria containing the resistance gene without the target gene including blue/white screening, target PCR, or gene sequencing.

	More recently, progress has been made with alternative techniques such as [http://en.wikipedia.org/wiki/Recombineering recombineering], which is takes advantage of homologous recombination in cells undergoing meiosis. The resulting mutated sequence in the target organism may be indistinguishable from a naturally occurring mutation, for example when single-base substitutions are created. Therefore, it is becoming doubtful whether some patents that are based on this technique are actually enforceable. The user of the modified organism could claim that this is a natural, random mutation and there is no way to prove that it is not.		More recently, progress has been made with alternative techniques such as [http://en.wikipedia.org/wiki/Recombineering recombineering], which is takes advantage of homologous recombination in cells undergoing meiosis. The resulting mutated sequence in the target organism may be indistinguishable from a naturally occurring mutation, for example when single-base substitutions are created. Therefore, it is becoming doubtful whether some patents that are based on this technique are actually enforceable. The user of the modified organism could claim that this is a natural, random mutation and there is no way to prove that it is not.

Poli at 13:58, 1 June 2018

2018-06-01T13:58:34Z

← Older revision		Revision as of 13:58, 1 June 2018
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	<iframe title="YouTube video player" width="480" height="390" src="https://www.youtube.com/embed//a6JpbIWej-E" frameborder="0" allowfullscreen></iframe></html>		<iframe title="YouTube video player" width="480" height="390" src="https://www.youtube.com/embed//a6JpbIWej-E" frameborder="0" allowfullscreen></iframe></html>

	==Implications of recent advances in ~~recombineering on biotech patents~~==		==Implications of recent advances in DNA synthesis, assembly, and synthetic biology==

	Traditionally, genetic engineering has relied on techniques such as gene cloning, restriction enzymes and ligation. Low rates of recombination often required the use of selection markers, such as antibiotic resistance sequences. Antibiotic selection fuses antibiotic resistance genes with the desired gene which is then inserted into a cell (in a process known as transformation). The antibiotic corresponding to the resistance gene is included in the media and kills (or slows the growth of) bacteria that do not contain the antibiotic resistance gene. There are a variety of techniques that are used to distinguish bacteria containing the fused (ligated) target gene from bacteria containing the resistance gene without the target gene including blue/white screening, target PCR, or gene sequencing.		Traditionally, genetic engineering has relied on techniques such as gene cloning, restriction enzymes and ligation. Low rates of recombination often required the use of selection markers, such as antibiotic resistance sequences. Antibiotic selection fuses antibiotic resistance genes with the desired gene which is then inserted into a cell (in a process known as transformation). The antibiotic corresponding to the resistance gene is included in the media and kills (or slows the growth of) bacteria that do not contain the antibiotic resistance gene. There are a variety of techniques that are used to distinguish bacteria containing the fused (ligated) target gene from bacteria containing the resistance gene without the target gene including blue/white screening, target PCR, or gene sequencing.

Poli at 13:57, 1 June 2018

2018-06-01T13:57:20Z

← Older revision		Revision as of 13:57, 1 June 2018
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	Open source biotechnology is in some ways more challenging than open source software, content or hardware. The unanswered question is: is there a place for an ecosystem based around free "software" running on biological processors ? Biological hacking has the potential to transform health care, address energy problems, mitigate climate change, and more. Or it could wreak environmental devastation and facilitate horrifying attacks by either individuals or governments.		Open source biotechnology is in some ways more challenging than open source software, content or hardware. The unanswered question is: is there a place for an ecosystem based around free "software" running on biological processors ? Biological hacking has the potential to transform health care, address energy problems, mitigate climate change, and more. Or it could wreak environmental devastation and facilitate horrifying attacks by either individuals or governments.

			=Open source biotechnology projects=

	==IGEM==		==IGEM==
	The International Genetically Engineered Machine competition (iGEM) is the premiere undergraduate Synthetic Biology competition. Student teams are given a kit of biological parts at the beginning of the summer from the Registry of Standard Biological Parts. Working at their own schools over the summer, they use these parts and new parts of their own design to build biological systems and operate them in living cells. This project design and competition format is an exceptionally motivating and effective teaching method. iGEM began in January of 2003 with a month-long course at MIT during their Independent Activities Period (IAP). The students designed biological systems to make cells blink. This design course grew to a summer competition with 5 teams in 2004, 13 teams in 2005 - the first year that the competition grew internationally - 32 teams in 2006, 54 teams in 2007, 84 teams in 2008, and 112 teams in 2009. Projects ranged from a rainbow of pigmented bacteria, to banana and wintergreen smelling bacteria, an arsenic biosensor, Bactoblood, and buoyant bacteria.		The International Genetically Engineered Machine competition (iGEM) is the premiere undergraduate Synthetic Biology competition. Student teams are given a kit of biological parts at the beginning of the summer from the Registry of Standard Biological Parts. Working at their own schools over the summer, they use these parts and new parts of their own design to build biological systems and operate them in living cells. This project design and competition format is an exceptionally motivating and effective teaching method. iGEM began in January of 2003 with a month-long course at MIT during their Independent Activities Period (IAP). The students designed biological systems to make cells blink. This design course grew to a summer competition with 5 teams in 2004, 13 teams in 2005 - the first year that the competition grew internationally - 32 teams in 2006, 54 teams in 2007, 84 teams in 2008, and 112 teams in 2009. Projects ranged from a rainbow of pigmented bacteria, to banana and wintergreen smelling bacteria, an arsenic biosensor, Bactoblood, and buoyant bacteria.

			==Community labs==

			==DIYbio==

	==Video==		==Video==

Rasmus: added images

2016-08-14T00:03:39Z

added images

← Older revision		Revision as of 00:03, 14 August 2016
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	[[File:lab_bench.jpg\|400px\|thumb\|right\|Lab bench]]		[[File:lab_bench.jpg\|400px\|thumb\|right\|Lab bench]]
			[[File:Ecoli bacteria.jpg\|400px\|thumb\|right\|E.coli - the traditional workhorse of biotechnology]]
			[[File:Bacteria-microbiology.jpg\|400px\|thumb\|right\|Bacterial culture]]

	Open source biotechnology is in some ways more challenging than open source software, content or hardware. The unanswered question is: is there a place for an ecosystem based around free "software" running on biological processors ? Biological hacking has the potential to transform health care, address energy problems, mitigate climate change, and more. Or it could wreak environmental devastation and facilitate horrifying attacks by either individuals or governments.		Open source biotechnology is in some ways more challenging than open source software, content or hardware. The unanswered question is: is there a place for an ecosystem based around free "software" running on biological processors ? Biological hacking has the potential to transform health care, address energy problems, mitigate climate change, and more. Or it could wreak environmental devastation and facilitate horrifying attacks by either individuals or governments.

Louie Louiie: /* Linkfest */

2014-11-17T02:05:02Z

Linkfest

← Older revision		Revision as of 02:05, 17 November 2014
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	==Linkfest==		==Linkfest==
	* [http://diybio.org/ DIYBio] - An Institution for the Amateur Biologist		* [http://diybio.org/ DIYBio] - An Institution for the Amateur Biologist
			* [http://counterculturelabs.org/ Counter Culture Labs]- Biohacking and Citizen Science lab in SF bay area
	* [http://www.igem.org IGEM] - International Genetically Engineered Machine competition - the premiere undergraduate Synthetic Biology competition		* [http://www.igem.org IGEM] - International Genetically Engineered Machine competition - the premiere undergraduate Synthetic Biology competition
	* [http://openwetware.org/wiki/Main_Page Open WetWare Wiki] - an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering		* [http://openwetware.org/wiki/Main_Page Open WetWare Wiki] - an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering

Poli: /* Related pages on OSE Wiki */

2012-06-10T15:48:19Z

Related pages on OSE Wiki

← Older revision		Revision as of 15:48, 10 June 2012
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	==Related pages on OSE Wiki==		==Related pages on OSE Wiki==
	*[[Microfluidics]], [[Biolab]],		*[[Microfluidics]], [[Biolab]], [[Fermentor]], [[Biorefinery]], [[Lignin]]

	==Linkfest==		==Linkfest==

Rasmus: /* Linkfest */ another link

2012-06-09T23:45:59Z

Linkfest: another link

← Older revision		Revision as of 23:45, 9 June 2012
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	* [http://bbf.openwetware.org/ BioBricks Foundation] - encourages the development and responsible use of technologies based on BioBrick™ standard DNA parts that encode basic biological functions		* [http://bbf.openwetware.org/ BioBricks Foundation] - encourages the development and responsible use of technologies based on BioBrick™ standard DNA parts that encode basic biological functions
	* [http://www.biofab.org/ The BIOFAB: International Open Facility Advancing Biotechnology]		* [http://www.biofab.org/ The BIOFAB: International Open Facility Advancing Biotechnology]
	* [http://www.indiebiotech.com/ Indie Biotech] - Open Source Biotechnology for Everyone		* [http://www.indiebiotech.com/ Indie Biotech] - Open Source Biotechnology for Everyone, featured in [http://www.technologyreview.com/news/426885/doing-biotech-in-my-bedroom/ this tech review article]
	* [http://www.bios.net/daisy/bios/home.html Biological Open Source (BiOS)] - an effort to develop new innovation ecosystems for disadvantaged communities and neglected priorities		* [http://www.bios.net/daisy/bios/home.html Biological Open Source (BiOS)] - an effort to develop new innovation ecosystems for disadvantaged communities and neglected priorities
	* [http://speakscience.org/ Genotyp] - open source biotech lab hardware, mainly intended for teaching institutions such as high schools		* [http://speakscience.org/ Genotyp] - open source biotech lab hardware, mainly intended for teaching institutions such as high schools

Rasmus: /* Linkfest */ added link

2012-06-09T23:25:51Z

Linkfest: added link

← Older revision		Revision as of 23:25, 9 June 2012
Line 28:		Line 28:
	* [http://bbf.openwetware.org/ BioBricks Foundation] - encourages the development and responsible use of technologies based on BioBrick™ standard DNA parts that encode basic biological functions		* [http://bbf.openwetware.org/ BioBricks Foundation] - encourages the development and responsible use of technologies based on BioBrick™ standard DNA parts that encode basic biological functions
	* [http://www.biofab.org/ The BIOFAB: International Open Facility Advancing Biotechnology]		* [http://www.biofab.org/ The BIOFAB: International Open Facility Advancing Biotechnology]
			* [http://www.indiebiotech.com/ Indie Biotech] - Open Source Biotechnology for Everyone
	* [http://www.bios.net/daisy/bios/home.html Biological Open Source (BiOS)] - an effort to develop new innovation ecosystems for disadvantaged communities and neglected priorities		* [http://www.bios.net/daisy/bios/home.html Biological Open Source (BiOS)] - an effort to develop new innovation ecosystems for disadvantaged communities and neglected priorities
	* [http://speakscience.org/ Genotyp] - open source biotech lab hardware, mainly intended for teaching institutions such as high schools		* [http://speakscience.org/ Genotyp] - open source biotech lab hardware, mainly intended for teaching institutions such as high schools

Poli: /* Implications of recent advances in recombineering on biotech patents */

2012-06-04T12:26:43Z

Implications of recent advances in recombineering on biotech patents

← Older revision		Revision as of 12:26, 4 June 2012
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	==Implications of recent advances in recombineering on biotech patents==		==Implications of recent advances in recombineering on biotech patents==

	Traditionally, genetic engineering has relied on techniques such as gene cloning, restriction enzymes and ligation. Low rates of recombination often required the use of selection markers, such as antibiotic resistance sequences. Antibiotic selection fuses antibiotic resistance genes with the desired gene which is then inserted into a cell (in a process known as transformation). The antibiotic corresponding to the resistance gene is included in the media and kills (or slows the growth of) bacteria that do not contain the antibiotic resistance gene. There are a variety of techniques that are used to distinguish bacteria containing the fused (ligated) target gene ~~containing~~ from bacteria containing the resistance gene without the target gene.		Traditionally, genetic engineering has relied on techniques such as gene cloning, restriction enzymes and ligation. Low rates of recombination often required the use of selection markers, such as antibiotic resistance sequences. Antibiotic selection fuses antibiotic resistance genes with the desired gene which is then inserted into a cell (in a process known as transformation). The antibiotic corresponding to the resistance gene is included in the media and kills (or slows the growth of) bacteria that do not contain the antibiotic resistance gene. There are a variety of techniques that are used to distinguish bacteria containing the fused (ligated) target gene from bacteria containing the resistance gene without the target gene including blue/white screening, target PCR, or gene sequencing.

	More recently, progress has been made with alternative techniques such as [http://en.wikipedia.org/wiki/Recombineering recombineering], which is takes advantage of homologous recombination in cells undergoing meiosis. The resulting mutated sequence in the target organism may be indistinguishable from a naturally occurring mutation, for example when single-base substitutions are created. Therefore, it is becoming doubtful whether some patents that are based on this technique are actually enforceable. The user of the modified organism could claim that this is a natural, random mutation and there is no way to prove that it is not.		More recently, progress has been made with alternative techniques such as [http://en.wikipedia.org/wiki/Recombineering recombineering], which is takes advantage of homologous recombination in cells undergoing meiosis. The resulting mutated sequence in the target organism may be indistinguishable from a naturally occurring mutation, for example when single-base substitutions are created. Therefore, it is becoming doubtful whether some patents that are based on this technique are actually enforceable. The user of the modified organism could claim that this is a natural, random mutation and there is no way to prove that it is not.