BME100 f2015:Group16 1030amL6

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BME 100 Fall 2015 Home
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Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
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Contents

OUR COMPANY

Steven Rojo
Steven Rojo
Jacob Baca
Jacob Baca
Javon Boaz
Javon Boaz
Sudarshan Kandel
Sudarshan Kandel
Aditya Konduri
Aditya Konduri
Nicolas March
Nicolas March


LAB 6 WRITE-UP

Bayesian Statistics

Overview of the Original Diagnosis System The class was split into their respected groups and were assigned 2 patients each. The patients were to be determined if they were positive for a SNP disease, which was to be determined with the use of a PCR. This was found be placing extracted DNA from the patients and known controls into a fluorimeter. In this fluorimeter, the fluorescence of the extracted DNA was measured and analyzed with the aid of a program called imageJ. The information was clear, but with the introduction of human error with the data, an additional step of utilizing a Bayes Statistics became necessary to insure the accuracy of the collected data.


What Bayes Statistics Imply about This Diagnostic Approach

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Intro to Computer-Aided Design

TinkerCAD
TinkerCAD is an user friendly 3D model designer program, that allows for simple models to be made in a quick fashion. As opposed to Solid Works, the program runs in browser and has the figures be aligned on a preset grid. The grid acts as a guide for the points & lines to follow so that common shapes can be easily made, where as in Solid Works, the points/lines are more liberal in their locations. Another aspect of TinkerCAD is that there is that since its browser based, it can be utilized on a Macintosh computer thus voiding the need of Bootcamp. Coinciding with this user friendly set-up, the program allows for color coordination to be used, with any shape or solid being capable of being assigned a color in a quick fashion.


Our Design

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  • The grayed out areas are the designated spots for holes to be in the actual device.*





Feature 1: Consumables

The essential consumables, which are the supplies included PCR kit (to allow for proper utilization), will be included with the newly designed version of the PCR machine. Said design will not require any additional consumables due to the changes being only dedicated to the loading aspect of the PCR. Any changes to the previously established list of materials, would be an increase in the amount of plastic tubes, in order to fulfill the increased amount of slots.


List of Consumables:

  • PCR Mix
  • Primer Solution
  • SYBR Green Solution
  • Buffer
  • Plastic Tubes
  • Glass Slides
  • Pipette Tips

Strengths: Strengths of the consumable resources include the fact that they are easy to use, relatively reliable, require minimal training to use, and are relatively inexpensive.


Weaknesses: Weaknesses of the consumable resources include that they are not very secure, they are quite fragile and delicate, and are difficult to fix and manipulate when a mistake is made.



Feature 2: Hardware - PCR Machine & Fluorimeter

Open PCR

Strengths: The machine is reliable and accurate with the collected data. The machine was also small and compact.

Weaknesses: Despite these attributes that the machine has, there were some faults in the design. For instance the amount of slots were quite limited and the lid had some issues closing. Another problem was that the PCR lacked a labeling system, which could have resulted in a mix-up of the solutions. These troubles were addressed in the new design with more available slots built in, and a coordinate system that will aid in keeping track of the pipettes. Another difficulty was inserting the tubes into the machine because the machine was small and difficult to operate given having to insert the tubes through the top of the machine. This problem was addressed with a sliding tray for the test tubes allowing for easier handling and access, which can be easily removed and inserted back into the machine. The new tray has a 36 slot capacity, over twice the capacity of the previous machine.


Fluorimeter System:

Strengths: The current device allowed for the necessary area to be darkened (for the photo to be taken) and with the current set-up, it was easy to take photos with the phone.

Weaknesses: The device was "shaky", in that it was not very stable, leading to the photos shifting with the moving system. Another weakness was that the slides for the test had to be manually held. It was difficult to set the camera in the right place and get a good focus without moving the rest of the elements of the system. The box being separate from the fluorimeter also proved to be a challenge to work with, because it was difficult to place the box in the correct space each time after a new slide was set up.



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