# BME103 s2013:T900 Group6 L3

(Difference between revisions)
 Revision as of 22:51, 15 April 2013 (view source) (→New System: Machine/ Device Engineering)← Previous diff Revision as of 22:56, 15 April 2013 (view source) (→New System: Protocols)Next diff → Line 153: Line 153: '''MATERIALS''' '''MATERIALS''' - + Supplied in Kit + *SYBR Green - 60 ug + *DNA Samples + *Fluorimeter + *Phone + *Micropipettes + * +

## Revision as of 22:56, 15 April 2013

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# OUR TEAM

 Name: Cyril Wassef - Design Strategy-Machine/Device Engineer Name: StudentRole(s) Name: StudentRole(s) Name: StudentRole(s) Name: StudentRole(s)

# LAB 3 WRITE-UP

## Original System: PCR Results

PCR Test Results

 Sample Name Ave. INTDEN* Calculated μg/mL Conclusion (pos/neg) Positive Control 7301649 62.48 N/A Negative Control 3786507.33 29.57 N/A Tube Label: 1-1 Patient ID: 72537 rep 1 7457625.66 63.94 pos Tube Label: 1-2 Patient ID: 72537 rep 2 9087739.66 79.2 pos Tube Label: 1-3Patient ID: 72537 rep 3 4817516.33 39.23 neg Tube Label: 2-1 Patient ID: 74083 rep 1 3558606.33 27.44 neg Tube Label: 2-2 Patient ID: 74083 rep 2 4247969.66 33.89 neg Tube Label:2-3 Patient ID: 74083 rep 3 4704281 38.17 neg

* 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 = Frequency of positive conclusions from cancer DNA sequence = 9/20 = .45
• B = Frequency of Total Positive DNA sequences = 26/60 = .433
• P (B|A) = Frequency of total positive DNA sequences given a positive conclusion = 25/26 = .962
• P(A|B) = .962

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

• A = Frequency of a mismatch for pos = 3/9 = .33
• B = Frequency of all mismatches = 5/9 = .55
• P (B|A) = Probability patient will get cancer = 3/10 = .3
• P(A|B) = .3

## New System: Design Strategy

We concluded that a good system Must Have:

• [Simple software. This is of vital importance due to the fact it will attract more user. The easier the software is to navigate and work with, the better sales will be. It will also in turn help interpret data easier by displaying results on a simple scale.]
• [Access to imaging results in a hasty manner. Being able to interpret images quickly after interpretation is important so the users can justify what they are analyzing quickly and precisely. This in turn will help develop more in-depth analysis' by revealing faster results for more trials. This will increase validity of the information obtained in the long run.]

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

• [Ease of access. The group concluded that the easier the system is to access from the outside in, the more improvement the group and developers can make on a more frequent basis. That being said, these frequent improvements allowed by this aspect will only increase the use of the PCR machine. The group will be able to make improvements on the machine whenever it seems fit and necessary; possibly leading to newer discoveries more frequently.]
• [Low cost. Although it is not always possible to have a low cost because of the parts put into the system, the group leans towards the machine being affordable. These low costs will increase sales and provide itself with a better outlook on the environment. Its gain in reputation would help our group further sales in the industry and promote additional add-ons to this product if deemed fit. ]

We concluded that a good system Must Not Have:

• [A Troublesome USB connectivity. If this is a factor in production, the PCR would almost be coined as worthless due to the fact it needs to be attached to a computer with the correct software to even record the results. It would also ruin the company's reputation in the process by not appealing to buyers. It's a must to keep these machines in mass production and on the market.]
• [A hazardous casing. With the prototype being made of wood for the outside casing, it causes a fire hazard due to the fact it's highly flammable. Something more durable would be deemed fit to encase the material that is of such a large investment. This would give potential buyers a sense of assurance that the product is not simply something fragile and easily disposed of, but can hold its own.

We concluded that a good system Should Avoid:

• [Time-consuming amplifications. While the prototype PCR machine took just over an hour and a half to fully amplify and denature, the group intends on making the new product a bit more time efficient by reducing this time interval to just under an hour. Although its not a necessity like the others, its something the group wants to avoid to aid in productivity with the machine. ]
• [Inaccurate time read-outs. Although the time difference normally is usually within a few seconds, the difference in this time could ultimately affect the denaturing of proteins in the long run. We want to avoid this to avoid inaccurate readings of the proteins due to harm during the process. Accurate readings of the DNA from the machine are vital.]

## New System: Machine/ Device Engineering

SYSTEM DESIGN

• The team planned on modifying the panels that encase the PCR system. By including shatter and scratch resistant Gorilla glass along with plexi glass for stability and glass for visibility, the system will seem more appealing to the user. It will also provide better stability for the system and do away with the potential fire hazard that was previously involved in the last design.

KEY FEATURES

We chose to include these new features

• We changed the side panels of the PCR machine to gorilla glass, the bottom to plexiglass, and the front to just glass. This will ensure that the machine won't set on fire.

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.

MATERIALS

Supplied in Kit

• SYBR Green - 60 ug
• DNA Samples
• Fluorimeter
• Phone
• Micropipettes

PROTOCOLS

• PCR Protocol

We chose keep the protocols the same as the original system

• Feature 1 - The PCR machine effectively amplifies the DNA with little error.
• Feature 2 - The software used in the PCR testing is very easy to use.
• Feature 3 - The flourimeter gave us a good idea whether a sample was positive or negative
• DNA Measurement and Analysis Protocol
1. Step 1: Gather materials and safety equipment
2. Step 2: Put flourimeter in dark box, keep one hatch open for ease of access
3. Step 3: Level the phone camera lens with flourimeter
4. Step 4: Calibrate flourimeter with water
5. Step 5: Dilute samples with SYBR green
6. Step 6: Run flourimeter again
7. Step 7: Take picture and repeat with the different samples
8. Step 8: Open image J
9. Step 9: Create a circle around the droplet in picture
10. Step 10: FInd the aveintdent for each droplet by clicking analyze, then measure

## 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.]