BME100 f2013:W900 Group15 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: Saiswathi Javangula Name: Justin Dombrowski Name: Gage Bebak Name: Ryan Fisher Name: student Name: student [Instructions: add the name of your team's company and/or product here] LAB 6 WRITE-UP Computer-Aided Design TinkerCAD TinkerCAD is an easy tool used to create digital designs that can be 3D printed into physical objects. TinkerCAD is specifically a program that allows modeling to form or refurbish a variety of products. During the previous lab, we used TinkerCAD to improve the construction of test tubes through design techniques. During the lab, we were given PCR tubes that needed minor adjustments, which could be accurately designed through TinkerCAD. One change that our group thought to make to the PCR machine was to add more holes, or places, for the test tubes in the tray under the heating pad. By doing so, there will be more accuracy in placing the test tubes perfectly in the given compartment. Also, we made the shapes of the lids into rectangles rather than circles to properly close the lids once the process was completed. We changed the layout of the test tubes by changing the shape of the lid into rectangles, which would ultimately allow for better usage of the test tubes. This would ensure for an easier and faster method to finishing up the test tube process. By adding in rectangle lids, it will cap easier and will ensure the tips to be in place when placing them inside rather than moving around too much. Also, by squaring the lids, it would ultimately allow for more space to add labels on top of the lids. By doing so, it would be much easier to know which tube is which immediately upon looking at it. Implications of Using TinkerCAD for Design TinkerCAD is an excellent tool for redesigning something like the PCR machine because it becomes very easy too start with design for the PCR machine and in TinkerCAD one can easily manipulate this design by changing the size, orientation, or completely adding something. For example, one change that our group thought to make to the PCR machine was to add more holes, or places, for the test tubes in the tray under the heating pad. By doing so, there will be more accuracy in placing the test tubes perfectly in the given compartment. We could easily illustrate this change through TinkerCAD by adding in more spaces between the test tubes, along with adding more holes between the test tubes to demonstrate the change that we want implemented. Also, we added in rectangular caps rather than circular ones to allow for easier finishing of the PCR process. This could be shown through TinkerCAD by using the shapes tool to add rectangles into the area of the lids, which clearly shows what we mean to portray. Using TinkerCAD is a very easy way when trying to add more of these rows of holes into the design specs. 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: TGATCTTCTATGTATGCAA Cancer-specific Reverse Primer: GTCCTAAAAACTCTTACAC 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 The consumables for the PCR kit which our company is creating will be tightly packed within the box that everything comes in so that it does not take up extra space and be both economically logical and will not create excessive waste. The kit will come with all necessary consumables and extras of all so that no separate purchases will be made by the consumer. It will come packaged with any liquids (including primers, etc.) on bottom so that if any leak or spill occurs there is less chance of the consumables being contaminated and as a second layer of protection, the consumables will be wrapped in plastic to reduce risk of contamination. Another goal of the way our consumables will be packaged is to have the packaging be usable to the consumer and act as a disposable tray that can hold all the pipette tips and a place in the packaging to dispose of the tips and excess liquids rather than using a trashcan or other method of disposal. In order to address the difficulty of cleaning the slide using the micropipettor which often did not completely clean the slide, we will include small disposable napkins that can be used to easily clean the slides and simply toss the napkin into the biohazard disposal bin. The edges of the slides were extremely sharp and could be very harmful if they were to cut someone so to avoid this issue the slides in our PCR testing kit will be made out of sturdy disposable plastic. in order to avoid measuring errors the micropipettors will come with a lock which will lock the dials into place to avoid bumping them and measuring the liquids wrong and wasting the primers, etc. Feature 3: PCR Machine Hardware Essentially, for our system, the PCR machine will basically be included in the same way as it was in the PCR kit. However, we will be making some changes to our own PCR machine. One of the main features we want to incorporate into our PCR system is an ability to have multiple testing abilities. For example, we would want the system to analyze multiple aspects such as cancer and diabetes. To do so, we would need to add more markers. By including more markers, or primers, we could redesign the PCR machine to test multiple diseases at once. The greatest advantage to adding multiple slots in the PCR machine is that it allows patients to properly assess information all at once, making it easier to use the machine to its fullest potential. Another function that we thought to be a major drawback for the PCR machine was the amount of time it took to perform an action. There is a relatively easy solution we would make to our own PCR machine by adding in more slots, which would mean a greater number of tubes to test a larger amount of DNA in the sample. By adding another row of holes for the test tubes or even two that could allow you to test not only 2 people at a time but 3 to 4 people. By allowing more tubes in the PCR machine, more DNA will be able to be tested, allowing more to get done in the time allocated. Therefore by adding two rows you could be essentially doubling the efficiency of the PCR device and or creating more trials to compare and thus create a larger data collection to analyze. Feature 4: Fluorimeter Hardware [Instructions: Summarize how you will include the fluorimeter 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 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 Calculation 3 for the Bayesian statistics is P(A I B). By calculating out the probability that the patient will develop cancer given a cancer DNA sequence, we received a a vary small value that was less than 1, which ultimately states that the value is not accurate. Likewise, for calculation 4, it was the same equation; however, it asked to find the probability that the patient will develop cancer given a non-cancer DNA sequence. After our calculation, we again received a very small value that was less than one, which again proves that the value is not very accurate. Both these calculates ultimately prove that the reliability of CHEK2 PCR is not very reliable for predicting cancer. One of the biggest reasons why CHEK2 PCR was found to be unreliable could have to been due to mistakes made during lab. Some of the trials could have accidentally used more or less of the sample than required, causing for a minor error in the reading. If the CHEK2 PCR was reliable, the values for calculations 3 and 4 would have closer to 1 rather than being so small.