BME100 f2015:Group2 8amL6

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BME 100 Fall 2015 Home
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Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
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Contents

OUR COMPANY

Name: Bryce GoldthwaiteRole(s)
Name: Bryce Goldthwaite
Role(s)
Name: Stephen LaneRole(s)
Name: Stephen Lane
Role(s)
Name: Samuel RiosRole(s)
Name: Samuel Rios
Role(s)
Name: Christian ManriquezRole(s)
Name: Christian Manriquez
Role(s)
Name: Yash DalviRole(s)
Name: Yash Dalvi
Role(s)


LAB 6 WRITE-UP

Bayesian Statistics

Calculations 1 and 2 The first two calculations in the Bayesian Statistics section determined the probability that a patient will have a positive final test conclusion given a positive PCR Reaction and the probability that a patient will have a negative final test conclusion given a negative PCR Reaction. These two statistics are good determining factors of if the final result is conclusive with the results from the PCR Reactions. For calculation one, the probability that a patient will have a positive final test conclusion given a positive PCR Reaction is .85. This means that 85% of the time that a patient has a positive final test conclusion, they have received a positive from a single PCR Reaction. For calculation two, the probability that a patient will have a negative final test conclusion given a negative PCR Reaction is .95. THis means that 95% of the time that a patient has a negative final test conclusion, they have received a negative from a single PCR Reaction.

Calculations 3 and 4 The final two calculations determine the probability of a patient developing the disease or not, given the infected DNA or not. Calculation three shows the probability of a patient developing the disease, given the SNP. The calculated percentage was 25%. This calculation means that when given the infected DNA sequence, the patient only develops the disease 25% of the time. Calculation four shows the probability that a patient will not develop the disease, given an uninfected DNA sequence. The calculated percentage for calculation four is 69%. This means that 69% of the time that a patient is given an uninfected DNA sequence, the patient does not develop the disease.


What Bayes Statistics Imply about This Diagnostic Approach

The first two calculations imply reliability and consistency throughout the entire test. The probability that a patient will have a positive or negative test conclusion compared to the probability that they have positive or negative PCR reactions. These percentages are both very good, for positive reactions, there is an 85% reliability through the test. For negative reactions, the percentage is even better, standing at 95%. Both of these are close to 100%, therefore proving to be reliable.


The second two calculations determine the probability of the disease developing given the infected or uninfected DNA sequence. Calculation three determines the probability that a patient will develop the disease given infected DNA sequences. The probability was very low, .25. This shows that even given the SNP sequences for the disease, it only develops in 1 out of every 4 patients. Calculation four determines the probability that a patient will not develop the disease given healthy DNA sequences. The percentage was closer to 75%, or three out of every four patients. This means that when a patient is given uninfected DNA, they have about a 75% chance of not developing the disease. Both of these show that either the test conducted was flawed, or the chances of actually developing the disease are very low.

Some sources of error in our team’s testing include mostly human error. The first major source of error was the possible contamination of the samples on the slide. Some drops of the sample occasionally were placed on the spots on the slide that were already used by other drops. This can contaminate the test that would go on a previously used surface. Another source of error was the phone camera being used. When setting a the iPhone 6 camera to the timer setting, it would flash on every second counting down. This could disrupt the green dye being used. The last source of error could be mistakes in the use of the ImageJ program. First time use can possibly cause errors in the data collection from the program.

Intro to Computer-Aided Design

TinkerCAD


Our Design

Image:Double Heating System.JPG Image:PCR handbook.JPG


Branding: Our new design is also known as the PCR machine, the Pretty Cool Reaction Machine. The new PCR machine resembles the standard PCR machine in all aspects; however, the difference in our machine is its higher performance.

Positioning: In the image, there are two smaller heating systems, rather than just one, that can be programmed to function at a slightly higher temperature than the standard PCR machine in order to speed up the DNA amplification process.

Target Markets: Our target market will not just include lab researchers, but will also include high school teachers, university professors, hospital staff such as doctors and medical scientists, and any other type of aspiring scientist aiming to learn or teach others about the mysteries of DNA.

Messaging: Along with the redesigned PCR machine is an instruction booklet to prevent possible damage or confusion when attempting to use the machine, in case users are new to or unfamiliar with the system.

Place: The "Pretty Cool Reaction" machine can be purchased at any major electronics store such as Best Buy, or major chain companies such as Target. It is also available to order at www.prettycoolreaction.machine.com



Feature 1: Consumables

The consumables of our product, including tubes, tips, a micropipettor, PCR mix, and primers, will be similar to those of a typical OpenPCR machine; however, as far as packaging, the tubes included with a typical PCR machine may be mixed up or confused by the consumer when working with the PCR mix, primers, or their DNA samples.

Our tubes will be both color coded and number labeled in order to prevent any mix up or confusion of the PCR mix, primers, or DNA samples as these errors could severely compromise the data. Additionally, the consumables kit will include new glass slides with small indentations, or wells, in order to prevent the DNA samples from moving around during image capture as this error could, and has occurred, with the standard glass slide, without a well.

Feature 2: Hardware - PCR Machine & Fluorimeter

Both the PCR machine and fluorimeter will be included in our system. In terms of utilizing the hardware, both pieces will be slightly redesigned in comparison to the standard PCR machine and standard fluorimeter.

The PCR machine will be redesigned in the terms of the heating system. The system will be redesigned to work and slightly increase the temperature at which the PCR machine functions in order to increase the time it takes amplify the DNA samples, and in return, reduce the time it takes to wait and analyze the DNA.

In terms of the fluorimeter system, all aspects will remain the same; however, there will be an addition to the system. Instead of having to separately capture images and then upload them to a PC, work through ImageJ, and finally analyze the DNA, the new fluorimeter system will work in unison with ImageJ. The image capturing device, such as a camera or cell phone, will be connected to a computer, and as the pictures are being taken, they will be sent to the computer to be automatically analyzed with the preferences previously chosen.






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