BME100 f2014:Group17 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
Course Logistics For Instructors
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Name: Lauren Britton
Name: Maribel Hernandez
Name: Talal Al-zouman
Name: Nermin Elsharawy
Name: Aron lopez-Jimenez


Bayesian Statistics

Overview of the Original Diagnosis System

There were 68 diagnosed patients where 32 teams of 6 students analyzed the data. BME 100 Group 17 tested 2 patients for the disease-associated SNP by using their DNA. From the acquired data there were some that were replicated and so it caused some errors in the calculations. In order to prevent these errors the data had to be looked over again to fix the calculation. In order to prevent errors in the imageJ calibration, the oval had to be drawn as accurate as possible to produce an accurate concentration result. Three drop images were used per PCR sample that decreased the chances of a having a bad image that would distort the results. The class' final data from the BME100_fa2014_PCRResults spreadsheet showed successful conclusions, inconclusive results and blank data as well. Successful conclusions were found when all three trials for some patients had the same results. There were also successful conclusions even when one of the three PCR trials revealed a different result. For certain patients some of the trials came out as inconclusive and therefore overall causing an inconclusive result for that patient. There was blank data present for certain patients which were marked as NO TEST for their conclusion. Overall there was a frequency of .48 for positive results and a frequency of 0.39 for negative results.

What Bayes Statistics Imply about This Diagnostic Approach

Bayesian Statistics helps with understanding the limitation of diagnostic tests. For this lab, Bayesian stats were used to determine whether a patient had cancer or not. By having a small value for calculation 3, it showed that CHECK2 PCR had a low sensitivity. Low sensitivity shows the chance that a person with the disease being tested, will result in a positive diagnosis for that disease. However, CHECK2 PCR had a high specificity for guessing cancer, because of the number that delivered from the Bayesian statistics of more than one calculation 4.

Computer-Aided Design


The tinker cad is a user-friendly website that is used for 3-d designing. it allows users to create any 3-D design within different work planes and utilize the wide variety of shapes. It is convenient because it lets you create the design by adding shapes solids or holes, and combing them to form your design. Furthermore, the tinkercad’s interface is simple, allowing you to drag, drop, and move objects into and out of other objects, and to zoom in and out with ease.

Our Design


Description of image Closedpcrsideview.jpg

The tinkercad website is more applicable than the open PCR design because it allows one to have a precise and accurate design, to where as the PCR design does not. Our Tinkercad design has a lot of storage inside to improve data inventory and to help establish organization of the sample DNA. The gray square on the Tinkercad design is the display screen/programming are of our PCR machine. With an HD display screen to make sure no reading is ever misread. The yellow is where the test tubes would be inserted in real time. Our new and improved design does not just look better, but works more efficiently, faster, and comes with more room to run more tests at once. These designs, while simple, make for more accuracy and precision in the lab.

Feature 1: Consumables Kit

A shortcoming of Open PCR was that there was a lot to keep track of, it was hard to organize what primers and PCR mix had already been used while doing the pipetting. To overcome this challenge and still be easy to use ClosedPCR has improved upon this design with our packaging. The test tubes will be available with in different colors in order to allow customers to color coordinate their samples, for instance controls will be one color, patients may be another, different concentrations another, and so on. Customers can customize their orders by selecting the number of different colors needed for their specific studies. Another feature that will aid in organization and management of samples will be that our tubes will have labels that may be written on and then affixed onto the tubes, as opposed to writing directly on the tubes, which may be sloppy and make it difficult to keep track of the samples.

Even though Open PCR was easy to use, a weakness was that it was difficult to keep the samples organized and keep track of which ones had been used with the micropipettor. Our packaging aims to address this shortcoming, thereby allowing easy organization and management of the samples for customers of ClosedPCR.

Feature 2: Hardware - PCR Machine & Fluorimeter

The ClosedPCR machine will resemble standard PCR machines, however it will be able to hold more samples than other PCR models, which will help our customers save time. However unlike other models, ClosedPCR does not need to be attached to a computer as its display screen will show the cycles and time remaining, all programming (cycles to be completed etc) will be imputed on the machines display screen instead of a computer.

Our fluorimeter is an improvement over other models as the device is already assembled in one unit, no more messing around making sure the phone cradle is in a decent position or messing with the lightbox. Since customers need have access to the inside of the fluorimeter, the bottom is able to slide in and out of the lightbox and locks in place in the proper position to take pictures. That is, the entire system is within the lightbox, the customer places it on a secure surface, slides the bottom out to affix the slides to the fluorimeter and place the smartphone camera into the phone cradle (also permanently attached to the bottom) and set the timer, then simply slide it back into the locked position, and close the open side of the lightbox.

Some weaknesses with other PCR machines is the lengthy process and problems with setting up the fluorimeter. Our design address these problems by allowing the PCR machine to hold more samples, allowing customers to complete more work in the same amount of time, and it has the added convenience of not needing to be attached to a computer. Our fluorimeter eliminates problems with the setup as it is all attached in one unit, samples and camera phones are placed by sliding the bottom tray out of the lightbox, when slid back inside the customer will know it is in the correct position because it locks in place.