BME100 f2015:Group11 8amL6

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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
Course Logistics For Instructors
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Tedward and CO.

Name: Dean Spyres
Name: Kyle Greenzweig
Name: Maria Roman
Name: Ryan Tenorio
Name: Theodore Valenzuela
Name: Kyra Temple


Bayesian Statistics

Overview of the Original Diagnosis System

BME 100 had 17 groups of 6 students to diagnose 34 patients. Different groups were given different samples to test for a positive PCR reaction. In order to keep the results accurate, there had be standard controls for PCR and ImageJ. These include the calibration, number of images used, the settings on the camera, and more. In order to get consistent results in diagnosing patients, it is crucial to have all the groups use the same procedure. The Bayesian statistics determined that the results were fairly accurate. The calculations showed very high accuracy in determining that a positive PCR reaction would result in a positive final test conclusion. There was also a high probability of a negative final test conclusion given a negative diagnostic signal. Although these results were accurate, the ones predicting whether or not the patient would actually develop the disease based off of the test conclusion were not as accurate.

What Bayes Statistics Imply about This Diagnostic Approach

Calculations 1 and 2 had a very high reliability in determining if a patient has SNP or not. The Bayes values were around 80 and 90 percent.

Calculations 3 and 4 were not nearly as accurate as 1 and 2. The Bayes values for predicting the development of the disease SNP were around 50 to 60 percent as opposed to the high reliability in concluding that someone already has the disease.

Sources of error could be in students not using the correct controls on imageJ. If someone had the wrong settings or distance for their camera while taking the drop images then that could have caused an error. Another possible source of error is if a group used the wrong number of drop images.

Intro to Computer-Aided Design


The TinkerCAD tool is very user friendly and easy to use once the controls are learned. My only criticism of the tool is that it is almost to simplistic. With Solid Works, the user can design and create almost anything with the right knowledge. However, in Tinker Cad, there are definitely some limitations with the detail and overall design of any project.

Our Design

We have a very basic design for our PCR machine, however, we did make several changes to the original PCR machine. The most notable change is the increase in the size of the heating block (red) and the cooling fan (blue). These two pieces of equipment were increased in order to run more PCR tests at once. The second change that we made is the size of the tray that the reaction tubes are placed into (green). The increase in size allows more tubes to be placed into the machine than before, allowing scientists and average consumers alike to run more PCR tests at once. The final change that we made to the overall machine was to the lid (purple and orange). The lid on the original PCR machine was clunky and hard to open/close. We scrapped that lid in favor of a half sphere design. This design allows the used to easily twist the top of the machine off. The lid is coated in a material that is easy to grip and twist off. All of these design changes lead to a better, more user freindly PCR experience.

Feature 1: Consumables

Consumables included in our kit: Micropipetter, tips, tubes, PCR mix, and primers.

Our PCR kit is overall going to be easier to use by simply having color identifications on the consumables. Having primers and PCR mixes that arent color-coded makes for much confusion regarding which samples have already been worked with or not. Having color-codes on our consumables will avoid this confusion and make the process overall much simpler. Ensuring that there will be no errors with the PCR mix and primers will lead to more accurate results with no invalid data.

Feature 2: Hardware - PCR Machine & Fluorimeter

PCR Machine The PCR machine is very good at replicating a very small amount of DNA and can be done with a high level of accuracy. Some of the main benefits of the machine is that it can be done within a very short time, usually in a matter of hours. In addition its very useful for detecting DNA sequences that appear in very small sample. Although the machine useful functions very well, like everything some times there can be mistakes, and one of the problems with the PCR is because of its replication process even a small amount of error would exponentially ruin the results.

Fluorimeter Overall, the fluorimeter was a practical tool because it was operated with ease. This device is fairly low cost in comparison to other similar devices that are used for the same task. Another benefit of the Fluorimeter is that it was easy to assemble, break apart, and put away. Also, It was easy to access the slides for the drop of solution. One of the downsides of the fluorimeter was the picture taking process. One of the most time consuming steps the group encountered was the set up of the phone or camera on a stand. The stand was too small for certain phones, or it did not hold the phone in place sturdy enough to achieve a good image. The height of the phone was inconsistent due to stacking books and other boxes under the stand this made it harder to set up each time as the new drops were added on the slides because the stand was moved out of the way. In order to improve the process of capturing the image, a new stand will be added to the kit. This new stand will act like a smaller version of a tripod with a base that can be lowered and raised up to the height of the machine itself, so that the camera is lined up straight with the drop. In addition, the tripod will have a simple holder with springs that extend and contract to fit various phone sizes. This piece of the tripod can be taken off the base for an easier method of storage. With this new camera holder, The spring will provide the phone with a sturdy base that will decrease the amount of blurry images. Along with the stand, an app for smartphones will be created so that the camera can take the pictures with a self timer mode. The phone app will also sort and upload the images to a computer automatically for easier access when analyzing with the computer program.