2020(S09) Lecture:week 10 - Revision history

Nkuldell at 16:11, 16 April 2009

Nkuldell — Thu, 16 Apr 2009 16:11:29 GMT

←Older revision		Revision as of 16:11, 16 April 2009
Line 105:		Line 105:
	After the challenge, we'll consider the following questions:		After the challenge, we'll consider the following questions:
	#Was it easy or difficult to license parts?		#Was it easy or difficult to license parts?
		+	*hard to license parts, wanted more $, limited # of patents to be had, competition for same parts,
	#What determined the value of a part? Did inventors tend to overvalue parts? Did investors tend to undervalue parts?		#What determined the value of a part? Did inventors tend to overvalue parts? Did investors tend to undervalue parts?
		+	*cost of production
		+	*how much the investor wanted
		+	*knowing how much the completed system is worth would have helped value the parts
		+	*if there's no other competition
		+
	#Were any parts licensed for free? Why?		#Were any parts licensed for free? Why?
		+	*no...but for the good of the many
	#The challenge system in today's class contained 12 parts. Would it be easier or more difficult to license the parts for a system that contained fewer parts (e.g., 3 parts)? What about more parts (e.g., 100 parts)?		#The challenge system in today's class contained 12 parts. Would it be easier or more difficult to license the parts for a system that contained fewer parts (e.g., 3 parts)? What about more parts (e.g., 100 parts)?
		+	*fewer parts easier...because it would drive down costs
		+	*or harder if more competitive
		+	*how many own enzymes or parts
		+	*net benefit
	#In the "real world" deals are often brokered between the same parties more than once...this year you have a deal for Eau d'coli, next year for something else. How would the fact that you may have to deal with the investor/inventor again change the dynamic of today's challenge?		#In the "real world" deals are often brokered between the same parties more than once...this year you have a deal for Eau d'coli, next year for something else. How would the fact that you may have to deal with the investor/inventor again change the dynamic of today's challenge?
		+	* I told other investors about existing deals...
		+	* inventor set minimum price
		+	*
	</div>		</div>
	\|}		\|}

Nkuldell: /* If you are an INVESTOR */

Nkuldell — Tue, 14 Apr 2009 01:53:13 GMT

If you are an INVESTOR

←Older revision		Revision as of 01:53, 14 April 2009
Line 108:		Line 108:
	#Were any parts licensed for free? Why?		#Were any parts licensed for free? Why?
	#The challenge system in today's class contained 12 parts. Would it be easier or more difficult to license the parts for a system that contained fewer parts (e.g., 3 parts)? What about more parts (e.g., 100 parts)?		#The challenge system in today's class contained 12 parts. Would it be easier or more difficult to license the parts for a system that contained fewer parts (e.g., 3 parts)? What about more parts (e.g., 100 parts)?
		+	#In the "real world" deals are often brokered between the same parties more than once...this year you have a deal for Eau d'coli, next year for something else. How would the fact that you may have to deal with the investor/inventor again change the dynamic of today's challenge?
	</div>		</div>
	\|}		\|}

Nkuldell: /* If you are an INVESTOR */

Nkuldell — Tue, 14 Apr 2009 01:43:25 GMT

If you are an INVESTOR

←Older revision		Revision as of 01:43, 14 April 2009
Line 91:		Line 91:
	===If you are an <font color = purple> INVESTOR </font color>===		===If you are an <font color = purple> INVESTOR </font color>===
	*Each investor is seeking to license the complete set of genetic parts needed to encode the Eau d'coli system.		*Each investor is seeking to license the complete set of genetic parts needed to encode the Eau d'coli system.
-	*The '''first''' investor who is able to acquire licenses for all the genetic parts needed to encode the full Eau d'coli system will earn '''real cash money'''!! The pay out will be told to ~~you~~ but should '''not''' be shared with the patent holders.	+	*The '''first''' investor who is able to acquire licenses for all the genetic parts needed to encode the full Eau d'coli system will earn '''real cash money'''!! The pay out will be told to the investor group but should '''not''' be shared with the inventors and patent holders.
	*The winning investor (if any) will be required to pay all inventors whatever fees might have been negotiated in obtaining the rights to use various genetic parts.		*The winning investor (if any) will be required to pay all inventors whatever fees might have been negotiated in obtaining the rights to use various genetic parts.
	*If the promised fees are less than the pay out then the investor can keep any additional cash (really).		*If the promised fees are less than the pay out then the investor can keep any additional cash (really).

Nkuldell: /* Week 10 Thursday */

Nkuldell — Tue, 14 Apr 2009 01:42:16 GMT

Week 10 Thursday

←Older revision		Revision as of 01:42, 14 April 2009
Line 65:		Line 65:

	=<center>Week 10 Thursday</center>=		=<center>Week 10 Thursday</center>=
-	<center>This challenge was originally developed and written by [[Drew Endy]]</center>	+	<center>This challenge was originally developed and written by [[Drew Endy]], then modified with help from Scott Kuldell</center>
	==<font color = blue>Ownership and Sharing Challenge</font color>==		==<font color = blue>Ownership and Sharing Challenge</font color>==
	Many useful genetic parts are currently protected by patents. For example, "uses of green fluorescent protein" is protected by [http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=5491084.PN.&s2=chalfie.INNM.&OS=PN/5491084+AND+IN/chalfie&RS=PN/5491084+AND+IN/chalfie United States Patent #5,491,084]. At least 200 more recent patents protect additional uses of various fluorescent proteins. Patents are a legislated form of "intellectual property" by which inventors are granted a limited-time monopoly (~17 years) during which they can control access to the patented technology (e.g., by selling exclusive or non-exclusive licenses). In establishing the U.S. patent system, the founders of our country wanted to balance the sharing of inventions (e.g., via the publishing of patent applications) while also encouraging the investment and profit needed to drive innovation.		Many useful genetic parts are currently protected by patents. For example, "uses of green fluorescent protein" is protected by [http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=5491084.PN.&s2=chalfie.INNM.&OS=PN/5491084+AND+IN/chalfie&RS=PN/5491084+AND+IN/chalfie United States Patent #5,491,084]. At least 200 more recent patents protect additional uses of various fluorescent proteins. Patents are a legislated form of "intellectual property" by which inventors are granted a limited-time monopoly (~17 years) during which they can control access to the patented technology (e.g., by selling exclusive or non-exclusive licenses). In establishing the U.S. patent system, the founders of our country wanted to balance the sharing of inventions (e.g., via the publishing of patent applications) while also encouraging the investment and profit needed to drive innovation.

Nkuldell at 01:41, 14 April 2009

Nkuldell — Tue, 14 Apr 2009 01:41:36 GMT

Nkuldell: /* If you are an INVESTOR */

Nkuldell — Mon, 13 Apr 2009 18:02:21 GMT

If you are an INVESTOR

←Older revision		Revision as of 18:02, 13 April 2009
Line 93:		Line 93:
	*The winning investor (if any) will be required to pay all inventors whatever fees might have been negotiated in obtaining the rights to use various genetic parts.		*The winning investor (if any) will be required to pay all inventors whatever fees might have been negotiated in obtaining the rights to use various genetic parts.
	*If the promised fees are less than $100 then the investor can keep any additional cash (really).		*If the promised fees are less than $100 then the investor can keep any additional cash (really).
-	*If the promised fees are greater than $100 then the investor must pay all additional licensing fees out of their own cash reserves. (~~not~~ really~~...~~it would be better to re-negotiate your licensing deals).	+	*If the promised fees are greater than $100 then the investor must pay all additional licensing fees out of their own cash reserves. (really, but it would be better to re-negotiate your licensing deals than to have this challenge cost you $$).
	<center>		<center>
	'''Good luck and, perhaps, great profits!'''		'''Good luck and, perhaps, great profits!'''

Nkuldell: /* If you are an INVENTOR */

Nkuldell — Mon, 13 Apr 2009 16:28:41 GMT

If you are an INVENTOR

←Older revision		Revision as of 16:28, 13 April 2009
Line 76:		Line 76:
	* Be aware that there are 12 components needed to produce a full Eau d'coli system, namely:		* Be aware that there are 12 components needed to produce a full Eau d'coli system, namely:
	#A genetically encoded "inverter"		#A genetically encoded "inverter"
-	#A "constitutive ~~PoPS source~~"	+	#A "constitutive promoter"
-	#A "stationary phase ~~PoPS source~~"	+	#A "stationary phase promoter"
	#A "transcription terminator"		#A "transcription terminator"
	#A "weak ribosome binding site"		#A "weak ribosome binding site"

Nkuldell: /* Week 10 Thursday */

Nkuldell — Mon, 13 Apr 2009 15:47:50 GMT

Week 10 Thursday

←Older revision		Revision as of 15:47, 13 April 2009
Line 65:		Line 65:

	=<center>Week 10 Thursday</center>=		=<center>Week 10 Thursday</center>=
		+	<center>This challenge was originally developed and written by [[Drew Endy]]</center>
	==<font color = blue>Ownership and Sharing Challenge</font color>==		==<font color = blue>Ownership and Sharing Challenge</font color>==
	Many useful genetic parts are currently protected by patents. For example, "uses of green fluorescent protein" is protected by [http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=5491084.PN.&s2=chalfie.INNM.&OS=PN/5491084+AND+IN/chalfie&RS=PN/5491084+AND+IN/chalfie United States Patent #5,491,084]. At least 200 more recent patents protect additional uses of various fluorescent proteins. Patents are a legislated form of "intellectual property" by which inventors are granted a limited-time monopoly (~17 years) during which they can control access to the patented technology (e.g., by selling exclusive or non-exclusive licenses). In establishing the U.S. patent system, the founders of our country wanted to balance the sharing of inventions (e.g., via the publishing of patent applications) while also encouraging the investment and profit needed to drive innovation.		Many useful genetic parts are currently protected by patents. For example, "uses of green fluorescent protein" is protected by [http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO2&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&co1=AND&d=PTXT&s1=5491084.PN.&s2=chalfie.INNM.&OS=PN/5491084+AND+IN/chalfie&RS=PN/5491084+AND+IN/chalfie United States Patent #5,491,084]. At least 200 more recent patents protect additional uses of various fluorescent proteins. Patents are a legislated form of "intellectual property" by which inventors are granted a limited-time monopoly (~17 years) during which they can control access to the patented technology (e.g., by selling exclusive or non-exclusive licenses). In establishing the U.S. patent system, the founders of our country wanted to balance the sharing of inventions (e.g., via the publishing of patent applications) while also encouraging the investment and profit needed to drive innovation.

-	For today's challenge, ~~many of your classmates~~ will act as the inventors and patent holders of various genetic parts~~; each patent holder may license the use of their patents for profit (exclusively~~ or ~~non-exclusively), or give away~~ the ~~rights for free. Other classmates will act as~~ investors ~~who are seeking~~ to ~~license the complete set of genetic parts needed to encode the now familiar Eau d'E.coli~~ system.	+	For today's challenge, you will act as EITHER the inventors and patent holders of various genetic parts or the investors hoping to assemble and earn $ off a completed system.

-	~~The first investor who is able~~ to ~~acquire licenses for all the genetic parts needed to encode the full Eau d'E~~.~~coli system~~ will ~~earn '''$100 in real cash~~ money~~.''' This winning investor (if any)~~ will be ~~required to pay all inventors whatever fees might have been negotiated in obtaining~~ the ~~rights to use various genetic parts. If~~ the ~~promised fees are less than $100 then~~ the investor ~~can keep any additional cash~~. If the ~~promised fees are greater than $100 then the investor must pay all additional licensing fees out~~ of their ~~own cash reserves~~.	+	===If you are an <font color = purple> INVENTOR </font color>===
-		+	* Each inventor holds a patent that will cost either $1 or $5 to secure. You will have to "pay" this money up front and will be reimbursed at the end of the day, either by the investor who will want to license your technology or by the clients/teachers.
-	~~The~~ 12 components needed to produce a full Eau d'coli system ~~are~~:	+	* Patent holders may license the use of their patents for profit (exclusively or non-exclusively), or give away the rights for free.
		+	* Be aware that there are 12 components needed to produce a full Eau d'coli system, namely:
	#A genetically encoded "inverter"		#A genetically encoded "inverter"
	#A "constitutive PoPS source"		#A "constitutive PoPS source"
Line 86:		Line 88:
	#The gene encoding the "THI3" enzyme		#The gene encoding the "THI3" enzyme

-	Good luck and, perhaps, great profits!	+	===If you are an <font color = purple> INVESTOR </font color>===
-		+	*Each investor is seeking to license the complete set of genetic parts needed to encode the Eau d'coli system.
-	After the challenge, consider the following questions:	+	*The '''first''' investor who is able to acquire licenses for all the genetic parts needed to encode the full Eau d'coli system will earn '''real cash money'''!! The pay out will be anywhere from $1 to $100 depending on what the market (i.e. the teachers) think the system is worth.
		+	*The winning investor (if any) will be required to pay all inventors whatever fees might have been negotiated in obtaining the rights to use various genetic parts.
		+	*If the promised fees are less than $100 then the investor can keep any additional cash (really).
		+	*If the promised fees are greater than $100 then the investor must pay all additional licensing fees out of their own cash reserves. (not really...it would be better to re-negotiate your licensing deals).
		+	<center>
		+	'''Good luck and, perhaps, great profits!'''
		+	</center>
		+	{\| cellspacing="2"
		+	\|- valign="top"
		+	\|width="670px" class="MainPageBG" style="border: 1px solid #336600; color: #000; background-color: #FFFFFF"\|
		+	<div style="padding: .4em .9em .9em">
		+	<center>'''Why are we doing this??'''</center>
		+	After the challenge, we'll consider the following questions:
	#Was it easy or difficult to license parts?		#Was it easy or difficult to license parts?
	#What determined the value of a part? Did inventors tend to overvalue parts? Did investors tend to undervalue parts?		#What determined the value of a part? Did inventors tend to overvalue parts? Did investors tend to undervalue parts?
	#Were any parts licensed for free? Why?		#Were any parts licensed for free? Why?
	#The challenge system in today's class contained 12 parts. Would it be easier or more difficult to license the parts for a system that contained fewer parts (e.g., 3 parts)? What about more parts (e.g., 100 parts)?		#The challenge system in today's class contained 12 parts. Would it be easier or more difficult to license the parts for a system that contained fewer parts (e.g., 3 parts)? What about more parts (e.g., 100 parts)?
		+	</div>
		+	\|}

Nkuldell: /* Week 10 Studio */

Nkuldell — Mon, 13 Apr 2009 15:34:53 GMT

Week 10 Studio

←Older revision		Revision as of 15:34, 13 April 2009
Line 61:		Line 61:
	=<center>Week 10 Studio</center>=		=<center>Week 10 Studio</center>=
	==<font color = blue>Join the Registry!</font color>==		==<font color = blue>Join the Registry!</font color>==
		+	Please designate one person from your team as the person who will request an account at the [http://partsregistry.org/Main_Page Registry of Standard Biological Parts.] The <font color = green> '''"log in/create account"''' </font color>button is in the upper right corner of the main page and the procedure for signing up should be pretty straight forward--just ignore references to "iGEM." Our group name is <font color = green> '''MIT BE 20.20--S09''' </font color> and our part range is <font color = green> '''BBa_M12000 to BBa_M12999.'''</font color> Once you have been approved as a member of our class registry group, you and your project team should identify a part that you'd like to spotlight from your project and then enter it into the Registry. See the details of this requirement [http://openwetware.org/wiki/20.20(S09):_Final_presentations here.]
	==<font color = blue> Project Redesign Day </font color>==		==<font color = blue> Project Redesign Day </font color>==
		+
	=<center>Week 10 Thursday</center>=		=<center>Week 10 Thursday</center>=
	==<font color = blue>Ownership and Sharing Challenge</font color>==		==<font color = blue>Ownership and Sharing Challenge</font color>==

Nkuldell at 15:04, 13 April 2009

Nkuldell — Mon, 13 Apr 2009 15:04:17 GMT

←Older revision		Revision as of 15:04, 13 April 2009
Line 29:		Line 29:
	The first challenge today addressed catastrophic failure--if breaking a paperclip can be called “catastrophic.” The activity makes clear how engineers can enhance reliability by anticipating then obviating failure modes. Certainly, weaknesses can be tested and quantified, leading to reliability terms such as the "MTTF" ('''M'''ean '''T'''ime '''T'''o '''F'''ailure). And certainly there are simple things to try that lengthen “MTTF” such as specifying operating conditions (“don’t repeatedly bend the open clip back and forth") or including redundant functions (“use two paper clips when in doubt”). But catastrophic failure is only one way to fail. Today’s second challenge will consider another mode of failure, namely unreliable performance. <br>		The first challenge today addressed catastrophic failure--if breaking a paperclip can be called “catastrophic.” The activity makes clear how engineers can enhance reliability by anticipating then obviating failure modes. Certainly, weaknesses can be tested and quantified, leading to reliability terms such as the "MTTF" ('''M'''ean '''T'''ime '''T'''o '''F'''ailure). And certainly there are simple things to try that lengthen “MTTF” such as specifying operating conditions (“don’t repeatedly bend the open clip back and forth") or including redundant functions (“use two paper clips when in doubt”). But catastrophic failure is only one way to fail. Today’s second challenge will consider another mode of failure, namely unreliable performance. <br>

-	The framework presented here is attributed to [http://openwetware.org/wiki/Reshma_Shetty Reshma Shetty] and the thesis work she ~~has undertaken~~ in the labs of Tom Knight and Drew Endy. She has developed a framework for characterizing transcription-based logic devices that we will modify to talk about system-level behavior.	+	The framework presented here is attributed to [http://openwetware.org/wiki/Reshma_Shetty Reshma Shetty] and the thesis work she did in the labs of Tom Knight and Drew Endy. She has developed a framework for characterizing transcription-based logic devices that we will modify to talk about system-level behavior.
		+
		+	To introduce digital devices and means for guiding reliable behavior, we'll watch the BioBuilder animation that introduces [http://biobuilder.org/device.html digital devices.]

	===Digital vs Analog Logic===		===Digital vs Analog Logic===
Line 40:		Line 42:
	[[Image:Overall MIT2006 Fullsystem.jpg]]		[[Image:Overall MIT2006 Fullsystem.jpg]]
	</center>[[Image:Analog+digitalcurves.png\|thumb\|left\|analog vs digital transfer curves]] [[Image:Thresholds vertical.png\|thumb\|right\|Thresholds for system operation]]		</center>[[Image:Analog+digitalcurves.png\|thumb\|left\|analog vs digital transfer curves]] [[Image:Thresholds vertical.png\|thumb\|right\|Thresholds for system operation]]
-	Mapping the log-to-stationary phase concentration of methylsalycilate <font color = green>(in green)</font color> to the digital transfer curve<font color = red> (in red)</font color>, you can see that activity of the green boxed wintergreen-generating device is swinging from a high value to a low value but the '''trip point''' (the input value at which the device inverts the output signal) is not precise. To impose digital logic on the analog signal, we'll have to impose '''thresholds.''' Thresholds designate a value above which the input for the device will be given a logic value = 1 and below which the logic value will = 0. ~~This idea is described in the Genetic Devices animation at [[http://biobuilder.org/device.html BioBuilder.]]~~ You'll note that the thresholds still leave some values that have unspecified consequences for the operation of the device. You'll also note that the steeper the slope of the curve, the more accurately the gated signals will perform.	+	Mapping the log-to-stationary phase concentration of methylsalycilate <font color = green>(in green)</font color> to the digital transfer curve<font color = red> (in red)</font color>, you can see that activity of the green boxed wintergreen-generating device is swinging from a high value to a low value but the '''trip point''' (the input value at which the device inverts the output signal) is not precise. To impose digital logic on the analog signal, we'll have to impose '''thresholds.''' Thresholds designate a value above which the input for the device will be given a logic value = 1 and below which the logic value will = 0. You'll note that the thresholds still leave some values that have unspecified consequences for the operation of the device. You'll also note that the steeper the slope of the curve, the more accurately the gated signals will perform.

	Please note that we have modified a framework that's useful for characterizing individual devices (e.g. sensors, logic devices, actuators) in order to describe the behavior of a system built with those devices. We've done this to help think about reliability in performance. Once your understanding of this description is solid for the system overall, it's worth thinking about the performance of each device that comprises the system and what the error rates might be for each. An example of an input/output analysis for the stationary phase sensor itself and in combination with the inverter is [http://parts.mit.edu/registry/index.php/Part:BBa_Q04401:Experience here.]		Please note that we have modified a framework that's useful for characterizing individual devices (e.g. sensors, logic devices, actuators) in order to describe the behavior of a system built with those devices. We've done this to help think about reliability in performance. Once your understanding of this description is solid for the system overall, it's worth thinking about the performance of each device that comprises the system and what the error rates might be for each. An example of an input/output analysis for the stationary phase sensor itself and in combination with the inverter is [http://parts.mit.edu/registry/index.php/Part:BBa_Q04401:Experience here.]

←Older revision		Revision as of 01:41, 14 April 2009
Line 72:		Line 72:

	===If you are an <font color = purple> INVENTOR </font color>===		===If you are an <font color = purple> INVENTOR </font color>===
-	* Each inventor holds a patent that ~~will~~ cost either $1 or $5 to secure. You will have to "pay" this money up front and will be reimbursed at the end of the day, either by the investor who will want to license your technology or by the clients/teachers.	+	* Each inventor holds a patent or two that cost either $1, $2 or $5 to secure. You will have to "pay" this money up front and will be reimbursed at the end of the day, either by the investor who will want to license your technology or by the clients/teachers.
-	* Patent holders may license the use of their patents for profit (exclusively or non-exclusively), or give away the rights for free.	+	* Patent holders may license the use of their patents for profit (exclusively or non-exclusively), or give away the rights for free
		+	* Patent holders will not know how much the final client/teachers are willing to pay for the complete Eau d'coli system
	* Be aware that there are 12 components needed to produce a full Eau d'coli system, namely:		* Be aware that there are 12 components needed to produce a full Eau d'coli system, namely:
	#A genetically encoded "inverter"		#A genetically encoded "inverter"
Line 90:		Line 91:
	===If you are an <font color = purple> INVESTOR </font color>===		===If you are an <font color = purple> INVESTOR </font color>===
	*Each investor is seeking to license the complete set of genetic parts needed to encode the Eau d'coli system.		*Each investor is seeking to license the complete set of genetic parts needed to encode the Eau d'coli system.
-	*The '''first''' investor who is able to acquire licenses for all the genetic parts needed to encode the full Eau d'coli system will earn '''real cash money'''!! The pay out will be ~~anywhere from $1~~ to ~~$100 depending on what~~ the ~~market (i~~.~~e. the teachers) think the system is worth.~~	+	*The '''first''' investor who is able to acquire licenses for all the genetic parts needed to encode the full Eau d'coli system will earn '''real cash money'''!! The pay out will be told to you but should '''not''' be shared with the patent holders.
	*The winning investor (if any) will be required to pay all inventors whatever fees might have been negotiated in obtaining the rights to use various genetic parts.		*The winning investor (if any) will be required to pay all inventors whatever fees might have been negotiated in obtaining the rights to use various genetic parts.
-	*If the promised fees are less than ~~$100~~ then the investor can keep any additional cash (really).	+	*If the promised fees are less than the pay out then the investor can keep any additional cash (really).
-	*If the promised fees are greater than ~~$100~~ then the investor must pay all additional licensing fees out of their own cash reserves. (really, but it would be better to re-negotiate your licensing deals than to have this challenge cost you $$).	+	*If the promised fees are greater than the pay out then the investor must pay all additional licensing fees out of their own cash reserves. (really, but it would be better to re-negotiate your licensing deals than to have this challenge cost you $$).
	<center>		<center>
	'''Good luck and, perhaps, great profits!'''		'''Good luck and, perhaps, great profits!'''