BME103 s2013:TEMPwu3: Difference between revisions

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<!-- Note: Delete any image placeholders that you do not need. -->
=LAB 3 WRITE-UP=


=LAB 2 WRITE-UP=
==Original System: PCR Results==


==Background Information==
'''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>


'''SYBR Green Dye'''<br>
''[A short summary describing SYBR green dye]''<br>


'''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>


'''Single-Drop Fluorimeter'''<br>
Bayes Theorem equation: P(A|B) = P(B|A) * P(A) / P(B)
''[A description of the single-drop fluorimeter device. Add a PHOTO for bonus points]''<br>




'''How the Fluorescence Technique Works'''<br>
Calculation 1: The probability that the sample actually has the cancer DNA sequence, given a positive diagnostic signal.<br>
''[In your own words, a summary of the information from page 9 of the worksheet]''  
* 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>
<br>
<!-- Note: Be sure to delete the text in brackets: ''[ ]'' -->


==Procedure==
==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. 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'':'''
* [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]
 
 
<br><br>
 
==New System: Machine/ Device Engineering==
<!-- This is the Machine operator's section -->


'''Smart Phone Camera Settings'''<br>
* ''[The type of smart phone you used and how you adjusted the camera settings, if applicable (see worksheet page 4).]''
** Flash:
** ISO setting:
** White Balance:
** Exposure:
** Saturation:
** Contrast:


* ''[If you used an additional phone, describe the other type of smart phone you used and how you adjusted the camera settings, if applicable (see worksheet page 4).]''
'''SYSTEM DESIGN'''<br>
** Flash:
** ISO setting:
** White Balance:
** Exposure:
** Saturation:
** Contrast:


<!-- 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 -->


'''Calibration'''<br>


''[Describe how to set up your camera in front of the fluorimeter. Add a PHOTO of this set-up for bonus points.]''
'''KEY FEATURES'''<br>


* Distance between the smart phone cradle and drop =
<!-- 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. -->
''[See worksheet page 5]''
'''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]


'''Solutions Used for Calibration''' ''[See worksheet page 5]''
<!-- 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-->
{| {{table}} width=700
'''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
| row 1 cell 1 || row 1 cell 2 || row 1 cell 3 || row 1 cell 4
* Feature 2 - explanation of how a pre-existing feature addresses any of the specifications in the "New System: Design Strategy" section
|-
* Etc.
| row 2 cell 1 || row 2 cell 2 || row 2 cell 3 || row 2 cell 4
 
|-
 
| row 3 cell 1 || row 3 cell 2 || row 3 cell 3 || row 3 cell 4
 
|}
'''INSTRUCTIONS''' <br>
''[Add more rows as needed]''
<!-- 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 --->
 
 
'''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'''


'''Placing Samples onto the Fluorimeter'''
<!--- 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. --->
* ''[Step one, in your OWN words]''
* ''[Step two, in your own words]''
* ''[Step three, in your own words]''
* ''[etc.]''


<br>
<!-- Note: Be sure to delete the text in brackets: ''[ ]'' -->


==Data Analysis==
'''DESIGN'''


'''Representative Images of Samples'''


''[Show an IMAGE <u>where you drew a circle around the droplet</u> with the freehand tool for a sample with no DNA]''
'''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.-->


''[Show an IMAGE <u>where you drew a circle around the droplet</u> with the freehand tool for a sample '''with''' DNA (positive signal)]''
<!-- 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.




'''Image J Values for All Samples''' ''[See worksheet page 5]''
<br><br>
{| {{table}} width=700
|-
| row 1 cell 1 || row 1 cell 2 || row 1 cell 3 || row 1 cell 4 || row 1 cell 5
|-
| row 2 cell 1 || row 2 cell 2 || row 2 cell 3 || row 2 cell 4 || row 2 cell 5
|-
| row 3 cell 1 || row 3 cell 2 || row 3 cell 3 || row 3 cell 4 || row 2 cell 5
|}
''[Add more rows as needed]''


==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.]


'''Fitting a Straight Line'''<br>
''[Place an IMAGE of your Excel plot with a line of best fit here. See worksheet page 8]''




<br>
<br>
<!-- Note: Be sure to delete the text in brackets: ''[ ]'' -->
<!-- Note: Be sure to delete the text in brackets: ''[ ]'' -->

Latest revision as of 12:28, 11 April 2013

BME 103 Spring 2013 Home
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Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
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OUR TEAM

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