BME100 s2016:Group10 W1030AM L6

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BME 100 Spring 2016 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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Ekta Patel
Joe Schreiber
Jade Nelson
Jordan Todd
Curtis McLoud
Gavin Steeber


Bayesian Statistics

Overview of the Original Diagnosis System

Seven teams with 6 students each diagnosed 34 patients in total. Having different groups processing different patients data, the results were available quicker. By dividing up the patients that were tested, groups performed separate procedures for performing the PCR. This could create differences in data. However, efforts were done to limit the amount of errors. For example, there were three replicates per patient that was tested, there was a calibration standard to ensure the system would function properly, and three drop images for each unique PCR sample. These controls would allow to have multiple samples to be tested and reduce the differences in data. Some of the challenges that were faced include positioning the phone camera on the cradle. Often times, the phone would shift and move, so the images that were gathered would be from slightly different angles. Also, the box to deflect light source would be placed on top of the fluorimeter differently each time. Based on the class's final data, 50% of the positive PCR results correctly corresponded to a positive doctor's diagnosis. 88.9% of the negative PCR results correctly corresponded to a negative doctor's diagnosis. There were two inconclusive PCR results, one corresponded to having the disease, another corresponded to not having the disease.

What Bayes Statistics Imply about This Diagnostic Approach

Based on the positive results from the PCR data, there is about an 80% reliability that the PCR test accurately concludes that a patient has the SNP disease. Based on the diagnosis results, there is about a 90% reliability that the PCR can predict the development of the disease. Three possible sources of error include:

  1. Contamination of solutions and/or using the incorrect mixtures
  2. Inaccurate photographs of the drop in fluorimeter, which influences Image J data
  3. Micropipette inaccuracy and incorrect volumes

Intro to Computer-Aided Design


TinkerCAD is a simplistic CAD software that allows the user to design simple 3-D objects. In the context of the lab, the software required several downloaded files off of The simple nature of the software makes it very user friendly, but limits it due to the need to download more complex objects. In comparison with Solid Works, TinkerCAD is far more simple and user friendly, but Solid Works allows the user to do far more complex designs. The TinkerCAD tutorials gave the user all the necessary experience needed to design the new products, and proved to be very simple to pick up. The ability to lock different pieces together proved to be an especially useful aspect of the software. TinkerCAD works as a simplistic user-friendly alternative to Solid Works.

Our Design

Remodeled Epi tube, now with pop cap, for easy opening!
Remodeled version of PCR, now including computer
Remodeled version of Fluorimeter, with built-in camera

We chose this design, because now there will not need to be a computer connected to the PCR machine, but rather a PCR machine that includes a built-in computer that can be set to an automatic timer and temperature.

Feature 1: Consumables

The consumables kit will include:

  1. Pipetter Tips
  2. Pop Cap Epi Tubes
  3. Micropipetter
  4. PCR Mix
  5. Primer Solution
  6. SYBR Green Solution
  7. Buffer
  8. Glass Slides

The change that our consumables kit will flaunt is the new and improved "Pop Cap" Epi Tubes. These tubes are the same design as regular epi tubes, however, they have a small mechanism on the cap, that pushed with one finger will pop open the tube for easy solution transferring.

Feature 2: Hardware - PCR Machine & Fluorimeter

The Open PCR machine replicates the DNA for easier analysis. The fluorimeter helps to show which samples of DNA have a positive reaction. Both devices will still be used in the experiment.

PCR - The Open PCR machine was redesigned to include a built-in computer. This allows the use of the PCR machine without the use of the computer since the run time and temperatures can be set from the machine itself. By adding a computer, the Open PCR machine becomes a stand-alone device and is easier to use.

Fluorimeter - The fluorimeter was redesigned to include a built-in camera on the fluorimeter itself. This eliminates the need for a webcam or camera phone to take a picture of each drop. This also ensures each picture is taken from the same height and distance from the drop so that the images are consistent and can be analyzed more accurately in ImageJ.