BME100 s2018:Group2 W1030 L6

BME 100 Spring 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: Ian Conley Name: Aisha Alsuwaidi Name: Sarah Davis LAB 6 WRITE-UP Bayesian Statistics Overview of the Original Diagnosis System The 16 patients our lab was assigned were evenly divided between 8 lab groups. Each group ran 2 patients as well as a positive and negative control. For each patient, 3 replicates were made to improve the probability of a successful diagnosis. Within each group, each member had the opportunity to dilute control and patient samples to the correct amount and run each sample. The caps on the micropipettes were replaced after every discharge of material to avoid error and contamination. ImageJ was used for the calibration as a way to find the positive and negative control values and compare them to the patients, as well as for each patient replicate, a photo was taken of the fluorescents three times. The final PCR result spreadsheet was filled with the correct data from each group, however, group 5 did not have data put in, so their results were not counted. No clear challenges presented themselves and the lab and data analysis ran smoothly. What Bayes Statistics Imply about This Diagnostic Approach Calculations 1 and 2 imply that the reliability of the individual PCR replicates for concluding correctly the presence of the SNP is not as high as it should be. For example, the positive test results were around 50% conclusive, and the negative results were around 75% conclusive. Equations 3 and 4 imply that the reliability of PCR for predicting the development of the disease (diagnosis) is close to 1.00 (100%). There are multiple sources of human and mechanical error that could have impacted the Bayes results in a negative way. Primarily, contamination was a very large error possibility. PCR is highly susceptible to contamination and it is very likely that at one point the samples were contaminated. Secondly, errors in data analysis and data interpretation to conclude positive or negative could be at fault for some error. A possible third error could come from faulty photos. The stand was not optimal and the cameras were not the same for all groups. This could cause one group to have significantly better photos--and therefore analysis--as compared to another group. An unlikely error could also be a false diagnosis by the doctor. Intro to Computer-Aided Design 3D Modeling For this part, our group used the program Tinkercad. This program is very useful in making the design of an object easily, but does not work as smoothly or as precisely as a program like Solidworks. Tinkercad was helpful in that it allowed you to easily construct basic forms, something that is more difficult to do in Solidworks, but as stated above, it sacrifices precision and options. For example, there was no option to round the edges of the object like there is in Solidworks. Overall, Tinkercad was a simple and useful program to run for creating basic objects. Our Design Our new fluorimeter design given the cardboard box a huge upgrade. With a jointed front face and lid, there is easy access to not only the slots for phones, but the top of the fluorimeter, where the sample is tested. On top of a redesigned outer shell, the new fluorimeter has multiple slots for phones which allow users to be able to take photos from multiple distances. Also, there is a half-cylinder cut out of the phone slots for easy access to the camera button on most phones. If this still doesn't work, many phones have an optional button on the outside of the phone, such as a volume control, to take the picture. The internal composition of the fluorimeter remains unchanged, but the design is placed on its side to make a more compact and ergonomic design. In addition to all this, our company offers multiple photo filters to be placed in front of the sample depending on the color of the fluorescence used. For example, if CYBR Green is used, the green photo filter should be placed in front of the slide so that when the photos are imported to ImageJ and changed to black and white, the green color is amplified, minimizing the 'background noise' of the photo as well. Feature 1: Consumables The consumables provided in our kit will be as follows: PCR mix A limited amount of PCR mix will be provided so that initial reactions can take place (this can be discarded if the lab has their own) Primer solution A primer solution will be provided with the lab however this can also be discarded if the lab is using different or special primers Buffers The Magnesium buffer will be provided in order to help increase the function of Taq polymerase Glass slides The glass slides provided are for use in the fluorimeter during the imaging stage Feature 2: Hardware - PCR Machine & Fluorimeter Our group did not alter the Open PCR machine, and solely focused on the fluorimeter design. Our system will provide an Open PCR machine in the package but it will be unaltered. Strength And Weakness of Fluorimeter System: Strength: The users are able to use the camera on the smartphones to take a picture of the sample. The setup was very simple and allowed for quick photos to be taken and the lab to be completed quickly. The box was movable so there was easy access to the slides and the camera. Weakness: The camera stand was very difficult to keep in place. Users constantly have to adjust the height and placement of the stand during the experiment resulting in different distances between the sample and the camera for every picture. Also, the lid did not close completely and in the end allowed some light to get into the box. On top of this, the who box had to be moved for access in the photo area. This was not a huge issue because once it was removed there was a large amount of space to work with, but then after you used set up the new sample, the group had to move the box back to the initial position to cover the sample and allow the next picture to be taken. Our Solution for the Fluorimeter System: One of the major weaknesses in the Fluorimeter is that the camera stand had to be readjusted multiple times with different sized plastic boxes during the experiment. To ensure the stability of the camera stand, our design will have an improved camera stand that will allow the users to modify the distance easily and can adjust the size of the camera holder for any smartphone. This provides the camera with a stable platform that is greater than the minimum recommended distance between the sample and camera to insure quality photos. The lid in the current fluorimeter system doesn't close completely. Our design will have a lid with hinges that allow the users to close the lid easily before the picture can be taken. Therefore, no light can enter the box as the phone is being prepared to take a photo. On top of this, the lid opens up the top as well for easy access to the sample that is being photographed. Additionally, our group's design will have new hardware included--transparent filters with different colors (red, blue and green). The quality of the picture would be better so the users of our device won't have to take extra steps in ImageJ to analyze the images they took on their smartphones.