BME100 f2018:Group8 T1030 L6

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Owwnotebook icon.png BME 100 Fall 2018 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: Ty Promreuk
Name: Sabrina Worley
Name: Sonja Brett
Name: Jaad Waters


Bayesian Statistics

Overview of the Original Diagnosis System

There were 17 teams of 4-5 students each, and we diagnosed 34 patients total. For each patient, we had three replicates. In order to further prevent error, we used positive and negative controls, in order to compare them to our patients. Our ImageJ calibration controls were used to ensure that ImageJ was working properly and would provide accurate results for our patients. Using three images per patient allowed us to ensure that the ImageJ images were accurate. There were a few inconclusive test results from the experiment; however, the inconclusive test results did not affect the conclusion of the PCR test. As a result of the inconclusive test results, there were inconclusive diagnoses for the patients. There was blank data for Group 1, which may have skewed the test results. We also encountered problems when micropipetting the soultions into the vials. This may have caused a mistake in our data and therefore cause a mistake in the class data.

What Bayes Statistics Imply about This Diagnostic Approach

The calculations 1 and 2 show the reliability of the test results in concluding whether or not patients have the disease SNP. Because the values we calculated for P(A|B) are close to 1.00 (100%) for both calculations 1 and 2, we can say that these results were reliable in diagnosing patients.

The P(A|B) value for calculations 3 implies that the reliability of the PCR test in diagnosing patients is low, under 50%. However, for calculation 4, the reliability of the PCR test is closer to 100%; therefore, it is a reliable test to predict development of the disease.

When calculating the area, mean, and RAWINTDEN data through ImageJ, variations in oval sizes due to human error could have occurred. Placement of the oval in the backdrop could have also caused error. Additionally, when calculating the final PCR concentrations, we may have incorrectly calculated values in Excel. Finally, rounding data values may have caused additional errors in calculated Bayesian statistical values.

Intro to Computer-Aided Design

3D Modeling
Our team used TinkerCad to develop the redesigned light box. This software was very easy to understand, given the simple features and straightforward tutorials that the website provided upon setting up an account. We were able to add and remove shapes, change colors, and dimension fairly easily. One of the minor setbacks was the difficulty of changing the perspective. Although there are preset options for point of view, we were not able to zoom into a particular point on our design if it was not within the preset parameters. Furthermore, it was difficult to capture images and recordings of the model because TinkerCad did not provide a recording tool. Overall, TinkerCad was very valuable in creating our design.

Our Design


Our redesigned light box has features that address issues like outside light interfering with photo quality and trouble lining up the fluorimeter and cell phone camera. The machine includes a sliding lid in order to easily keep light out when capturing images. The front side of the box has a small peep hole that is level to the fluorimeter, as well as a magnetized surface. The light box couples with a phone stand with a magnetic back, which allows for the stand to be adjustable and compatible with various sizes of phones. We chose this design because we had difficulties with stacking the cartons and positioning the phone to make the light box high enough for us to capture pictures.

Feature 1: Consumables

Since we did not make changes to the PCR machine itself and only changed the set up of the lightbox, standard sized consumables may still be used without issue. We will utilize the same consumables as the iteration of the PCR machine and process that we worked with in previous labs. Our consumable parts are interchangeable with those used in standard PCR experiments- standard micropipettors, liquid reagents, PCR tubes and tube racks, and so on. Therefore, our product does not include specific "very important" consumable parts that are only applicable to our kit; our product consists of our original lightbox design, a fluorimeter, and and our magnetized stand.

Feature 2: Hardware - PCR Machine & Fluorimeter

The OpenPCR machine did not go any changes in our design and will still be used in the same manner. We changed the design of the light box in order to make the fluorimeter setup less difficult; the fluorimeter will simply be placed into an elevated platform inside our light box, which has a sliding lid and a peephole in order to more completely block out light. We will use other standard processes and equipment in order to perform the remaining steps of the PCR reaction.