BME100 f2015:Group7 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: Carson Minarik
Name: Haley Archambault
Name: Hannah Graff
Name: Courtney Gadbois
Name: Elizabeth Meneses
Name: Thalia Dinh


Bayesian Statistics

Overview of the Original Diagnosis System

The division labor of how BME100 tested patients for the disease-associated SNP, there was 17 teams of 6 students each diagnosed 34 patients, each group had a total of two patients.The things that were done to prevent error were labeling each patients ID number in order to not get them confused. Each patient has a total of three DNA samples, there was also a positive and negative control to compare to each sample. For each sample we took three pictures, with a total of twenty four pictures. For each picture, we used the ImageJ program to split channels and each result was labeled and put onto a table.the overall results for the BME 100 PCR were successfully conclusive with positive and negative results,however there was a few inconclusive results. There was also one group that had blank data because of technical difficulties. Some of the difficulties may have effected our data was that for the flourimeter it wasn't completely dark and some light interfere and may have alter the results by the time the images were analyze by ImageJ program.

What Bayes Statistics Imply about This Diagnostic Approach

Calculation 1 was close to 75%, which means that there is a high probability that a positive test result will occur given that there is a positive PCR reaction. Calculation 2 was close to 100%, which means that there is a very high probability that a negative final test result will occur, given a negative diagnostic signal. Both calculations 1 and 2 seem to have a high reliability.

Calculation 3 is close to 25%, which indicates that there is a low probability that the patient will develop the disease, given a positive final test result. Calculation 4 is close to 90%, which indicates that there is a high probability that a patient will not develop a disease given a negative final test result. There is a low reliability because the probabilities are very different.

Three possible errors: Measuring could have been compromised, pipettes may have been in device for wrong period of time, lids may not have been closed tight enough.

Consumables: plastics, pipettor, and reagents (PCR mix, primers) STRENGTH: Disposable, inexpensive, abundancy, easy to use. WEAKNESS: bad for the environment, because they are disposable there is the need to use many consumables.

The OpenPCRmachine and software STRENGTH: the time was reasonable for the PCR to be copied. WEAKNESS: sample space is limited.

The Fluorimeter system(including slides, stand, etc.) STRENGTH: the functionality of the overall fluorimeter WEAKNESS: the size, it was hard to adjust the height.

Intro to Computer-Aided Design

TinkerCAD is a website that allows the user to build a 3D model of an instrument. The group designed a fluorimeter machine that better the original machine. The original machine was used during the PCR lab using DNA. The TinkerCAD tool was very helpful when brainstorming the redesign. When changing the design of the device the overall design of the original device was strong and was kept within the redesign. The new designed did in fact add a strength feature. This feature was adding a scissor lift to the bottom of the device to create the ability to change the height of the device. This change will create a better viewing environment for the viewer. Also, the camera was added and a screen that can be read for information.

Our Design

The new design is the original design, with an added scissor lift on the bottom. This design was chosen because the original design was not easily viewed. Plates were stacked underneath the device in order to add height. This was not a sturdy way of adding height. This lift will create an operable height change that will increase the functionality of the device and view. In addition, a camera was added to the device along with a processing system image j that analyzes the captured image and produces the percentage of green. There is also a screen on the device that is how the experimenter views this calculation.

Feature 1: Consumables

The consumables used with the experiment are glass slides, tubing, PCR mix, primer solution, SYBR Green solution, buffer, pipettor, and a PCR machine. The kit that comes along with the Fluorimeter includes a PCR device, a pipetter, and glass slides.

Feature 2: Hardware - PCR Machine & Fluorimeter

The PCR and the fluorimeter will both be included in the package system. The Fluorimeter is the only device that will be improved. The PCR device will be left unchanged. The group decided to make the Fluorimeter have a machine operated height system. The original Fluorimeter was not tall enough to be viewed at a high enough level for viewers or a camera. The new design creates a better functioning viewing experience. The Fluorimeter will have a switch that can lower and higher the device using a scissor lift. Another change to the Fluorimeter will be a screen that tells the experimenter what the percentage of the green is in the liquid. The device will include a camera that will capture an image of the light and use an image j system to calculate the percentage of green in the liquid.