BME100 f2013:W1200 Group6 L6: Difference between revisions
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'''Implications of | '''Implications of using TinkerCAD for design'''<br><br> | ||
One possible redesign of the OpenPCR machine would be to design a better camera holder. We had a lot of difficulty keeping the camera in one place. It was very easy to bump it and then everything would have to be set up again. Even a slight variation in the distance between the camera and the fluorimeter would change the image making it difficult analyze accurately in imageJ.<br><br> | One possible redesign of the OpenPCR machine would be to design a better camera holder. We had a lot of difficulty keeping the camera in one place. It was very easy to bump it and then everything would have to be set up again. Even a slight variation in the distance between the camera and the fluorimeter would change the image making it difficult analyze accurately in imageJ.<br><br> | ||
Using TinkerCAD, one | Using TinkerCAD, one can attach the camera holder to the fluorimeter. This attachment will be adjustable to allow the camera holder to be placed in the correct position to focus, making it adaptable to all phone models. Once in the correct position, a knob would hold the assembly in place so that the camera holder would stay in place, reducing the chance of error. TinkerCAD is useful in designing prototypes to be tested before having to manufacture a product on a more massive scale. | ||
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We will use a cardboard box with a styrofoam block | We will use a cardboard box with a styrofoam block inside to safely protect the materials. The micropipette, primer and mix will be held in place so that it will not move during packaging. Also, there will be plastic baggies to hold the tubes so that the kit is neatly organized and nothing gets mixed around. On the side of the styrofoam box will be the instructions manual. The outside of the box will have pictures that will demonstrate its uses and make it look professional.The logo and slogan will also be displayed on the outside of the box in a prominent position. | ||
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Weaknesses in the last kit was that the SYBR green dye kept going faulty. The SYBR green dye needs to be kept out of the light so that it doesn't get bleached and become ineffective. We made the SYBR green tubes black so that light will not degrade the dye. Another weakness was the labeling of the microtubes. We made the tubes better by adding labels to the side of the tubes. These labels not only identified the tubes, but also used as a grip so it does not fall from your fingertips on accident. | Weaknesses in the last kit was that the SYBR green dye kept going faulty. The SYBR green dye needs to be kept out of the light so that it doesn't get bleached and become ineffective. We made the SYBR green tubes black so that light will not degrade the dye. Another weakness was the labeling of the microtubes. We made the tubes better by adding labels to the side of the tubes. These labels not only identified the tubes, but also used as a grip so it does not fall from your fingertips on accident. | ||
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The PCR machine is | The PCR machine is improved and will be able to test more samples at once. The machine will run more smoothly and will be able to run cycles simultaneously on the open PCR program. This will make the machine more time efficient and it will allow hospitals to do more tests at once for a high demand of samples. | ||
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[[Image:Fluorup3.png|500px|]] | [[Image:Fluorup3.png|500px|]] | ||
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==Feature 4: Fluorimeter Hardware== | ==Feature 4: Fluorimeter Hardware== | ||
The fluorimeter will | The fluorimeter will use its same methods when its incorporated in the system design. It will still detect DNA in the our system and transmit light that will detect a fluorescence for a concentration of DNA. Adding grips and connecting the cradle to the fluorimeter box will make the device easier to use and more accurate when collecting data. | ||
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Latest revision as of 12:08, 27 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 COMPANYLAB 6 WRITE-UPComputer-Aided DesignTinkerCAD TinkerCAD is an online site that allows the user to create 3D designs easily. By combining and manipulation basic shapes, any design can be created. There are special tools and shapes that allow the user to create precise details. Once designed, it can be sent to a 3D printer to get a physical model by using a standard STL file.
We used TinkerCAD to modify a set of tubes used in PCR.
Feature 1: Cancer SNP-Specific PrimersBackground on the cancer-associated mutation A genome is an organism's entire genetic makeup. The human genome is composed of billions of base pairs. When the genome is copied to make a new cell it is not always perfect because a single base pair may: get deleted, added, or substituted. An example of this is when one DNA sequence is CTAAGTA and the other DNA sequence is CTAGGTA (this sequence should be CTAAGTA). The two DNA sequences seem identical; however, they differ at one nucleotide position. Variation or mutation in a single base pair creates a single nucleotide polymorphism (SNP). Our DNA is actually made up of millions of SNPs; this accounts for the many differences (e.g. physical characteristics, development of diseases or our systems’ response to pharmaceutical drugs) we have to each other. Furthermore, the SNP rs17879961 is linked to a high risk of cancers to homo sapiens. It commonly occurs on chromosome number 22 with a clinical significance of a pathogenic allele (i.e. it is in the human gene checkpoint kinase 2 or also called CHEK2). The CHEK2 gene provides codes for making proteins called checkpoint kinase 2. Checkpoint kinase 2 is stimulated when the dsDNA is damaged for whatever reason (e.g. disturbance of homeostasis). Ultimately, it acts as a tumor suppressor by inhibiting cancer cells from rapidly dividing and affecting healthy cells. Primer design
How the primers work: Feature 2: Consumables Kit
We will use a cardboard box with a styrofoam block inside to safely protect the materials. The micropipette, primer and mix will be held in place so that it will not move during packaging. Also, there will be plastic baggies to hold the tubes so that the kit is neatly organized and nothing gets mixed around. On the side of the styrofoam box will be the instructions manual. The outside of the box will have pictures that will demonstrate its uses and make it look professional.The logo and slogan will also be displayed on the outside of the box in a prominent position.
Feature 3: PCR Machine Hardware
Feature 4: Fluorimeter HardwareThe fluorimeter will use its same methods when its incorporated in the system design. It will still detect DNA in the our system and transmit light that will detect a fluorescence for a concentration of DNA. Adding grips and connecting the cradle to the fluorimeter box will make the device easier to use and more accurate when collecting data.
Bonus Opportunity: What Bayesian Stats Imply About The BME100 Diagnostic Approach
Calculation 4 tests specificity. It analyzes the probability that the patient will not develop cancer, given a non-cancer DNA sequence. Our result from calculation 4 was larger than calculation 3, but still not close to 1. So, a non-cancerous DNA would often still return a positive result.
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