BME100 f2015:Group12 1030amL6: Difference between revisions
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<!-- Instructions: Write a medium-length summary (~10 - 20 sentences) of how BME100 tested patients for the disease-associated SNP. Describe (A) the division of labor (e.g., 17 teams of 6 students each diagnosed 34 patients total...etc.), (B) things that were done to prevent error, such as the number of replicates per patient, PCR controls, ImageJ calibration controls, and the number of drop images that were used for the ImageJ calculations (per unique PCR sample), and (C) the class's final data from the BME100_Fa2015_PCRresults spreadsheet (successful conclusions, inconclusive results, blank data). Also, if applicable, discuss any challenges or problems you encountered that may have affected your data. --> | <!-- Instructions: Write a medium-length summary (~10 - 20 sentences) of how BME100 tested patients for the disease-associated SNP. Describe (A) the division of labor (e.g., 17 teams of 6 students each diagnosed 34 patients total...etc.), (B) things that were done to prevent error, such as the number of replicates per patient, PCR controls, ImageJ calibration controls, and the number of drop images that were used for the ImageJ calculations (per unique PCR sample), and (C) the class's final data from the BME100_Fa2015_PCRresults spreadsheet (successful conclusions, inconclusive results, blank data). Also, if applicable, discuss any challenges or problems you encountered that may have affected your data. --> | ||
For this lab, 17 teams of approximately 6 students each worked to diagnose a total of 34 patients. Each team was assigned two patients to complete three PCR trials on. In each group, one or two team members would handle wet lab duties such as pipetting samples and working with the fluorimeter while the remaining team members focused on ImageJ analysis. Several measures were taken to prevent error while working, including using positive and negative PCR control samples. The positive control came from someone who is known to have the disease SNP in question, while the negative control came from someone who is known to lack that SNP. These allowed the group to set baselines for positive and negative results, as even negative results yielded positive results for the fluorescence calculations. In addition, completing three trials for each patient ensured that our results were reliable and made it easy to see whether or not a result was anomalous. Using three drop images for each trial further increased our confidence in the results and helped prevent error. In ImageJ, | For this lab, 17 teams of approximately 6 students each worked to diagnose a total of 34 patients. Each team was assigned two patients to complete three PCR trials on. In each group, one or two team members would handle wet lab duties such as pipetting samples and working with the fluorimeter while the remaining team members focused on ImageJ analysis. Several measures were taken to prevent error while working, including using positive and negative PCR control samples. The positive control came from someone who is known to have the disease SNP in question, while the negative control came from someone who is known to lack that SNP. These allowed the group to set baselines for positive and negative results, as even negative results yielded positive results for the fluorescence calculations. In addition, completing three trials for each patient ensured that our results were reliable and made it easy to see whether or not a result was anomalous. Using three drop images for each trial further increased our confidence in the results and helped prevent error. In ImageJ, the same size of ellipse was used for each drop image so as to maintain the number of pixels to ensure image processing was consistent. | ||
''Final Data:'' | ''Final Data:'' |
Revision as of 23:05, 24 November 2015
BME 100 Fall 2015 | 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-UPBayesian StatisticsOverview of the Original Diagnosis System For this lab, 17 teams of approximately 6 students each worked to diagnose a total of 34 patients. Each team was assigned two patients to complete three PCR trials on. In each group, one or two team members would handle wet lab duties such as pipetting samples and working with the fluorimeter while the remaining team members focused on ImageJ analysis. Several measures were taken to prevent error while working, including using positive and negative PCR control samples. The positive control came from someone who is known to have the disease SNP in question, while the negative control came from someone who is known to lack that SNP. These allowed the group to set baselines for positive and negative results, as even negative results yielded positive results for the fluorescence calculations. In addition, completing three trials for each patient ensured that our results were reliable and made it easy to see whether or not a result was anomalous. Using three drop images for each trial further increased our confidence in the results and helped prevent error. In ImageJ, the same size of ellipse was used for each drop image so as to maintain the number of pixels to ensure image processing was consistent. Final Data:
Intro to Computer-Aided DesignExisting Design Assessment
Planning
TinkerCAD TinkerCAD is a simple 3D design and 3D printing that can be used by all with its simple and all encompassing array of tools. TinkerCAD provides an easy to use design studio for any and all. The essence of TinkerCAD is the use of basic building blocs and tools to construct simple or complex designs. With two simple design tools, adding shapes to your design as solids or holes and combining shapes together, creating any 3 dimensional design is at your finger tips. forming a new shape.TinkerCad also provides you with pre-existing shapes as well as the ability to upload your own. It is also possible to import a 2D image and convert it in to a 3D design that is printable. Our Design
Feature 1: ConsumablesFeature 2: Hardware - PCR Machine & FluorimeterFrom our experience using the open PCR machine and the fluorimeter and others experience, we found the PCR machine to meet and and exceed portable PCR standards. This PCR machine provided us with accurate results with the variations in results due to variations in samples not inconsistent performance by your thermocycler. The compatibility with computers is also handy providing users with easy to use software where users can adjust the time and the temperature and with in hours you will have plenty of DNA for sorting and sequencing. However the fluorimeter that was used to analyze the the samples seemed to have far to many variables to be accounted for. With the fluorimeter, there were three separate moving parts to the fluorimeter, the camera stand, the actual fluorimeter, and the dark box. These three moving parts are not connected causing the high possibility of the movement of any part effecting the other moving parts position. This can effect the accuracy of the data. The camera stand, which does not stand hold the camera in the first place, had to be placed 9 to 11 inches way from the fluorimeter. The black box had to removed to place a sample on the fluorimeter and placed over the fluorimeter and camera stand to reduce outside light. This process of removing and placing the box back on did in fact bump the fluorimeter, camera stand set up, altering the set up and in the end slightly altering our data. In order to prevent this, we decided to connect the black box to the fluorimeter and the camera stand with detachable and adjustable connections combined with a weighed base to the fluorimeter to prevent unnecessary movement. Be black box would be connected to the back of the fluorimeter through a rotating hinge that would allow the user to pull back the black box and have it rest on it's back side face. This would reduce the ill effects of having to constantly remove and place the black box. For the stand we created a a more mobile phone friendly stand, that can be adjusted to the proper distance, in inches, from the fluorimeter. This whole set up can disassembled and placed in the black box for easy storage. Open PCR. No changes were made to the PCR machine The black box, fluorimeter and camera stand were connected together to form a more secure system that reduces the variability in the data.
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