BME103 s2013:TEMPwu3: Difference between revisions
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=LAB | =LAB 3 WRITE-UP= | ||
==Original System: PCR Results== | ==Original System: PCR Results== | ||
'''PCR Test Results''' | |||
{| {{table}} | |||
|- | |||
| Sample Name || Ave. INTDEN* || Calculated μg/mL || Conclusion (pos/neg) | |||
|- | |||
| Positive Control || --- || --- || N/A | |||
|- | |||
| Negative Control || --- || ---|| N/A | |||
|- | |||
| Tube Label:___ Patient ID: ____ rep 1 || --- || --- || --- | |||
|- | |||
| Tube Label:___ Patient ID: ____ rep 2 || --- || --- || --- | |||
|- | |||
| Tube Label:___ Patient ID: ____ rep 3 || --- || --- || --- | |||
|- | |||
| Tube Label:___ Patient ID: ____ rep 1 || --- || --- || --- | |||
|- | |||
| Tube Label:___ Patient ID: ____ rep 2 || --- || --- || --- | |||
|- | |||
| Tube Label:___ Patient ID: ____ rep 3 || --- || --- || --- | |||
|} | |||
<nowiki>* Ave. INTDEN = Average of ImageJ integrated density values from three Fluorimeter images</nowiki> | |||
'''Bayesian Statistics'''<br> | |||
These following conditional statistics are based upon all of the DNA detection system results that were obtained in the PCR lab for 20 hypothetical patients who were diagnosed as either having cancer or not having cancer.<br> | |||
Bayes Theorem equation: P(A|B) = P(B|A) * P(A) / P(B) | |||
Calculation 1: The probability that the sample actually has the cancer DNA sequence, given a positive diagnostic signal.<br> | |||
* A = [text description] = [frequency shown as a fraction] = [final numerical value] | |||
* B = [text description] = [frequency shown as a fraction] = [final numerical value] | |||
* P (B|A) = [text description] = [frequency shown as a fraction] = [final numerical value] | |||
* '''P(A|B) = [answer]''' | |||
<br> | |||
<!-- Bonus points for Calculation 2! | |||
Calculation 2: The probability that the sample actually has a non-cancer DNA sequence, given a negative diagnostic signal.<br> | |||
* A = [text description] = [frequency shown as a fraction] = [final numerical value] | |||
* B = [text description] = [frequency shown as a fraction] = [final numerical value] | |||
* P (B|A) = [text description] = [frequency shown as a fraction] = [final numerical value] | |||
* '''P(A|B) = [answer]''' --> | |||
<br> | |||
Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence.<br> | |||
* A = [text description] = [frequency shown as a fraction] = [final numerical value] | |||
* B = [text description] = [frequency shown as a fraction] = [final numerical value] | |||
* P (B|A) = [text description] = [frequency shown as a fraction] = [final numerical value] | |||
* '''P(A|B) = [answer]''' | |||
<br> | |||
<!-- Bonus points for Calculation 4! | |||
Calculation 4: The probability that the patient will not develop cancer, given a non-cancer DNA sequence.<br> | |||
* A = [text description] = [frequency shown as a fraction] = [final numerical value] | |||
* B = [text description] = [frequency shown as a fraction] = [final numerical value] | |||
* P (B|A) = [text description] = [frequency shown as a fraction] = [final numerical value] | |||
* '''P(A|B) = [answer]''' --> | |||
<br> | |||
==New System: Design Strategy== | ==New System: Design Strategy== | ||
<!--The whole team is responsible for completing this section. This is where you get to express/ argue why certain aspects fall under Must Have, Want, Must Not Have, or Should Avoid. List the two aspects that your team picked from each category in class.--> | <!--The whole team is responsible for completing this section. This is where you get to express/ argue why certain aspects fall under Must Have, Want, Must Not Have, or Should Avoid. List the two aspects that your team picked from each category in class. You are allowed to create new aspects, as long as they are relevant to your new design.--> | ||
'''We concluded that a good system Must Have:''' | '''We concluded that a good system ''Must Have'':''' | ||
* [Must have #1 - why? short, ~4 or 5 sentences] | * [Must have #1 - why? short, ~4 or 5 sentences] | ||
* [Must have #2 - why? short, ~4 or 5 sentences] | * [Must have #2 - why? short, ~4 or 5 sentences] | ||
'''We concluded that we would | '''We concluded that we would ''Want'' a good system to have:''' | ||
* [Want #1 - why? short, ~4 or 5 sentences] | * [Want #1 - why? short, ~4 or 5 sentences] | ||
* [Want #2 - why? short, ~4 or 5 sentences | * [Want #2 - why? short, ~4 or 5 sentences] | ||
'''We concluded that a good system Must Not Have:''' | '''We concluded that a good system ''Must Not Have'':''' | ||
* [Must | * [Must Not Have #1 - why? short, ~4 or 5 sentences] | ||
* [Must | * [Must Not Have #2 - why? short, ~4 or 5 sentences] | ||
'''We concluded that a good system Should Avoid:''' | '''We concluded that a good system ''Should Avoid'':''' | ||
* [Should Avoid #1 - why? short, ~4 or 5 sentences] | * [Should Avoid #1 - why? short, ~4 or 5 sentences] | ||
* [Should Avoid #2 - why? short, ~4 or 5 sentences] | * [Should Avoid #2 - why? short, ~4 or 5 sentences] | ||
<br><br> | |||
==New System: Machine/ Device Engineering== | ==New System: Machine/ Device Engineering== | ||
Line 51: | Line 114: | ||
'''DESIGN | '''SYSTEM DESIGN'''<br> | ||
<!-- If your design goals include modifying the Open PCR machine, include an image or images from the Open PCR Solid Works 3D rendering exercise. Write a short paragraph that summarizes what your team is going to modify --> | |||
<!-- If your goal includes modifying the Fluorimeter, include a labeled image or images of the Fluorimeter. There is no Solid Works file for the Fluorimeter. Write a short paragraph that summarizes what your team is going to modify --> | |||
<!-- If your goal does not require any changes in the machinery/ devices, include labeled images of the OpenPCR machine and the Fluorimeter. Write a short paragraph that summarizes what each one of the machines does --> | |||
<!-- If your team decided to change any of the machinery, summarize | |||
'''KEY FEATURES'''<br> | |||
<!-- If your team decided to change any of the machinery/ devices, summarize the new features here and delete the '''We chose keep the devices the same as the original system''' section. --> | |||
'''We chose to include these new features''' | '''We chose to include these new features''' | ||
* Feature 1 - explanation of how this addresses any of the | * Feature 1 - explanation of how this addresses any of the specifications in the "New System: Design Strategy" section | ||
* Feature 2 - | * Feature 2 - explanation of how this addresses any of the specifications in the "New System: Design Strategy" section | ||
* Etc. | |||
[OR] | [OR] | ||
<!-- If your team decided NOT to change any of the machinery/ devices, explain why here and delete the '''We chose to include these new features''' section above--> | |||
'''We chose keep the devices the same as the original system''' | |||
* Feature 1 - explanation of how a pre-existing feature addresses any of the specifications in the "New System: Design Strategy" section | |||
* Feature 2 - explanation of how a pre-existing feature addresses any of the specifications in the "New System: Design Strategy" section | |||
* Etc. | |||
'''INSTRUCTIONS''' <br> | |||
<!-- Changing the machine will require new instructions for using the machine. Write a short step-by-step list of instructions on how to set up and use the new machine. The instructions must be specific to your new design. --> | |||
<!-- If your team decided not to change any of the machinery/ devices, write a short step-by-step list of instructions on how to set up and use each machine. You may want to consider modifying the instructions to improve ease of use. --> | |||
<br><br> | |||
==New System: Protocols== | |||
'''DESIGN''' | |||
<!-- If your team decided to change the PCR and/or the Fluorimeter imaging protocols, summarize the new approaches/ features here and delete the '''We chose keep the protocols the same as the original system''' section. --> | |||
'''We chose to include these new approaches/ features''' | |||
* Feature 1 - explanation of how this addresses any of the specifications in the "New System: Design Strategy" section | |||
* Feature 2 - explanation of how this addresses any of the specifications in the "New System: Design Strategy" section | |||
* Etc. | |||
[OR] | |||
<!-- If your team decided NOT to change any of the machinery/ devices, explain why here and delete the '''We chose to include these new features''' section above--> | |||
'''We chose keep the protocols the same as the original system''' | |||
* Feature 1 - explanation of how a pre-existing feature addresses any of the specifications in the "New System: Design Strategy" section | |||
* Feature 2 - explanation of how a pre-existing feature addresses any of the specifications in the "New System: Design Strategy" section | |||
* Etc. | |||
''' | '''MATERIALS''' | ||
<!--- Place your two tables "Supplied in the kit" and "Supplied by User" here ---> | <!--- Place your two tables "Supplied in the kit" and "Supplied by User" here ---> | ||
''' | '''PROTOCOLS''' | ||
* '''PCR Protocol''' | |||
<!-- Create a step-by-step procedure for setting up and running PCR reactions. Your instructions should include everything from adding reagents to the tubes, to programming the PCR machine and running the reaction.--> | |||
# Step 1 | |||
# Step 2 | |||
# Etc. | |||
* '''DNA Measurement and Analysis Protocol''' | |||
<!-- Create a step-by-step procedure for measuring DNA amplification in the PCR reactions. Your instructions should include everything from diluting the samples in SYBR Green, to placing the drops onto the fluorimeter (if your group is using the fluorimeter), to collecting and processing images in Image J. Don't forget to provide instructions on how to set up the calf thymus DNA samples for calibration, and how to convert INTDEN values into concentrations.---> | |||
# Step 1 | |||
# Step 2 | |||
# Etc. | |||
<br><br> | |||
==New System: Research and Development== | |||
'''BACKGROUND''' | |||
<!--- A description of the CHEK2 gene, it's associated SNP, and the cancer-related function of the gene. Use the information from your Week 13 worksheet. ---> | |||
'''DESIGN''' | |||
''' | '''Primers for PCR'''<br> | ||
<!-- If your team decided to only amplify cancer-associated DNA, list the "Cancer allele forward primer" sequence and the "Cancer allele reverse primer" sequence. Include a paragraph that explains why a disease allele will give a PCR product and the non-disease allele will not.--> | |||
<!-- | <!-- If your team chose an alternative approach to amplify the DNA, list all relevant primers. Include a paragraph that explains how your system works.--> | ||
'''Our primers address the following design needs''' | |||
* Design specification 1 - explanation of how an aspect of the primers addresses any of the specifications in the "New System: Design Strategy" section | |||
* Design specification 2 - explanation of how an aspect of the primers addresses any of the specifications in the "New System: Design Strategy" section | |||
* Etc. | |||
<br><br> | |||
==New System: Software== | |||
[THIS SECTION IS OPTIONAL. If your team has creative ideas for new software, and new software is a key component included in your new protocols, R&D, or machine design, you may describe it here. You will not receive bonus points, but a solid effort may raise your overall page layout points. If you decide not to propose new software, please delete this entire section, including the <nowiki>==New System: Software==</nowiki> header.] | |||
Latest revision as of 12:28, 11 April 2013
BME 103 Spring 2013 | Home People Lab Write-Up 1 Lab Write-Up 2 Lab Write-Up 3 Course Logistics For Instructors Photos Wiki Editing Help | |||||||||||||||||||||||||||||||||||||||||
OUR TEAMLAB 3 WRITE-UPOriginal System: PCR ResultsPCR Test Results
* Ave. INTDEN = Average of ImageJ integrated density values from three Fluorimeter images
Bayes Theorem equation: P(A|B) = P(B|A) * P(A) / P(B)
Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence.
New System: Design StrategyWe concluded that a good system Must Have:
New System: Machine/ Device EngineeringSYSTEM DESIGN
KEY FEATURES We chose to include these new features
[OR] We chose keep the devices the same as the original system
INSTRUCTIONS
New System: ProtocolsDESIGN We chose to include these new approaches/ features
[OR] We chose keep the protocols the same as the original system
PROTOCOLS
New System: Research and DevelopmentBACKGROUND
DESIGN
New System: Software[THIS SECTION IS OPTIONAL. If your team has creative ideas for new software, and new software is a key component included in your new protocols, R&D, or machine design, you may describe it here. You will not receive bonus points, but a solid effort may raise your overall page layout points. If you decide not to propose new software, please delete this entire section, including the ==New System: Software== header.]
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