BME100 f2016:Group5 W8AM L6

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Owwnotebook icon.png BME 100 Fall 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
Course Logistics For Instructors
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Name: Chris Kaufman
Name: Edgar Garcia
Name: Pranav Sista
Name: Megan Hiruko

Our Brand Name


Bayesian Statistics

Overview of the Original Diagnosis System

A. Each patient was diagnosed by three students.

B. Pos/Neg PCR samples, sterile pipette, timed reactions to keep time constant


What Bayes Statistics Imply about This Diagnostic Approach

For calculations 1 and 2, the closer the probability is to 1 or 100%, this means that the reliability of each individual PCR replicate is extremely high when coming to the conclusion that the specific person tests positive for the SNP disease. When it is close to 50%, the data showed the values to be inconclusive. A potential reason could be that based on the tests conducted, we are not certain about the progression of the disease, and thus the reliability begins to come into question, and therefore a decisive conclusion cannot be made. And when the probability is very small, this means that the the conclusion can be made that the patient will in most likelihood to test negative for the SNP disease.
For calculations 3 and 4, the closer the probability was to 100%, the higher the reliability and accuracy of the test is with regards to being able to predict and conclude that the patient is positive, or negative with respect to calculation 4. When the probability is roughly 50%, this means that when the test makes a prediction to whether the patient tests positive or negative, there is a 50/50 chance that when making the prediction, there's a 50% chance it predicts whether the patient has it or not correctly. Lastly, when the probability is 0%, this means that reliability is ineffective, and the test will show that even if the test shows positive, the chances are that the patient is negative, due to the reliability being very small.
First, the micropipettes that were being used, could have been a potential error, due to the fact that, when putting in 80 micro liters, it is highly possible that one sample could have had 79 micro liters, and another had 78, and the same result for the rest. Maybe, the entirety of the sample wasn't put in as instructed. Another error could be the flash from the phone, due to the fact that the sample are sensitive to a light environment which can affect the results. And lastly, the amount for each sample can also be varied, during a specific reaction, which can result in different Bayes values.

Intro to Computer-Aided Design

3D Modeling

We used tinkercad over solidworks. Tinkercad was a little difficult to move around the plane and adjust the views. We also had trouble picking up newly uploaded parts because the parts would end up in the middle of the box we had already constructed so we would have to take apart the box to grab the new piece. However, uploading the new parts and getting the pieces aligned was pretty easy and smooth. Also there were many indicators on how to move or rotate the object which was very helpful.

Our Design


We chose to add handles on the side to the new design because the last PCR machine was difficult to move around. We also removed the nob on the top that screwed because we thought the lid needed to be unscrewed and lifted and screwed when closed but later found out that we did not need the screw. To help life the lid, we added a nob that was not adjustable to sway any confusion. We also located the nob farther away from the hinge to indicate which side of the lid lifted and add ease to opening the lid.

Feature 1: Consumables

The packaging would be similar to the original. The tubes for the PCR machine would be the same. There will be half as many tips in the packaging. There will be a total of three pipettes. The PCR reaction samples would come in the same tubes and same with the calf thymus DNA but the buffers will come in a single container and same with the SYBR Green.

The packaging would include three different micropipettes. One micropipette would be used to transfer the different PCR reaction samples and the Calf Thymus DNA using separate tips for each set. However to save tips, one pipette will be dedicated to SYBR Green and the other will be strictly for the buffers. The two pipettes dedicated to a single solution would consume all of the given solution and then release only 80units each time. The SYBR Green will come in a darker tube that will block out light rather than have to cover the tubes with tin foil.

Feature 2: Hardware - PCR Machine & Fluorimeter

The PCR Machine would generally remain the same. There will be handles included on the side to make the machine more portable. There would also be a new nob on thee lid located in a more convenient place to open the lid with ease and will also take away the confusion of having to unscrew the lid when opening or not. The fluorimeter would have a wider slit for the glass so the glass can slide in and out more easily. The fluorimeter will also have an adjustable stand to change the height to match the phone more easily. The phone case stand would be more thin so thee phone isn't leaning or moving around. The stand should also be attached to the fluorimeter, but still adjustable so the phone stand position doesn't change when the phone is moved out of the way to change the slides or to take a new photo.