BME100 f2018:Group2 T0800 L6

BME 100 Fall 2018	Home People Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3 Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6 Course Logistics For Instructors Photos Wiki Editing Help
Our Company Name: Kayla Charles Name: Youssef Serag Name: Itzel Pineda Name: Tim Sayre Name: Ami Asodji KAIYTech LAB 6 WRITE-UP Bayesian Statistics Overview of the Original Diagnosis System Each group in the BME 100 lab were given 2 patients with 3 replicas of each giving us a total of 90 patients to diagnose. Each group were given three replicas to minimize the percentage of error in the calculations done on the final step. Each group also had a PCR control group to refer to as a golden standard. Certain collaborations on ImageJ were used to prevent variability in measurements such as the mean, and area of the droplet. To further prevent error, 3 images were taken for each droplet, and the mean of the 3 images were calculated. After all groups submitted their data to the spreadsheet, the results were observed. For the most part, the groups’ PCR results were successful. The inconclusive results were obtained because of accidents that occured in the lab. Another factor that may have played a role in the variability of the results was the usage of ImageJ. While calculating the area of the droplet, there might have been a variability in the area of the droplet depending on how large was the oval that was drawn. Calculation 1: What is the probability that a patient will get a positive final test conclusion, given a positive PCR reaction? Variable Description Numerical Value A Probability of positive final conclusions .37 B Probability of positive PCR reaction .33 P B/A Probability of positive PCR reactions given positive final conclusions .83 P A/B Probability of positive final conclusions given positive PCR reactions .93 Calculation 2: What is the probability that a patient will get a negative final test conclusion, given a negative diagnostic signal? Variable Description Numerical Value A Probability of negative final conclusions .53 B Probability of negative diagnostic signals .49 P B/A Probability of negative diagnostic signals given the probability of negative final conclusions .89 P A/B Probability of negative final conclusions given the probability of negative final conclusions .96 Calculation 3: What is the probability that a patient will develop the disease, given a positive final test conclusion? Variable Description Numerical Value A Probability of a yes diagnosis .33 B Probability of POS final test conclusion .37 P B/A Probability of POS final test conclusion given the probability of a yes diagnosis .36 P A/B Probability of yes diagnosis given the probability of POS final test .32 Calculation 4: What is the probability that a patient will not develop the disease, given a negative final test conclusion? Variable Description Numerical Value A Probability of a no diagnosis .67 B Probability of a negative final test conclusion .53 P B/A Probability of a negative final test conclusion given the probability of a no diagnosis .69 P A/B Probability of a no diagnosis given a probability of a negative final test conclusion .87 Which calculation describes the sensitivity of the system regarding the ability to detect the disease SNP? P A/B in Calculation table 1 (0.93) Which calculation describes the sensitivity of the system regarding the ability to predict the disease? P A/B in Calculation table 3 (0.32) Which calculation describes the specificity of the system regarding the ability to detect the disease SNP? P A/B in Calculation table 2 (0.96) Which calculation describes the specificity of the system regarding the ability to predict the disease? P A/B in calculation table 4 (0.87) Intro to Computer-Aided Design 3D Modeling Consumables: plastics, pipeor, and reagents (PCR mix, primers) Open PCR Machine and Software Fluorimeter system Strength: The consumables provided were completely functional, and no large improvements would be necessary. Weakness: Packaging and label what is needed for a complete reaction, and hand out packaged ‘bags’ instead of distributing each item individually. Weakness: We could fit in more samples in the PCR machine.There is a difficulty in opening the box. Strength: The LED light in the system is well designed. It makes it very clear to know if we have DNA present in the sample or not.Weakness: The Fluorimeter system is not well elevated, which makes it more difficult to take clear images. The box that we put over the system. Because of the box, we are forced to shove the system into the end of the box. Our Design #1 File:34.png #2 File:35.png #3 Strengths of new design: The strength of the new design is that is allows easier adjustability between the phone and the sample. One only has to worry about setting everything once and covering the content inside the box. Features: The new holder for the design is completely adaptable to any phone size. The distance between the phone and the phone sampler is adjustable in two directions up and down and inward and outward. Feature 1: Consumables Consumables Kit ‐ how could you pre‐package the tubes, ps, micropipeor, PCR mix, and primers so that you can fix the major weakness you described? All of the items listed above would be packaged together, in units that provide everything needed for 1 PCR cycle. This would make acquiring each item much easier, and would provide assurance that no lab member is missing a stray part for their experiment. Feature 2: Hardware - PCR Machine & Fluorimeter Hardware: PCR Machine – how will you redesign the PCR machine to improve the major weakness you described? We would fit the PCR machine with a lid that is more intuitive and easier to open, and we also would add another row of slots for test tubes within the chamber in order to increase the amount of trials that can be run at one time. We would also build the machine to be more sustainable, and make sure that all the screws and parts are aligned and placed correctly. Hardware: Fluorimeter ‐ how will you redesign the Fluorimeter system to improve the major weakness you described? We will redesign it by attaching the phone holder and the Fluorimeter to a single box. The Fluorimeter will be sitting on an adjustable stand that will allow it to align properly with the phone camera.