BME103 s2013:TEMPwu3

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(New System: Design Strategy)
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(Original System: PCR Results)
 
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{| {{table}}
{| {{table}}
|-
|-
-
| Sample Name || ng/mL || Conclusion (pos/neg)
+
| Sample Name || Ave. INTDEN* || Calculated μg/mL || Conclusion (pos/neg)
|-
|-
-
| Positive Control || --- || N/A
+
| Positive Control || --- || --- ||  N/A
|-
|-
-
| Negative Control || --- || N/A
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| Negative Control || --- || ---|| N/A
|-
|-
-
| Tube Label:___ Patient ID: ____ rep 1 || --- ||  
+
| Tube Label:___ Patient ID: ____ rep 1 || --- || ---  ||  ---
|-
|-
-
| Tube Label:___ Patient ID: ____ rep 2 || --- ||  
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| Tube Label:___ Patient ID: ____ rep 2 || --- || --- ||  ---
|-
|-
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| Tube Label:___ Patient ID: ____ rep 3 || --- ||  
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| Tube Label:___ Patient ID: ____ rep 3 || --- || --- ||  ---
|-
|-
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| Tube Label:___ Patient ID: ____ rep 1 || --- ||  
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| Tube Label:___ Patient ID: ____ rep 1 || --- || --- ||  ---
|-
|-
-
| Tube Label:___ Patient ID: ____ rep 2 || --- ||  
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| Tube Label:___ Patient ID: ____ rep 2 || --- || --- ||  ---
|-
|-
-
| Tube Label:___ Patient ID: ____ rep 3 || --- ||  
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| Tube Label:___ Patient ID: ____ rep 3 || --- || --- ||  ---
|}
|}
 +
<nowiki>* Ave. INTDEN = Average of ImageJ integrated density values from three Fluorimeter images</nowiki>
'''Bayesian Statistics'''<br>
'''Bayesian Statistics'''<br>
-
These statistics are based upon all of the DNA detection system results that were obtained in the PCR lab for 34 hypothetical patients who were diagnosed as either having cancer or not having cancer.<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)
Bayes Theorem equation: P(A|B) = P(B|A) * P(A) / P(B)
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==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'':'''
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-
'''DESIGN STRATEGY'''<br>
+
'''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 your 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'''
 
-
* Feature 1 - explanation of how this addresses any of the the Must Have/ Must Not Have items in the
 
-
* Feature 2 - description * Etc.
 
 +
'''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'''
 +
* 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]
[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.
-
<!-- If your team decided NOT to change any of the machinery, 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'''<br>
 
-
[Short paragraph explaining why the original system satisfies the design needs that you listed above]
 
 +
'''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. -->
-
'''DESIGN APPROACH'''
 
-
<!-- If your goal is to modify 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
 
 +
<br><br>
-
'''Instructions'''<br>
 
 +
==New System: Protocols==
-
<!--- From Week 4 exercise --->
+
'''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.
-
<br><br>
+
[OR]
-
==Protocols==
+
<!-- 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.
-
<!--- Design a new protocol based on your group's new PCR design. Make a step-by-step list of how someone should use your method
 
-
Things to consider:
 
-
How should the PCR machine be set up? Does it need to be plugged in?
 
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How many samples will fit into a single 2-hour run?
 
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How many replicates should be created per patient?
 
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What should the final volume of the reaction be?
 
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Will signal reading be integrated into the PCR machine or remain separate?
 
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If it is separate, you will need to include instructions on how to use the fluorimeter.
 
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How should the user calculate the about of signal amplified?
 
-
etc.
 
-
--->
 
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'''Materials'''
+
'''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 --->
-
'''PCR Protocol'''
+
'''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.
-
'''DNA Measurement Protocol'''
+
<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. --->
-
==Research and Development==
 
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<!--- Bonus: explain how Bayesian statistics can be used to assess the reliability of your team's method. Just write the equation using variables that are relevant to your team's new test. You do not need actual numbers --->
+
'''DESIGN'''
-
'''Background on Disease Markers'''
+
'''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.-->
-
<!--- A description of the diseases and their associated SNP's (include the database reference number and web link) --->
+
<!-- If your team chose an alternative approach to amplify the DNA, list all relevant primers. Include a paragraph that explains how your system works.-->
-
 
+
-
 
+
-
 
+
-
 
+
-
'''Primer Design'''
+
-
 
+
-
<!--- Include the sequences of your forward and reverse primers. Explain why a disease allele will give a PCR product and the non-disease allele will not. --->
+
 +
'''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>
-
'''Illustration'''
+
==New System: Software==
-
<!--- Include an illustration that shows how your system's primers allow specific amplification of the disease-related SNP --->
+
[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.]

Current revision

BME 103 Spring 2013 Home
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Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
Photos
Wiki Editing Help
Image:BME494_Asu_logo.png

Contents

OUR TEAM

Name: StudentRole(s)
Name: Student
Role(s)
Name: StudentRole(s)
Name: Student
Role(s)
Name: StudentRole(s)
Name: Student
Role(s)
Name: StudentRole(s)
Name: Student
Role(s)
Name: StudentRole(s)
Name: Student
Role(s)

LAB 3 WRITE-UP

Original System: PCR Results

PCR Test Results

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 --- --- ---

* Ave. INTDEN = Average of ImageJ integrated density values from three Fluorimeter images


Bayesian Statistics
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.

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.

  • 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]



Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence.

  • 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]



New System: Design Strategy

We concluded that a good system Must Have:

  • [Must have #1 - why? short, ~4 or 5 sentences]
  • [Must have #2 - why? short, ~4 or 5 sentences]


We concluded that we would Want a good system to have:

  • [Want #1 - why? short, ~4 or 5 sentences]
  • [Want #2 - why? short, ~4 or 5 sentences]


We concluded that a good system Must Not Have:

  • [Must Not Have #1 - why? short, ~4 or 5 sentences]
  • [Must Not Have #2 - why? short, ~4 or 5 sentences]


We concluded that a good system Should Avoid:

  • [Should Avoid #1 - why? short, ~4 or 5 sentences]
  • [Should Avoid #2 - why? short, ~4 or 5 sentences]




New System: Machine/ Device Engineering

SYSTEM DESIGN


KEY FEATURES

We chose to include these new 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]

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





New System: Protocols

DESIGN

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]

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


PROTOCOLS

  • PCR Protocol
  1. Step 1
  2. Step 2
  3. Etc.


  • DNA Measurement and Analysis Protocol
  1. Step 1
  2. Step 2
  3. Etc.



New System: Research and Development

BACKGROUND


DESIGN


Primers for PCR


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.




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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