BME100 f2013:W1200 Group17 L6

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 Name: Sonia Malek File:Cox.jpg Name: Mickie Cox Name: Andrew Prindle Name: Kevin Luong Name: Jason Yang Name: student [Instructions: add the name of your team's company and/or product here] LAB 6 WRITE-UP Computer-Aided Design TinkerCAD [Instructions: A short summary (up to five sentences) of the TinkerCAD tool and how you used it in lab on November 20th] The TinkerCAD tool is a simple and effective application used to redesign models that can be printed out with 3D printers. In lab, the TinkerCAD tool was used to redesign the consumable kits of the PCR hardware, PCR hardware, and fluorimeter hardware system. By using TinkerCAD, adjustments can be made to complement each of the hardware designs to create a more faster, efficient, and simpler experiment. The remodeling of the hardware pieces consist of redesigning the PCR test tubes, and changing the lid of the PCR, and stabilizing the fluorimeter. These new designs will drastically improve the efficiency of measuring and performing the experiment. Implications of Using TinkerCAD for Design There were a lot of improvements that were made on the PCR test tubes. The test tube that is shown on the image now has a label at the center. This further improves data inventory and helps establish organization on the samples itself. Not only are labels added to the test tubes, but also an attachment component has been added on the tubes. The attachment is just a simple plastic that hooks on to the other tube. It's designed to simply attach and detach from each other with little hassle. This then creates a more flexible way into attaching test tubes together and improves time when applying DNA samples to the test tubes itself. Now users can just attach several test tubes into one and this allows them to save more time when using the pipettes and applying samples into the test tubes. 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 Forward Primer: [Instructions: write the sequence of the forward primer] Cancer-specific Reverse Primer: [Instructions: write the sequence of the forward primer] 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 Kit [Instructions: Summarize how the consumables will be packaged in your kit. You may add a schematic image. An image is OPTIONAL and will not get bonus points, but it will make your report look awesome and easy to score.] The consumables will be packaged into a box. In the box, there will be a bin with 3 drawers. The first drawer will contain the tubes where you put all the mixtures for the PCR machine reaction. The tube case will have areas to clearly label the tubes. The second drawer will have the PCR mix and the third drawer will have the primers. All 3 drawers will also be clearly labeled. The box will also include a soft, velvet pocket for the micropipette and a plastic box of sterile micropipette tubes. [Instructions: IF your consumables packaging plan addresses any major weakness discussed by your group or mentioned by others (see the Virtual Comment Board Powerpoint files on Blackboard, Lab Week 12) explain how in an additional paragraph. ] A major weakness was not having enough area to label the DNA tubes. We addressed this issue by adding flat areas to label directly onto the tubes. Also there are spots to label on the tube case. The tubes were easily mixed up and disorganized so we added a hooking feature to the tubes inorder to help them stay connected and be separated more easily. Feature 3: PCR Machine Hardware [Instructions: Summarize how you will include the PCR machine in your system. You may add a schematic image. An image is OPTIONAL and will not get bonus points, but it will make your report look really awesome and easy to score.] [Instructions: IF your group has decided to redesign the PCR machine to address any major weakness discussed by your group or mentioned by others (see the Virtual Comment Board Powerpoint files on Blackboard, Lab Week 12) explain how in an additional paragraph.] One weakness is only being able to to one PCR at a time. The problem with this is that in a class of over a hundred students, it is more efficient to buy something that does 4 PCRs with one machine rather than 4 different machines. Also in reasearch labs, researchers may be doing multiple PCRs so it's convenient to have 4 different PCRs going in one machine rather than 4 machines.We designed the PCR machine to have 4 different sections to do 4 different PCRs at once and at different times. The PCR was also slow and hard to read so we put in a smarter, more accurate software. The screen will display the progress of each reaction and the correct amount of time left for the PCR to finish. Feature 4: Fluorimeter Hardware The fluorimeter is used to hold the glass slide in place horizontally as the light is moved from one end of the fluorimeter to the other. In the new group design the fluorimeter is accompanied with a black box, a stand with a camera attached, and pieces of velcro that will help hold the box, flourimeter, and stand in place. An image is OPTIONAL and will not get bonus points, but it will make your report look really REALLY awesome and easy to score.] [Instructions: IF your group has decided to redesign the fluorimeter to address any major weakness discussed by your group or mentioned by others (see the Virtual Comment Board Powerpoint files on Blackboard, Lab Week 12) explain how in an additional paragraph.] 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.]