BME100 f2014:Group16 L6

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Owwnotebook icon.png BME 100 Fall 2014 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: Christopher Saar
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Name: Gurpaul Sidhu
Role(s): Wiki editor, researcher
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Name: Emily Angeles Mancinas
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Name: Leslie Bernardino
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Name: Romann Arizmendi


Bayesian Statistics

Overview of the Original Diagnosis System

A The division of Labor
The PCR project was divided into wet-lab, lab procedure and data reclamation. These data point were labeled and sent to data analysis through ImageJ which was run at least 2 times for every data point. All data point were imported into excel for complete calculation and statistical analysis. The group was split three groups of two, wet lab and photo collection was acquired where three photos were collected for every data trial. All data trials were sent to the second group where ImageJ calculations were run twice and imported into excel. The third group was tasked to import the data into OpenWetWare and wiki coded to accurately and quick translate qualitative and quantitative data into tables and charts.

B Error Prevention
Error reduction was prevented through the acquisition of multiple data point for every trial which helped to eliminated outliers and data variance which could misdirect calculations. For all trials for both patients strict pipette protocols were practiced to reduce contamination errors, each trial was recorded by photo three times to establish a better data reference. Once an image was taken the ImageJ program was run twice for one data set to help further smooth data and reduce outlier data.

C PCR Results for the Class
Date across the PCR was extensive and directed several observations. The indications towards positive results relative to a positive control, and resulted of positive results with a positive diagnosis were indicated through calculations of 87percent and 7 precent respectively. The negative relative to the negative control and negative towards a negative diagnosis was low at 30 percent to 46 percent respectively. This data is far from a 99 percent accuracy but give constraints has some data considerate of data analysis and interpretation.

What Bayes Statistics Imply about This Diagnostic Approach

Based upon the result of calculation 1 was extremely close to 100% which means that the PCR replicates are effective at concluding that a person has a disease SNP. Similarly, `the result of calculation 2 was also relatively high which means that if someone did not have the disease SNP the PCR replicates were efficacious in its conclusions. The first source of error was due to the fact that it was difficult to focus the camera which led to a certain degree of blurriness in the pictures. The second source of error was that there was no way to completely prevent light from entering the photo apparatus. The final error could have occurred due to the fact that he PCR reaction went past class time and therefore the DNA samples were forced to sit for an entire week.

The numerical value of calculation 3 was very low which means that the PCR is not effective at diagnosing or predicting the development of the disease. The same can be said about calculation 4 even though the value was slightly higher. The numerical value was not high enough for it to be claimed that the PCR reaction was effective at diagnosing the disease.||

Computer-Aided Design

The TinkerCAD tool functions similarly to Solidworks but instead utilizes a community based database for shapes to help complete designs. The tool was utilized to manipulate the size and holes present with the PCR machine.

Our Design

This design is an improvement of the original PCR design because it is larger in volume. Therefore, it can accommodate larger numbers of samples at one time. It also has a larger area to store samples which also aids in its ability to test more efficiently. It is also equipped with a button that allows for real time manipulation of the PCR process. This button is especially useful if experimenters feel as though there is a deficiency in the machine itself.

Feature 2: Consumables Kit

There were no significant issues that arose based on the packaging that was utilized in this experiment. Therefore, the liquid reagents and small plastics will be packaged in the same way that they were packaged in this study. The only difference will be the plate on which the vials are stored will be wider. This is due to the change in the PCR machine design that allows it to react more reagents at once. This is not necessarily a weakness in the current kit but instead a change that is analogous to the changes that were made when the PCR machine was improved.

Feature 3: Hardware - PCR Machine & Fluorimeter

The PCR, as pictured, will operate the same within the experimental system but will be able to hold more samples and offer better user control. The fluorimeter will be unchanged, except, the button that operates the PCR machine can be detached and used on the fluorimeter. The button would be connected directly to the camera, allowing pictures to be taken without allowing light into the apparatus. This would improve the design by giving better images of the PCR results. Furthermore, the efficiency of the PCR machine would compensate for human error by increasing the window of redoing trials.