BME100 f2015:Group10 8amL6

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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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OUR COMPANY: Star Biomed

Name: Jose Luis Rivera
Role(s):Intro to CAD, Feature 1 & 2
Name: Amity Jackson
Role(s): Bayesian Stats
Name: Jarrett Eshima
Role(s): Intro to CAD, Feature 1 & 2
Name: Sheldon Cummings
Role(s):TinkerCAD model, Feature 1 & 2
Name: Diba Pourazar
Role(s): Intro to CAD, Feature 1 & 2
Name: Katarina Junio
Role(s): Bayesian Stats

Star Biomed

LAB 6 WRITE-UP

Bayesian Statistics

Overview of the Original Diagnosis System For the PCR lab, each group was assigned two DNA samples to test for the disease-associated SNP. Since there are seventeen teams, there were a total of 34 patients being tested for this disease. This made the lab easier to manage, and overall made the data easier to interpret for all of the patients. In order to prevent error of diagnosis, three replicate images were taken for each of the patients. To compare these images of known concentrations, calibration standard pictures were taken and evaluated through Image J to compare the RAWINTDEN of the calibrations (known concentrations) to the unknown samples. Based on the final data, Group 1 had successful conclusions for both patients. Group 2 had blank data for both patients. Group 3 had inconclusive data for Patient 32924, and successful data for their other patient. Groups 4, 5, 7, 8, 9, 10, 11, 12, 14, and 17 had successful data for both of their patients. Group 6 had inconclusive data for both patients. Group 13 had one successful test, and one inconclusive, and Groups 15 and 16 had no tests data for their patients. Problems that may have effected our data may have stemmed from inaccurate picture taking due to incorrect angles, camera settings etc.


What Bayes Statistics Imply about This Diagnostic Approach Calculation 1 numbers indicate that there is approximately a 1 in 3 chance of the final test conclusion and the positive PCR reaction to occur. There is close to 1.00 probability of a positive PCR reaction to occur given a positive final test conclusion result. There is more than a 3 out of 4 chance that the probability of a positive final test conclusion occurring given a positive PCR reaction result. Calculation 2 indicates that there is approximately a 50% chance that a negative final test conclusion and a negative PCR reaction to occur. There is a 3 out of 4 chance that a negative PCR reaction will occur when a negative final test conclusion result is found. There is a close to 1.00 probability of a negative final test conclusion occurring given a negative PCR reaction result. Calculations 3 indicated that there would be about a 1 out of 3 chance of testing positive for the disease, 1 out of 3 chance of a positive final test conclusion, a 1 out of 4 chance of a positive final test conclusion given a positive disease, and a 1 out of 4 chance of a positive disease given a positive final test conclusion. The PCR appears to be not very reliable in predicting the development of the disease. Calculations 4 indicated that there would be about a 3 out of 4 chance of testing negative for the disease, about 50% chance of a negative final test conclusion, about a 50% chance of a negative final test conclusion given a negative test for the disease, and about 70% chance of testing negative for the disease given a negative final test conclusion.



Intro to Computer-Aided Design

TinkerCAD

The TinkerCAD program was used to import in the multiple files and bring them together. This was challenging because unlike Solid Works, TinkerCAD does not have any "mate" tools and so edges are difficult to align perfectly. After the PCR Machine was assembled, edits on the design took place. This involved dragging in the correct base shape, editing them to the right size, and attaching them into the design. This was much more streamlined and easier than Solid Works, since it involves a click and drag dynamic. However, it was also a lot less precise than Solid Works, because exact measurements are hard to use, and most things were "eyeballed" into the correct positions. All in all, the TinkerCAD program is favored for this application because it is much faster and user friendly, as well as intuitive. It is designed to create proposals and conceptual designs, that do not worry about the exact dimensions yet. Solid Works is favored when creating something that needs to be accurate and precise. When building a file to 3D print, Solid Works is the stronger program.


Our Design


This top view shows the new improved handle attachment as well as the larger display screen

This isometric view shows the new improved handle attachment as well as the larger display screen

This side view shows the new improved handle attachment as well as the larger display screen



Our design kept the inside of the OpenPCR machine the same in order to ensure that the device was still capable of performing PCR. However, we did choose to alter the lid and display screen of the OpenPCR machine. Our group removed the black knob on the top of the device and replaced it with a more convenient handle. Additionally, we increased the size of the display screen to allow for more clear readings and to allow for the display of additional information such as a timer and which cycle the PCR machine is on. Our design is different from the original OpenPCR design because our design provides a more useful handle and allows for more information to be displayed on the screen. The additional information can be useful when determining how many cycles have been completed in order to determine approximate number of replications.


Feature 1: Consumables

The "very important" consumables include: micro-pipetting equipment and the reagents such as PCR mix and primers. Since our group did not alter the inside of the OpenPCR machine, we do not need to change any of the consumables. However, idealistically our group would be able to create cheaper reagents that still worked and pipetting equipment designed specifically for the concentrations needed in PCR.

Feature 2: Hardware - PCR Machine & Fluorimeter

We decided to include the Open PCR machine and the fluorimeter in our system. Our group's resign includes a new handle for the lid and a larger display screen. Our group chose to keep the Flourimeter the same, however the main weakness we noted was the stand for the smart phone. If we were to change the Flourimeter, we would include a built in smart phone stand that would be adjustable so that the desired length from the drop can be achieved. Additionally, a ruler would be etched into the adjustable stand so that the increments would be easy to determine.