Endy:Measkit draft - Revision history

Jason R. Kelly: /* Jason's Summary */

Jason R. Kelly — Wed, 17 Sep 2008 00:13:31 GMT

Jason's Summary

←Older revision		Revision as of 00:13, 17 September 2008
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	**Cells, media, polymerase per cell, et cetera		**Cells, media, polymerase per cell, et cetera

-	*Instruments could be calibrated across labs	+	*Instruments could be calibrated across labs ('''would also require controls for things like plasmid copy number since that is part of the "instrument" as well. Which would be difficult to control for.''')
	**For example, distribute purified GFP, beads, et cetera		**For example, distribute purified GFP, beads, et cetera

Jason R. Kelly: /* Jason's Summary */

Jason R. Kelly — Mon, 25 Aug 2008 03:41:55 GMT

Jason's Summary

←Older revision		Revision as of 03:41, 25 August 2008
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	*PoPS is a unit for measuring or quantifying promoter activity (and also other objects)		*PoPS is a unit for measuring or quantifying promoter activity (and also other objects)
	**PoPS is a ''derived'' or ''compound'' unit, and thus does not need a reference standard of its own (for now)		**PoPS is a ''derived'' or ''compound'' unit, and thus does not need a reference standard of its own (for now)
-	**PoPS is a 'ratio scale' as defined in the 4 classes of "On the theory of scales of measurement" (~~Stephens~~, Science, 1946) since it has an absolute zero.	+	**PoPS is a 'ratio scale' as defined in the 4 classes of "On the theory of scales of measurement" (Stevens, Science, 1946) since it has an absolute zero.

	*If we want to enable the measurement of promoter activity in PoPS then we need to provide:		*If we want to enable the measurement of promoter activity in PoPS then we need to provide:

Jason R. Kelly: /* Jason's Summary */

Jason R. Kelly — Mon, 25 Aug 2008 02:54:07 GMT

Jason's Summary

←Older revision		Revision as of 02:54, 25 August 2008
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	*PoPS is a unit for measuring or quantifying promoter activity (and also other objects)		*PoPS is a unit for measuring or quantifying promoter activity (and also other objects)
	**PoPS is a ''derived'' or ''compound'' unit, and thus does not need a reference standard of its own (for now)		**PoPS is a ''derived'' or ''compound'' unit, and thus does not need a reference standard of its own (for now)
-	**PoPS is a 'ratio scale' as defined in the 4 classes of "On the theory of scales of measurement" (Stephens, Science, 1946)	+	**PoPS is a 'ratio scale' as defined in the 4 classes of "On the theory of scales of measurement" (Stephens, Science, 1946) since it has an absolute zero.

	*If we want to enable the measurement of promoter activity in PoPS then we need to provide:		*If we want to enable the measurement of promoter activity in PoPS then we need to provide:

Jason R. Kelly: /* Jason's Summary */

Jason R. Kelly — Mon, 25 Aug 2008 02:53:36 GMT

Jason's Summary

←Older revision		Revision as of 02:53, 25 August 2008
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	*PoPS is a unit for measuring or quantifying promoter activity (and also other objects)		*PoPS is a unit for measuring or quantifying promoter activity (and also other objects)
	**PoPS is a ''derived'' or ''compound'' unit, and thus does not need a reference standard of its own (for now)		**PoPS is a ''derived'' or ''compound'' unit, and thus does not need a reference standard of its own (for now)
		+	**PoPS is a 'ratio scale' as defined in the 4 classes of "On the theory of scales of measurement" (Stephens, Science, 1946)

	*If we want to enable the measurement of promoter activity in PoPS then we need to provide:		*If we want to enable the measurement of promoter activity in PoPS then we need to provide:

Jason R. Kelly: /* Other places where parts characteristics are very dependent on conditions or where relative measurement across many conditions has proven more valuable than a single 'absolute' measurement in one condition */

Jason R. Kelly — Fri, 22 Aug 2008 18:29:04 GMT

Other places where parts characteristics are very dependent on conditions or where relative measurement across many conditions has proven more valuable than a single 'absolute' measurement in one condition

←Older revision		Revision as of 18:29, 22 August 2008
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	===Other places where parts characteristics are very dependent on conditions or where relative measurement across many conditions has proven more valuable than a single 'absolute' measurement in one condition===		===Other places where parts characteristics are very dependent on conditions or where relative measurement across many conditions has proven more valuable than a single 'absolute' measurement in one condition===
	*[http://en.wikipedia.org/wiki/Georges_Cuvier#Principle_of_correlation_of_parts Comparative anatomy?]		*[http://en.wikipedia.org/wiki/Georges_Cuvier#Principle_of_correlation_of_parts Comparative anatomy?]
-	**Today comparative anatomy has reached such a point of perfection that, after inspecting a single bone, one can often determine the class, and sometimes even the genus of the animal to which it belonged, above all if that bone belonged to the head or the limbs. ... This is because the number, direction, and shape of the bones that compose each part of an animal's body are always in a necessary relation to all the other parts, in such a way that - up to a point - one can infer the whole from any one of them and vice versa.	+	**"Today comparative anatomy has reached such a point of perfection that, after inspecting a single bone, one can often determine the class, and sometimes even the genus of the animal to which it belonged, above all if that bone belonged to the head or the limbs. ... This is because the number, direction, and shape of the bones that compose each part of an animal's body are always in a necessary relation to all the other parts, in such a way that - up to a point - one can infer the whole from any one of them and vice versa."

Jason R. Kelly: /* Other places where parts are dependent on conditions or where relative measurement across many conditions has proven more valuable than a single 'absolute' measurement in one condition */

Jason R. Kelly — Thu, 21 Aug 2008 15:03:27 GMT

Other places where parts are dependent on conditions or where relative measurement across many conditions has proven more valuable than a single 'absolute' measurement in one condition

←Older revision		Revision as of 15:03, 21 August 2008
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	**I think that the first option is likely to be the right one, but I think it could be influenced by the answer to the first question above.		**I think that the first option is likely to be the right one, but I think it could be influenced by the answer to the first question above.

-	===Other places where parts are dependent on conditions or where relative measurement across many conditions has proven more valuable than a single 'absolute' measurement in one condition===	+	===Other places where parts characteristics are very dependent on conditions or where relative measurement across many conditions has proven more valuable than a single 'absolute' measurement in one condition===
	*[http://en.wikipedia.org/wiki/Georges_Cuvier#Principle_of_correlation_of_parts Comparative anatomy?]		*[http://en.wikipedia.org/wiki/Georges_Cuvier#Principle_of_correlation_of_parts Comparative anatomy?]
	**Today comparative anatomy has reached such a point of perfection that, after inspecting a single bone, one can often determine the class, and sometimes even the genus of the animal to which it belonged, above all if that bone belonged to the head or the limbs. ... This is because the number, direction, and shape of the bones that compose each part of an animal's body are always in a necessary relation to all the other parts, in such a way that - up to a point - one can infer the whole from any one of them and vice versa.		**Today comparative anatomy has reached such a point of perfection that, after inspecting a single bone, one can often determine the class, and sometimes even the genus of the animal to which it belonged, above all if that bone belonged to the head or the limbs. ... This is because the number, direction, and shape of the bones that compose each part of an animal's body are always in a necessary relation to all the other parts, in such a way that - up to a point - one can infer the whole from any one of them and vice versa.

Jason R. Kelly at 15:02, 21 August 2008

Jason R. Kelly — Thu, 21 Aug 2008 15:02:55 GMT

←Older revision		Revision as of 15:02, 21 August 2008
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	**We could alternatively define the SPU as = 1 PoPS.		**We could alternatively define the SPU as = 1 PoPS.
	**I think that the first option is likely to be the right one, but I think it could be influenced by the answer to the first question above.		**I think that the first option is likely to be the right one, but I think it could be influenced by the answer to the first question above.
		+
		+	===Other places where parts are dependent on conditions or where relative measurement across many conditions has proven more valuable than a single 'absolute' measurement in one condition===
		+	*[http://en.wikipedia.org/wiki/Georges_Cuvier#Principle_of_correlation_of_parts Comparative anatomy?]
		+	**Today comparative anatomy has reached such a point of perfection that, after inspecting a single bone, one can often determine the class, and sometimes even the genus of the animal to which it belonged, above all if that bone belonged to the head or the limbs. ... This is because the number, direction, and shape of the bones that compose each part of an animal's body are always in a necessary relation to all the other parts, in such a way that - up to a point - one can infer the whole from any one of them and vice versa.

Endy: /* Jason's Summary */

Endy — Thu, 21 Aug 2008 00:28:54 GMT

Jason's Summary

←Older revision		Revision as of 00:28, 21 August 2008
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	***NOTE. If only the reference standard is measured, without calibration of the instrument, then differences in conditions (but not instruments) can be accounted for; this allows for measurement of relative, but not actual, promoter activities under those measurement conditions.		***NOTE. If only the reference standard is measured, without calibration of the instrument, then differences in conditions (but not instruments) can be accounted for; this allows for measurement of relative, but not actual, promoter activities under those measurement conditions.
	****Interestingly, a single measure of relative promoter activity '''may''' be a more useful or less confusing than reporting the actual activity of both the sample promoter and the reference promoters.		****Interestingly, a single measure of relative promoter activity '''may''' be a more useful or less confusing than reporting the actual activity of both the sample promoter and the reference promoters.
-	*****Stated differently, there are three options for measuring a new promoter. First, calibrate the instrument (e.g., purified GFP) and control for variation in conditions (e.g., ref promoter) thereby allowing for reporting of both promoters in actual units. Second, do not perform an instrument calibration, but only perform the conditions control, thereby only allowing for a relative measurement. Third, only perform the instrument calibration thereby allowing for reporting of activity of promoter (but only under those specific conditions).	+	*****Stated differently, there are three options for measuring a new promoter.
		+	******First, calibrate the instrument (e.g., purified GFP) and control for variation in conditions (e.g., ref promoter) thereby allowing for reporting of both promoters in both relative and actual units.
		+	******Second, do not perform an instrument calibration, but only perform the conditions control, thereby only allowing for a relative measurement.
		+	******Third, only perform the instrument calibration thereby allowing for reporting of the activity of the sample promoter in actual units (but only under those specific conditions).

	*Note, stating a seemingly obvious but subtle point, accounting for conditions only matters if one is interested in the activity of a promoter across different conditions.		*Note, stating a seemingly obvious but subtle point, accounting for conditions only matters if one is interested in the activity of a promoter across different conditions.

Endy: /* Jason's Summary */

Endy — Thu, 21 Aug 2008 00:26:17 GMT

Jason's Summary

←Older revision		Revision as of 00:26, 21 August 2008
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	****Interestingly, a single measure of relative promoter activity '''may''' be a more useful or less confusing than reporting the actual activity of both the sample promoter and the reference promoters.		****Interestingly, a single measure of relative promoter activity '''may''' be a more useful or less confusing than reporting the actual activity of both the sample promoter and the reference promoters.
	*****Stated differently, there are three options for measuring a new promoter. First, calibrate the instrument (e.g., purified GFP) and control for variation in conditions (e.g., ref promoter) thereby allowing for reporting of both promoters in actual units. Second, do not perform an instrument calibration, but only perform the conditions control, thereby only allowing for a relative measurement. Third, only perform the instrument calibration thereby allowing for reporting of activity of promoter (but only under those specific conditions).		*****Stated differently, there are three options for measuring a new promoter. First, calibrate the instrument (e.g., purified GFP) and control for variation in conditions (e.g., ref promoter) thereby allowing for reporting of both promoters in actual units. Second, do not perform an instrument calibration, but only perform the conditions control, thereby only allowing for a relative measurement. Third, only perform the instrument calibration thereby allowing for reporting of activity of promoter (but only under those specific conditions).
		+
		+	*Note, stating a seemingly obvious but subtle point, accounting for conditions only matters if one is interested in the activity of a promoter across different conditions.

	===Starting Comments===		===Starting Comments===

Endy: /* Jason's Summary */

Endy — Thu, 21 Aug 2008 00:23:17 GMT

Jason's Summary

←Older revision		Revision as of 00:23, 21 August 2008
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	**Measure a reference promoter (any promoter measured previously as described here) under current conditions in order to establish an empirical model that accounts for the effect of differences in conditions on activity.		**Measure a reference promoter (any promoter measured previously as described here) under current conditions in order to establish an empirical model that accounts for the effect of differences in conditions on activity.
	***NOTE. If only the reference standard is measured, without calibration of the instrument, then differences in conditions (but not instruments) can be accounted for; this allows for measurement of relative, but not actual, promoter activities under those measurement conditions.		***NOTE. If only the reference standard is measured, without calibration of the instrument, then differences in conditions (but not instruments) can be accounted for; this allows for measurement of relative, but not actual, promoter activities under those measurement conditions.
		+	****Interestingly, a single measure of relative promoter activity '''may''' be a more useful or less confusing than reporting the actual activity of both the sample promoter and the reference promoters.
		+	*****Stated differently, there are three options for measuring a new promoter. First, calibrate the instrument (e.g., purified GFP) and control for variation in conditions (e.g., ref promoter) thereby allowing for reporting of both promoters in actual units. Second, do not perform an instrument calibration, but only perform the conditions control, thereby only allowing for a relative measurement. Third, only perform the instrument calibration thereby allowing for reporting of activity of promoter (but only under those specific conditions).

	===Starting Comments===		===Starting Comments===