BME103:T930 Group 6 - Revision history

Amanda Noel Sweig: Undo revision 655873 by Amanda Noel Sweig (Talk)

Amanda Noel Sweig — Thu, 15 Nov 2012 06:35:18 GMT

Undo revision 655873 by Amanda Noel Sweig (Talk)

←Older revision		Revision as of 06:35, 15 November 2012
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	[[Image:Calfthymus2.jpg\|300px\|thumb\|Calf Thymus DNA Test]]		[[Image:Calfthymus2.jpg\|300px\|thumb\|Calf Thymus DNA Test]]

-		+	<!--- Enter the values from your group's Data Analyzer table below. E6, F6, etc. are the excel cells from which you should copy your data. --->
		+	{\| {{table}}
	\|- style="background:#f0f0f0;"		\|- style="background:#f0f0f0;"
	\| '''Sample''' \|\| '''Integrated Density''' \|\| '''DNA μg/mL''' \|\| '''Conclusion'''		\| '''Sample''' \|\| '''Integrated Density''' \|\| '''DNA μg/mL''' \|\| '''Conclusion'''

Amanda Noel Sweig: /* Results */

Amanda Noel Sweig — Thu, 15 Nov 2012 06:33:27 GMT

Results

←Older revision		Revision as of 06:33, 15 November 2012
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	[[Image:Calfthymus2.jpg\|300px\|thumb\|Calf Thymus DNA Test]]		[[Image:Calfthymus2.jpg\|300px\|thumb\|Calf Thymus DNA Test]]

-	~~<!--- Enter the values from your group's Data Analyzer table below. E6, F6, etc. are the excel cells from which you should copy your data. --->~~	+
-	~~{\| {{table}}~~	+
	\|- style="background:#f0f0f0;"		\|- style="background:#f0f0f0;"
	\| '''Sample''' \|\| '''Integrated Density''' \|\| '''DNA μg/mL''' \|\| '''Conclusion'''		\| '''Sample''' \|\| '''Integrated Density''' \|\| '''DNA μg/mL''' \|\| '''Conclusion'''

Amanda Noel Sweig: /* Protocols */

Amanda Noel Sweig — Thu, 15 Nov 2012 06:31:25 GMT

Protocols

←Older revision		Revision as of 06:31, 15 November 2012
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-	'''~~Flourimeter~~ Measurements'''<br>	+	'''Fluorometer Measurements'''<br>

-	[[Image:Biosetup.jpg\|250px\|thumb\|Assembled ~~Flourimeter~~]]	+	[[Image:Biosetup.jpg\|250px\|thumb\|Assembled Fluorometer]]

-	''~~Flourimeter~~ Assembly Procedure''	+	''Fluorometer Assembly Procedure''

	1. Remove lid from black box and invert the box, open the front flap.		1. Remove lid from black box and invert the box, open the front flap.

Alexandra Nazareno: /* Results */

Alexandra Nazareno — Thu, 15 Nov 2012 05:46:40 GMT

Results

←Older revision		Revision as of 05:46, 15 November 2012
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	* '''Integrated Density''' = Integrated density is sum of the values of the pixels in the selected image on ImageJ. In this case, the selected area was the DNA mixture and SYBR Green, and each pixel was given a value. These values of all the pixels in the image were added together to determine the integrated density.		* '''Integrated Density''' = Integrated density is sum of the values of the pixels in the selected image on ImageJ. In this case, the selected area was the DNA mixture and SYBR Green, and each pixel was given a value. These values of all the pixels in the image were added together to determine the integrated density.
	* '''DNA μg/mL''' = The DNA concentration (in micro grams per milliliter) was determined by dividing the integrated density of the given sample by the integrated density of the calf thymus, then multiplying that quotient by two.		* '''DNA μg/mL''' = The DNA concentration (in micro grams per milliliter) was determined by dividing the integrated density of the given sample by the integrated density of the calf thymus, then multiplying that quotient by two.
-	* '''Conclusion''' = ~~based~~ on the DNA concentration, whether or not the patient sample contained the cancer gene sequence. Positive ~~indicates the presence of~~ the gene, while negative means there is no ~~suuch~~ gene was detected.	+	* '''Conclusion''' = Based on the DNA concentration, the conclusion indicates whether or not the patient sample contained the cancer gene sequence. Positive means the gene was present, while negative means there is no such gene was detected.

Alexandra Nazareno: /* Research and Development */

Alexandra Nazareno — Thu, 15 Nov 2012 05:42:50 GMT

Research and Development

←Older revision		Revision as of 05:42, 15 November 2012
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	Relation to Bayes' Rule:		Relation to Bayes' Rule:
-	Bayers' rule is used to determine the probability of true positives, false positives, and false negatives to predict the reliability of the process in detecting the cancer sequence in patients.	+	Bayers' rule is used to determine the probability of true positives, false positives, and false negatives to predict the reliability of the process in detecting the cancer sequence in patients.<br<

-	P(A\|B) = P(B\|A)P(A) / P(B)	+	The equation for Bayes' Rule is '''P(A\|B) = P(B\|A)P(A) / P(B)''', wherein '''P(A)''' represents the initial belief in the occurrence of A, '''P(A\|B)''' represents the degree of belief in A with regards to B, an known factor, and '''P(B\|A) / P(B)''' represents the support B has for A.

	<br><br>		<br><br>

Alexandra Nazareno: /* Research and Development */

Alexandra Nazareno — Thu, 15 Nov 2012 05:35:39 GMT

Research and Development

←Older revision		Revision as of 05:35, 15 November 2012
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	* Since the primer is purposely selected to bind to the specific sequence of nucleotides that makes up the cancer gene, if the cancer gene is not present in the DNA, then the primers will not attach to the seperated DNA strands and replication will not take place, resulting in a negative result. However, if the cancer gene is present then the primers will attach and Taq Polymerase will begin the replication creating an exponential copies of the desired gene resulting in a positive result.		* Since the primer is purposely selected to bind to the specific sequence of nucleotides that makes up the cancer gene, if the cancer gene is not present in the DNA, then the primers will not attach to the seperated DNA strands and replication will not take place, resulting in a negative result. However, if the cancer gene is present then the primers will attach and Taq Polymerase will begin the replication creating an exponential copies of the desired gene resulting in a positive result.

-	Relation to ~~Bayers~~' Rule:	+	Relation to Bayes' Rule:
	Bayers' rule is used to determine the probability of true positives, false positives, and false negatives to predict the reliability of the process in detecting the cancer sequence in patients.		Bayers' rule is used to determine the probability of true positives, false positives, and false negatives to predict the reliability of the process in detecting the cancer sequence in patients.

		+	P(A\|B) = P(B\|A)P(A) / P(B)

	<br><br>		<br><br>

Alexandra Nazareno: /* Results */

Alexandra Nazareno — Thu, 15 Nov 2012 04:09:51 GMT

Results

←Older revision		Revision as of 04:09, 15 November 2012
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	* '''Sample''' = A sample is small collection of information regarding the area being researched. For this experiment, the sample was small fragments of DNA from two patients and a positive and negative control to test for a cancer gene.		* '''Sample''' = A sample is small collection of information regarding the area being researched. For this experiment, the sample was small fragments of DNA from two patients and a positive and negative control to test for a cancer gene.
	* '''Integrated Density''' = Integrated density is sum of the values of the pixels in the selected image on ImageJ. In this case, the selected area was the DNA mixture and SYBR Green, and each pixel was given a value. These values of all the pixels in the image were added together to determine the integrated density.		* '''Integrated Density''' = Integrated density is sum of the values of the pixels in the selected image on ImageJ. In this case, the selected area was the DNA mixture and SYBR Green, and each pixel was given a value. These values of all the pixels in the image were added together to determine the integrated density.
-	* '''DNA μg/mL''' = ~~<!--- how you calculated this --->~~	+	* '''DNA μg/mL''' = The DNA concentration (in micro grams per milliliter) was determined by dividing the integrated density of the given sample by the integrated density of the calf thymus, then multiplying that quotient by two.
-	* '''Conclusion''' = ~~<!--- explain~~	+	* '''Conclusion''' = based on the DNA concentration, whether or not the patient sample contained the cancer gene sequence. Positive indicates the presence of the gene, while negative means there is no suuch gene was detected.

Alexandra Nazareno: /* Initial Machine Testing */

Alexandra Nazareno — Thu, 15 Nov 2012 03:54:54 GMT

Initial Machine Testing

←Older revision		Revision as of 03:54, 15 November 2012
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	'''The Original Design'''<br>		'''The Original Design'''<br>
	The OpenPCR is an enclosed DNA processing and replication tool. It uses cycles of heating and cooling to replicate the desired DNA. The heating unit, LED controls, and all processing components are encased in a wooden box. A hinged lid covers and insulates the DNA heating plate to facilitate the replication process.<br>		The OpenPCR is an enclosed DNA processing and replication tool. It uses cycles of heating and cooling to replicate the desired DNA. The heating unit, LED controls, and all processing components are encased in a wooden box. A hinged lid covers and insulates the DNA heating plate to facilitate the replication process.<br>
-	[[Image:Labeled OpenPCR.png\|300px\|thumb\|Open PCR]]	+	[[Image:Labeled OpenPCR.png\|300px\|thumb\|Open PCR Machine]]

	'''Experimenting With the Connections'''<br>		'''Experimenting With the Connections'''<br>

Alexandra Nazareno: /* Initial Machine Testing */

Alexandra Nazareno — Thu, 15 Nov 2012 03:54:29 GMT

Initial Machine Testing

←Older revision		Revision as of 03:54, 15 November 2012
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	'''The Original Design'''<br>		'''The Original Design'''<br>
	The OpenPCR is an enclosed DNA processing and replication tool. It uses cycles of heating and cooling to replicate the desired DNA. The heating unit, LED controls, and all processing components are encased in a wooden box. A hinged lid covers and insulates the DNA heating plate to facilitate the replication process.<br>		The OpenPCR is an enclosed DNA processing and replication tool. It uses cycles of heating and cooling to replicate the desired DNA. The heating unit, LED controls, and all processing components are encased in a wooden box. A hinged lid covers and insulates the DNA heating plate to facilitate the replication process.<br>
-	[[Image:~~Open_PCR_Screenshot~~.png\|300px\|thumb\|Open PCR]]	+	[[Image:Labeled OpenPCR.png\|300px\|thumb\|Open PCR]]

	'''Experimenting With the Connections'''<br>		'''Experimenting With the Connections'''<br>
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	<br><br>		<br><br>
		+
	==Protocols==		==Protocols==

Nicholas Sterkowitz: /* OUR TEAM */

Nicholas Sterkowitz — Thu, 15 Nov 2012 02:47:22 GMT

OUR TEAM

←Older revision		Revision as of 02:47, 15 November 2012
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	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[Image:~~BME103student~~.~~jpg~~\|100px\|thumb\|Name: Nicholas Sterkowitz<br>Open PCR machine engineer]]	+	\| [[Image:Snapshot_20121114.JPG\|100px\|thumb\|Name: Nicholas Sterkowitz<br>Open PCR machine engineer]]
	\| [[Image:D.jpg‎\|100px\|thumb\|Name: Dominic Ilardi<br>Open PCR machine engineer]]		\| [[Image:D.jpg‎\|100px\|thumb\|Name: Dominic Ilardi<br>Open PCR machine engineer]]
	\| [[Image:new_york.jpg\|100px\|thumb\|Name: Alexandra Nazareno<br>Experimental Protocol Planner]]		\| [[Image:new_york.jpg\|100px\|thumb\|Name: Alexandra Nazareno<br>Experimental Protocol Planner]]

←Older revision		Revision as of 02:47, 15 November 2012
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	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[Image:~~BME103student~~.~~jpg~~\|100px\|thumb\|Name: Nicholas Sterkowitz<br>Open PCR machine engineer]]	+	\| [[Image:Snapshot_20121114.JPG\|100px\|thumb\|Name: Nicholas Sterkowitz<br>Open PCR machine engineer]]
	\| [[Image:D.jpg‎\|100px\|thumb\|Name: Dominic Ilardi<br>Open PCR machine engineer]]		\| [[Image:D.jpg‎\|100px\|thumb\|Name: Dominic Ilardi<br>Open PCR machine engineer]]
	\| [[Image:new_york.jpg\|100px\|thumb\|Name: Alexandra Nazareno<br>Experimental Protocol Planner]]		\| [[Image:new_york.jpg\|100px\|thumb\|Name: Alexandra Nazareno<br>Experimental Protocol Planner]]