BME100 f2015:Group2 1030amL6

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BME 100 Fall 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: Gage Schrantz
Name: Amar Joshi
Name: Colleen Rice
Name: Anton Voronov
Name: Lydia Chen
Name: Cindy Crockett

Safety Box


Bayesian Statistics

Overview of the Original Diagnosis System Our first task was to prepare the solutions for PCR. Primarily, we had two people acquire all of the supplies that we needed. This included the PCR test tubes, the extracted DNA, the two variants of primers, and safety equipment. Two people had the task of marking the tubes in order to label what amount of solutions are designated into that tube. We had two people handle the transferring the correct solutions into the marked tubes. There were three drop images used for determining the values. In order to prevent error, we had two PCR reaction sample controls. A negative control, and a positive control. Additionally, for each patient, we had 3 different replicates in order to be as accurate as possible. For the class’s final data, we had in total 32 total diagnoses. 10 concluded that there is a disease, while 22 concluded that there is not. Additionally, 17 groups in their final conclusions, stated that the results were negative, while 13 stated they were positive. Only 2 of the groups ended up with an inconclusive conclusion. When looking at the frequencies, we can conclude that the test results were relatively consistent with the actual.

What Bayes Statistics Imply about This Diagnostic Approach

Calculation one describes the probability that, given a positive PCR reaction, a patient will receive a positive final test conclusion. This number was close to 75%, therefore it was fairly high. This means that the test is reliable. Calculation two, on the other hand, describes the probability that, given a negative PCR reaction, a patient will get a negative final test conclusion. This number was close to 100%. This means that the test is reliable.

Calculation three describes the probability that if a patient receives a positive final test conclusion they will develop the disease. Only a small number of those who received a positive final test conclusion developed the disease meaning the test is not very accurate despite its reliability. Calculation four determines the probability that a person will not develop the disease if the final test conclusion is negative. This number was almost 100% meaning that the test is accurate when it says someone does NOT have the disorder.

One possible source of human error is if the solution gets contaminated with a foreign substance, which could adversely affect the fluorimeter data. Another possible source of error is if the fluorescent dye is exposed to light for an extended period of time, it would also affect the results. Last, if there were a bad photo quality, it could make it hard to determine the results.

Intro to Computer-Aided Design

After clicking the "Create a new design", we found Import term on the right line. Then we found six images which are separately six parts(sides) of the Saftybox in the file and inserted them into the thinker cad in order. According to PCR machine's characters of a cubic shape, it could be assembled in terms of geometry principle. Meanwhile, in terms of the embedded holes on each board, the process of joining could be done more exactly. This 3-D cubic shaped PCR machine will be used to relevantly show our design goals and subject. Our Design

This design incorporates the Fluorometer with the PCR machine. Since it is enclosed, it provides an efficient and compact solution to the inconvenience of a primitive, and difficult to use fluorometer. Specifically, it replaces the cardboard box that previously enclosed the Fluorometer.

Feature 1: Consumables

Strength: They are easy to use and are precise

Weakness: If the fluorescent primer is exposed to light for an extended period of time it will not be as effective

The small pipet tips are conveniently packaged so you can insert the pipeter into the pipet tips. The PCR mix is separated into multiple test tubes, with each of them containing a specific amount of solution and different amount of solution. The primer solution is also in test tubes but it covered in aluminum foil to make sure there isn't a loss in efficiency when exposed to light.

Feature 2: Hardware - PCR Machine & Fluorimeter


Strengths: cheap and easy to build.

Weaknesses: It takes long time to do the PCR process.

There is a 4 x 4 row where you can place the test tubes. The PCR Machine goes through a thermal cycle in which it warms the tubes in a specfic pattern in order to promote the PCR and replicate the DNA.

Fluorimeter System:

Strengths: cheap system

Weaknesses: The phone had to be in a "makeshift" upright position and the stand had to be closed right after the picture was taken which could pose a problem.

A sliding mechanism that is placed on the top of the Fluorimeter that helps get rid of the light in a much easier way. Then there is a place in which you can put your phone in a fixed position that is attached to Fluorimeter and it is able to slide in and out in order to adjust the focus of the camera.