Open Biotech/PCR - Revision history

Juul at 04:46, 17 March 2013

2013-03-17T04:46:14Z

← Older revision		Revision as of 21:46, 16 March 2013
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	The goal of this project is to build a PCR machine as part of the open biolab. The device should be simple enough that people with a basic skillset can build it on their own while being cheap and simple to produce in a 100x to 500x quantity.		The goal of this project is to build a PCR machine as part of the open biolab. The device should be simple enough that people with a basic skillset can build it on their own while being cheap and simple to produce in a 100x to 500x quantity.

	The current target for the entire kit is $~~300~~ (PCR, centrifuge, shaking incubator, gel electrophoresis box, micropipette + chemistry/biology/plastics for 3+ experiments). This may turn out to be too low for the first run, but we're aiming at making this as affordable as possible while maintaining a quality that's good enough for day-to-day citizen science work.		The current target for the entire kit is $500 (PCR, centrifuge, shaking incubator, gel electrophoresis box, micropipette + chemistry/biology/plastics for 3+ experiments). This may turn out to be too low for the first run, but we're aiming at making this as affordable as possible while maintaining a quality that's good enough for day-to-day citizen science work.

	= Bill of materials and pricing =		= Bill of materials and pricing =

208.87.217.74: /* Discussion */

2013-02-18T10:33:47Z

Discussion

← Older revision		Revision as of 03:33, 18 February 2013
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	I've been looking at the specs of some Peltier chips (see https://docs.google.com/file/d/1u2m--LONYCOyvcp76spoAP3wN3nWroROwfTtoJx9TpeeeMYY1WVNb1-KCXOk/edit?usp=sharing ) and on some of them, they seem to be designed for lower temperature operation and the lifetime of the device will be significantly reduced if you operate them at a high temperature (the limits of the device in the attached spec device, for example, is 80C.) At 95C, the hot side quickly ramps up from the cold side temp, which is starting at 95C, I've heard as much as 4x the rate of the cold side. By the time you got to 80C on the cold side, you could easily exceed 150C if your heat sink isn't able to pump that much heat that quickly. I think to ensure against damage or reduced life, you have to carefully control the amount of volatge/current applied. A feedback loop to limit applied voltage based on temp of hot side seems to be a sensible addition. I'm still trying to figure this out for a temperature controlled minielectrophoresis unit that I am designing (to be open source). [[User:Hbergeronx\|Hbergeronx]].		I've been looking at the specs of some Peltier chips (see https://docs.google.com/file/d/1u2m--LONYCOyvcp76spoAP3wN3nWroROwfTtoJx9TpeeeMYY1WVNb1-KCXOk/edit?usp=sharing ) and on some of them, they seem to be designed for lower temperature operation and the lifetime of the device will be significantly reduced if you operate them at a high temperature (the limits of the device in the attached spec device, for example, is 80C.) At 95C, the hot side quickly ramps up from the cold side temp, which is starting at 95C, I've heard as much as 4x the rate of the cold side. By the time you got to 80C on the cold side, you could easily exceed 150C if your heat sink isn't able to pump that much heat that quickly. I think to ensure against damage or reduced life, you have to carefully control the amount of volatge/current applied. A feedback loop to limit applied voltage based on temp of hot side seems to be a sensible addition. I'm still trying to figure this out for a temperature controlled minielectrophoresis unit that I am designing (to be open source). [[User:Hbergeronx\|Hbergeronx]].

	:~~Interesting information! I knew there was some problems~~ with ~~the peltier elements at higher temperatures but~~ it'~~s good~~ to ~~have some numbers~~. One solution would be to just not switch them on at the higher temperatures. We can see how much of an effect the peltier will have above 80 C. My guess is that it will be fairly small. Another solution is to either PWM control the MOSFET, perhaps through a capacitor, or even better, to use the analog output of the microcontroller and a non-charge-pumped MOSFET to gradually control the peltier based on the temperature. We may want to do this with the heating element as well. [[User:Juul\|Juul]]		:Yeah. The temperature sensor + MOSFET + microcontroller allows us this dynamic control :-) (also, please put three tilde characters to tag comments with your name) - [[User:Juul\|Juul]]
			::A cheap unit becomes not so cheap if after a handful of runs, you have to fix it: not trying to imply that you haven't thought of this or to be a downer, but just raising awareness of something that only recently came to my attention. [[User:Hbergeronx\|Hbergeronx]]
			:::My apologies for the brief comment before. I was in a hurry. Interesting information indeed! One solution would be to just not switch them on at the higher temperatures. We can see how much of an effect the peltier will have above 80 C. My guess is that it will be fairly small. Another solution is to either PWM control the MOSFET, perhaps through a capacitor, or even better, to use the analog output of the microcontroller and a non-charge-pumped MOSFET to gradually control the peltier based on the temperature. We may want to do this with the heating element as well. [[User:Juul\|Juul]]
	A cheap unit becomes not so cheap if after a handful of runs, you have to fix it: not trying to imply that you haven't thought of this or to be a downer, but just raising awareness of something that only recently came to my attention.

	= Heating =		= Heating =

208.87.217.74 at 10:29, 18 February 2013

2013-02-18T10:29:53Z

← Older revision		Revision as of 03:29, 18 February 2013
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	:Could not find anything cheaper on digikey.		:Could not find anything cheaper on digikey.
	:It looks like searching for '12709 Tec' can yield small lots of a very very similar device for $5 a piece.		:It looks like searching for '12709 Tec' can yield small lots of a very very similar device for $5 a piece.

			=== Discussion ===

			I've been looking at the specs of some Peltier chips (see https://docs.google.com/file/d/1u2m--LONYCOyvcp76spoAP3wN3nWroROwfTtoJx9TpeeeMYY1WVNb1-KCXOk/edit?usp=sharing ) and on some of them, they seem to be designed for lower temperature operation and the lifetime of the device will be significantly reduced if you operate them at a high temperature (the limits of the device in the attached spec device, for example, is 80C.) At 95C, the hot side quickly ramps up from the cold side temp, which is starting at 95C, I've heard as much as 4x the rate of the cold side. By the time you got to 80C on the cold side, you could easily exceed 150C if your heat sink isn't able to pump that much heat that quickly. I think to ensure against damage or reduced life, you have to carefully control the amount of volatge/current applied. A feedback loop to limit applied voltage based on temp of hot side seems to be a sensible addition. I'm still trying to figure this out for a temperature controlled minielectrophoresis unit that I am designing (to be open source). [[User:Hbergeronx\|Hbergeronx]].

			:Interesting information! I knew there was some problems with the peltier elements at higher temperatures but it's good to have some numbers. One solution would be to just not switch them on at the higher temperatures. We can see how much of an effect the peltier will have above 80 C. My guess is that it will be fairly small. Another solution is to either PWM control the MOSFET, perhaps through a capacitor, or even better, to use the analog output of the microcontroller and a non-charge-pumped MOSFET to gradually control the peltier based on the temperature. We may want to do this with the heating element as well. [[User:Juul\|Juul]]


			A cheap unit becomes not so cheap if after a handful of runs, you have to fix it: not trying to imply that you haven't thought of this or to be a downer, but just raising awareness of something that only recently came to my attention.

	= Heating =		= Heating =
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	== Peltier ==		== Peltier ==
			Note: Comments moved to different section of this page: Temperature control -> Cooling.
	~~I've been looking at the specs of some Peltier chips (see https~~:~~//docs.google.com/file/d/1u2m--LONYCOyvcp76spoAP3wN3nWroROwfTtoJx9TpeeeMYY1WVNb1-KCXOk/edit?usp=sharing ) and on some of them, they seem~~ to ~~be designed for lower temperature operation and the lifetime~~ of the device will be significantly reduced if you operate them at a high temperature (the limits of the device in the attached spec device, for example, is 80C.) At 95C, the hot side quickly ramps up from the cold side temp, which is starting at 95C, I've heard as much as 4x the rate of the cold side. By the time you got to 80C on the cold side, you could easily exceed 150C if your heat sink isn't able to pump that much heat that quickly.

	I think to ensure against damage or reduced life, you have to carefully control the amount of volatge/current applied. A feedback loop to limit applied voltage based on temp of hot side seems to be a sensible addition. I'm still trying to figure this ~~out for a temperature controlled minielectrophoresis unit that I am designing (to be open source).~~
	:~~Yeah. The temperature sensor + MOSFET + microcontroller allows us this dynamic~~ control ~~:-) (also, please put three tilde characters to tag comments with your name)~~ - ~~[[User:Juul\|Juul]] ([[User talk:Juul\|talk]])~~

	A cheap unit becomes not so cheap if after a handful of runs, you have to fix it: not trying to imply that you haven't thought of this or to be a downer, but just raising awareness of something that only recently came to my attention.

	== MOSFETs ==		== MOSFETs ==

Juul: /* Peltier */

2013-02-16T22:44:50Z

Peltier

← Older revision		Revision as of 15:44, 16 February 2013
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	I've been looking at the specs of some Peltier chips (see https://docs.google.com/file/d/1u2m--LONYCOyvcp76spoAP3wN3nWroROwfTtoJx9TpeeeMYY1WVNb1-KCXOk/edit?usp=sharing ) and on some of them, they seem to be designed for lower temperature operation and the lifetime of the device will be significantly reduced if you operate them at a high temperature (the limits of the device in the attached spec device, for example, is 80C.) At 95C, the hot side quickly ramps up from the cold side temp, which is starting at 95C, I've heard as much as 4x the rate of the cold side. By the time you got to 80C on the cold side, you could easily exceed 150C if your heat sink isn't able to pump that much heat that quickly.		I've been looking at the specs of some Peltier chips (see https://docs.google.com/file/d/1u2m--LONYCOyvcp76spoAP3wN3nWroROwfTtoJx9TpeeeMYY1WVNb1-KCXOk/edit?usp=sharing ) and on some of them, they seem to be designed for lower temperature operation and the lifetime of the device will be significantly reduced if you operate them at a high temperature (the limits of the device in the attached spec device, for example, is 80C.) At 95C, the hot side quickly ramps up from the cold side temp, which is starting at 95C, I've heard as much as 4x the rate of the cold side. By the time you got to 80C on the cold side, you could easily exceed 150C if your heat sink isn't able to pump that much heat that quickly.

	I think to ensure against damage or reduced life, you have to carefully control the amount of volatge/current applied. A feedback loop to limit applied voltage based on temp of hot side seems to be a sensible addition. I'm still trying to figure this out for a temperature controlled minielectrophoresis unit that I am designing (to be open source). A cheap unit becomes not so cheap if after a handful of runs, you have to fix it: not trying to imply that you haven't thought of this or to be a downer, but just raising awareness of something that only recently came to my attention.		I think to ensure against damage or reduced life, you have to carefully control the amount of volatge/current applied. A feedback loop to limit applied voltage based on temp of hot side seems to be a sensible addition. I'm still trying to figure this out for a temperature controlled minielectrophoresis unit that I am designing (to be open source).
			:Yeah. The temperature sensor + MOSFET + microcontroller allows us this dynamic control :-) (also, please put three tilde characters to tag comments with your name) - [[User:Juul\|Juul]] ([[User talk:Juul\|talk]])

			A cheap unit becomes not so cheap if after a handful of runs, you have to fix it: not trying to imply that you haven't thought of this or to be a downer, but just raising awareness of something that only recently came to my attention.

	== MOSFETs ==		== MOSFETs ==

Hbergeronx: /* Documentation */

2013-02-16T19:06:19Z

Documentation

← Older revision		Revision as of 12:06, 16 February 2013
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	= Documentation =		= Documentation =

			== Peltier ==

			I've been looking at the specs of some Peltier chips (see https://docs.google.com/file/d/1u2m--LONYCOyvcp76spoAP3wN3nWroROwfTtoJx9TpeeeMYY1WVNb1-KCXOk/edit?usp=sharing ) and on some of them, they seem to be designed for lower temperature operation and the lifetime of the device will be significantly reduced if you operate them at a high temperature (the limits of the device in the attached spec device, for example, is 80C.) At 95C, the hot side quickly ramps up from the cold side temp, which is starting at 95C, I've heard as much as 4x the rate of the cold side. By the time you got to 80C on the cold side, you could easily exceed 150C if your heat sink isn't able to pump that much heat that quickly.

			I think to ensure against damage or reduced life, you have to carefully control the amount of volatge/current applied. A feedback loop to limit applied voltage based on temp of hot side seems to be a sensible addition. I'm still trying to figure this out for a temperature controlled minielectrophoresis unit that I am designing (to be open source). A cheap unit becomes not so cheap if after a handful of runs, you have to fix it: not trying to imply that you haven't thought of this or to be a downer, but just raising awareness of something that only recently came to my attention.

	== MOSFETs ==		== MOSFETs ==

Juul: /* Fans and heatsinks */

2013-02-16T05:31:04Z

Fans and heatsinks

← Older revision		Revision as of 22:31, 15 February 2013
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	== Fans and heatsinks ==		== Fans and heatsinks ==

	5 or 12 vdc 5x5 cm.		Should be 5 or 12 vdc 5x5 cm. We should use standard CPU coolers since they are cheap an easy to find, which is important since this is the only moving part in the PCR machine and will likely need to be replaced at some point by the user.

	*[http://www.digikey.com/product-detail/en/KDE1205PHV2%20MS.A.GN/259-1357-ND/1021206 $4 fan from digikey] (drops to $2.90 for 100).		*[http://www.digikey.com/product-detail/en/KDE1205PHV2%20MS.A.GN/259-1357-ND/1021206 $4 fan from digikey] - no heatsink included (drops to $2.90 for 100).
	*[https://www.sparkfun.com/products/9648 $5 fan from sparkfun		*[https://www.sparkfun.com/products/9648 $5 fan from sparkfun] - no heatsink.
	*Fan with built in heatsink for $6.20 [http://www.google.com/shopping/product/13394255327842041335?q=cpu%20fan&hl=en&psj=1&bav=on.2,or.r_gc.r_pw.r_qf.&bvm=bv.42261806,d.cGE&biw=1024&bih=613&sa=X&ei=SvkZUamMBaKsjAKMhYDwAQ&ved=0CH8Q8wIwAA&prds=scoring:tp via google]		*Fan with built in heatsink for $6.20 [http://www.google.com/shopping/product/13394255327842041335?q=cpu%20fan&hl=en&psj=1&bav=on.2,or.r_gc.r_pw.r_qf.&bvm=bv.42261806,d.cGE&biw=1024&bih=613&sa=X&ei=SvkZUamMBaKsjAKMhYDwAQ&ved=0CH8Q8wIwAA&prds=scoring:tp via google]
	*Fan with built in heatsink, but a bit too big for $5.00 [http://www.outletpc.com/c1987.html?utm_source=c1987&utm_medium=shopping%2Bengine&utm_campaign=googleproducts via outletpc.com]		*Fan with built in heatsink, but a bit too big for $5.00 [http://www.outletpc.com/c1987.html?utm_source=c1987&utm_medium=shopping%2Bengine&utm_campaign=googleproducts via outletpc.com]
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	Assuming the fans are 12 volts, the NPN 2N3904 can be used (but it's max 200 mA) [https://www.sparkfun.com/products/521 via sparkfun] at $0.75 but they're less than 10 cents at 100x.		Assuming the fans are 12 volts, the NPN 2N3904 can be used (but it's max 200 mA) [https://www.sparkfun.com/products/521 via sparkfun] at $0.75 but they're less than 10 cents at 100x.


	= Power supply =		= Power supply =

Juul at 05:26, 16 February 2013

2013-02-16T05:26:34Z

← Older revision		Revision as of 22:26, 15 February 2013
Line 3:		Line 3:

	The current target for the entire kit is $300 (PCR, centrifuge, shaking incubator, gel electrophoresis box, micropipette + chemistry/biology/plastics for 3+ experiments). This may turn out to be too low for the first run, but we're aiming at making this as affordable as possible while maintaining a quality that's good enough for day-to-day citizen science work.		The current target for the entire kit is $300 (PCR, centrifuge, shaking incubator, gel electrophoresis box, micropipette + chemistry/biology/plastics for 3+ experiments). This may turn out to be too low for the first run, but we're aiming at making this as affordable as possible while maintaining a quality that's good enough for day-to-day citizen science work.

			= Bill of materials and pricing =

			*[https://docs.google.com/spreadsheet/ccc?key=0Akog0JI0-bB9dDA0cTRLWFhlTkVOdGdhSUN4SE5NVEE&usp=sharing#gid=2 Order list for prototype materials]
			:Our initial prototype order. Based on aluminum block PCR tube holder. Does not include case.
			*[https://docs.google.com/spreadsheet/ccc?key=0Akog0JI0-bB9dDA0cTRLWFhlTkVOdGdhSUN4SE5NVEE&usp=sharing#gid=1 Pricing for between 100 and 500 units unit].
			:Some prices estimated. Not including taxes and shipping.

	= PCR tube holder =		= PCR tube holder =

Juul at 05:12, 16 February 2013

2013-02-16T05:12:14Z

Show changes

Juul: /* Possible materials */

2013-02-12T08:06:05Z

Possible materials

← Older revision		Revision as of 01:06, 12 February 2013
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	*[http://www.mcmaster.com/#standard-aluminum-sheets/=lfqnfz Aluminum bars from McMaster-Carr]		*[http://www.mcmaster.com/#standard-aluminum-sheets/=lfqnfz Aluminum bars from McMaster-Carr]
	:1 cm x 4 cm x 6 feet for $35 (enough for 45 4x4 cm tube holders)		:1 cm x 4 cm x 6 feet for $35 (enough for 45 4x4 cm tube holders)
	:1 cm x 4 cm x 6 feet for $44 (enough for 36 5x5 cm tube holders)		:1 cm x 5 cm x 6 feet for $44 (enough for 36 5x5 cm tube holders)
	:1 cm x 2.5 cm x 6 feet for $23		:1 cm x 2.5 cm x 6 feet for $23

Juul: /* Useful links */

2013-02-12T00:14:56Z

Useful links

← Older revision		Revision as of 17:14, 11 February 2013
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	== Useful links ==		== Useful links ==
			*[http://hackteria.org/wiki/index.php/Jugaad_PCR_Thermocyclers Hackteria PCR notes]

	* [http://openwetware.org/wiki/DIYbio:Notebook/Open_Thermal_Cycler DIYbio:Notebook/Open Thermal Cycler]		* [http://openwetware.org/wiki/DIYbio:Notebook/Open_Thermal_Cycler DIYbio:Notebook/Open Thermal Cycler]
	* [http://russelldurrett.com/lightbulbpcr.html The Light Bulb PCR Machine]		* [http://russelldurrett.com/lightbulbpcr.html The Light Bulb PCR Machine]