BME100 s2015:Group5 12pmL6

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BME 100 Spring 2015 Home
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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Name: Brandon Favre
Name: Daniella Orlando
Name: Martisha Clyde
Name: David Shumate
Name: Nick Valverde
Name: Fernanda Diva


Bayesian Statistics

Overview of the Original Diagnosis System

The division of labor was quite unequal. There were 34 teams of 6 students each that all performed the experiment and determined the diagnosis. However, due to faulty diagnoses (whether be due to human error, lack of time, etc.) not all 68 patients were diagnosed correctly. The tasks that were done to prevent error were that each group was given different patients in order to get a large spectrum of the diagnosis. The equipment that was given for the experiment was fairly accurate and provided accurate enough measurements for each group to conduct the PCR test. The ImageJ software was used, which was more helpful in the diagnoses process, which helps prevent error as well. However, the final data resulted in faulty and skewed data. About 20 out of the 68 patients weren't diagnoses correctly, therefore skewing the data. 8 of the patients didn't have any test done on them, and 4 of them were inconclusive for whatever reason. There was, though, a larger number of successful conclusions that inconclusive results.

What Bayes Statistics Imply about This Diagnostic Approach

The results from calculations what in two show that there's a higher probability that a patient will not result in negative test results for the SNP disease given the frequency of negative PCR test results compared to the probability of positive test results given that positive for SNP. The Bayes values for each though, was fairly low and relatively very small. Three possible sources of human error are that the number of drops measured during the experiment weren't correct. Another could be that the ImageJ analysis could have been off when performing analysis with ImageJ. Also, sources of error could have been when conducting the experiment the proper steps weren't taken, therefore, mixing patient results in each group, skewing the data, and resulting in false negatives/positives.

The results from calculations 3 and f imply that the reliability of PCR for predicting the development of disease is fairly accurate. The Bayes values concluded from these calculations showed high probabilities for each, but under 1. These values were reliable and showed a representation of the diagnosis of SNP, given the tests that were able to be used.

Computer-Aided Design


TinkerCAD is an online modeling software that allows users to create files, shape by shape, to model whatever they need. It was used during the Computer-Aided Design lab to model the OpenPCR machine, and to demonstrate the improvements that were conceived of for it, Our Design

The overall shape of the OpenPCR machine was not changed significantly, save for the addition of a fluorimeter module at the bottom of the machine.

The fluorimeter at the bottom of the OpenPCR machine features a built in, pre-calibrated camera that will snap shots when the shutter (light pink) is closed, saving the data to flash drive, SD card, or computer that is connected to it. There is a drawer that slides out to make pipetting fluids onto the slide accessible. Further, because the fluorimeter is underneath and attached to the OpenPCR machine, it will not move, and will be completely covered in darkness to enhance the image quality.

To avoid contamination and wasting pipette tips due to carelessly setting the pipette down on a lab bench or other surface, a pipette holder has been added to the top of the OpenPCR machine, to suspend any pipette AND its tip to avoid contamination. It is a snap-in, meaning that the tip will not swing around and hit the OpenPCR machine, further avoiding contamination.

The USB drive on the OpenPCR machine was updated to accommodate modern USB-drive shapes, so as to allow more versatility in the connection of the OpenPCR machine to the computer. Further, this allows for data to be accessed and written onto flash drives, which makes analyzing data at home or other locations away from the lab easier. Further, an SD card drive was added, to increase storage space for the images taken by the fluorimeter module.

Feature 1: Consumables Kit

The consumables in the kit will be packaged in the same box as the Enzyme PCR Tower (the name of the unit), in a separate, light-shielded area of the box (two compartments, one is the main tower with its components, and the other is the light-shielded reagents packaging). The consumables, being packaged in reflective and light-avoiding material, will avoid any harm coming to the SYBER green reagent. Further, the pipette tips will come in their own, usual box to prevent any touching of the tips with anything else. Finally, the liquid reagents will be held in Syrofoam packaging to prevent any breaking of glass or denting of plastic, further increasing the security of the packaging.

Feature 2: Hardware - PCR Machine & Fluorimeter

See above for the re-designed PCR machine, now called the Enzyme PCR Tower. The PCR machine and Fluorimeter will come in the same box as the reagents, but will be packaged in a separate compartment as the rest of the reagents to prevent any crushing, damage, or contamination by the PCR Tower. The fluorimeter and PCR machine are now one unit, and will be shipped and packaged as such.