BME100 f2013:W1200 Group3 L6: Difference between revisions
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After using the fluorimeter hardware in another system, we have decided to make several changes that we see necessary. These changes will mainly be concerning the amount of variables in operation. The original fluorimeter hardware was very difficult to set up because of the large quantity of variables. We place on creating a more effective camera stand that is adjustable for different cellular phones that may be used by the consumers. The camera stand will also be attached to the device so that the distance from the camera to the lights will become constant. We hope to improve the results of the machine by making the product more user-friendly and by reducing the chance of user error. | |||
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Revision as of 14:45, 26 November 2013
BME 100 Fall 2013 | Home People 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 Photos Wiki Editing Help | |||||
OUR COMPANY
LAB 6 WRITE-UPComputer-Aided DesignTinkerCAD
Implications of Using TinkerCAD for Design
Feature 1: Cancer SNP-Specific Primers[Instructions: This information will come from the Week 9 exercises you did in lab. Your notes should be in a pdf file that is saved on Blackboard under your group.] Background on the cancer-associated mutation [Instructions: Use the answers from questions 3, 4, 5, and 7 to compose, in your own words, a paragraph about rs17879961]
Primer design
How the primers work: [Instructions: explain what makes the primers cancer-sequence specific. In other words, explain why the primers will amplify DNA that contains the cancer-associated SNP rs17879961, and will not exponentially amplify DNA that has the non-cancer allele.]
Feature 2: Consumables KitThe small tubes are typically placed all together in a plastic bag. Instead the tubes would be placed in a holder similar to the one the micro-pipette tips are in. This makes for a more convenient set-up and organization. As well the tubes would be perforated so that the there could be any amount in a set, not just four. Lastly, to secure all of the tubes there would be lid to go over the container to help prevent spillage. Feature 3: PCR Machine HardwareThe PCR machine will be redesigned to address a few small issues that were found with the original version. Using the original version of the PCR machine was a large time consuming processes, so we are redesigning our PCR machine to reduce the run time. Another problem we saw with the PCR machine was that the performance was not reliable. Our redesigned machine aims to be accurate 100% of the time. We did not see a problem with the PC software; most people interested in using a PCR machine will have access to a computer. By putting the software on the computer, we are able to minimize the size of the machine. The last change that we are going to make to the machine is the size of the sample tray. Originally the PCR machine was only able to use 16 samples, but we thought this number was much too low. The improved PCR machine will be able to run 96 samples in each run."
Feature 4: Fluorimeter HardwareAfter using the fluorimeter hardware in another system, we have decided to make several changes that we see necessary. These changes will mainly be concerning the amount of variables in operation. The original fluorimeter hardware was very difficult to set up because of the large quantity of variables. We place on creating a more effective camera stand that is adjustable for different cellular phones that may be used by the consumers. The camera stand will also be attached to the device so that the distance from the camera to the lights will become constant. We hope to improve the results of the machine by making the product more user-friendly and by reducing the chance of user error.
Bonus Opportunity: What Bayesian Stats Imply About The BME100 Diagnostic Approach[Instructions: This section is OPTIONAL, and will get bonus points if answered thoroughly and correctly. Here is a chance to flex some intellectual muscle. In your own words, discuss what the results for calculations 3 and 4 imply about the reliability of CHEK2 PCR for predicting cancer. Please do NOT type the actual numerical values here. Just refer to them as being "less than one" or "very small." The instructors will ask you to submit your actual calculations via e-mail. We are doing so for the sake of academic integrity and to curb any temptation to cheat.] The results from calculation 3 give the probability of a person with cancerous DNA receiving a positive PCR diagnosis. This calculation has very low percentage meaning that the cancerous DNA will most likely not return a positive result from the PCR machine. The PCR instrument may not be the best device to use for this experiment. Calculation 4 tests specificity, giving the probability that a non-cancerous DNA sample will test negative using the PCR test. The calculated percentage for calculation 4 was also very small meaning that the PCR diagnosis test will likely return a positive result for a non-cancerous DNA sample. This suggests that the PCR machine would not be a good instrument to use to test for a non-cancerous negative result. |