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. | |||
In our final data, there were 16 successful conclusions (where the conclusion matched the disease diagnosis) and 16 unsuccessful conclusions (that got a negative conclusion for someone with the disease, a positive conclusion for someone without the disease, or were inconclusive). Two results were inconclusive. One team failed to process their PCR samples and contribute their results, so two patients do not have any test results. | |||
''Final Data:'' | ''Final Data:'' | ||
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'''What Bayes Statistics Imply about This Diagnostic Approach''' | '''What Bayes Statistics Imply about This Diagnostic Approach''' | ||
<!-- Instructions: In your own words, discuss what the results for calculations 1 and 2 imply about the reliability of the individual PCR replicates for concluding that a person has the disease SNP or not. Please do NOT type the actual numerical values here. Just refer to the Bayes values in general terms (for example, "close to 1.00 (100%)", "about 50%", "very small", etc.). --> | |||
Calculation 1 implies that close to 80% of patients with a positive PCR reaction will receive a positive final test conclusion, and that the reverse is also true: the probability that a patient with a positive final test conclusion has a positive PCR reaction is close to 80%. In other words, close to 80% of people for which the PCR test comes back positive will be concluded to have the SNP, and people who are concluded to have the SNP will receive positive PCR tests around 80% of the time. Similarly, calculation 2 implies that people with negative final test conclusions will receive negative PCR reaction results about 80% of the time, while patients who receive a negative PCR result will get a negative final test conclusion about 90% of the time. This slightly higher percentage may indicate that the class' results favored negative test conclusions. | |||
<!-- Instructions: In your own words, discuss what the results for calculations 3 and 4 imply about the reliability of PCR for *predicting the development of the disease* (diagnosis). Please do NOT type the actual numerical values here. Just refer to the Bayes values in general terms (for example, "close to 1.00 (100%)", "about 50%", "very small", etc.). --> | <!-- Instructions: In your own words, discuss what the results for calculations 3 and 4 imply about the reliability of PCR for *predicting the development of the disease* (diagnosis). Please do NOT type the actual numerical values here. Just refer to the Bayes values in general terms (for example, "close to 1.00 (100%)", "about 50%", "very small", etc.). --> | ||
Calculation 3 implies that the probability that a patient who actually has the SNP and is diagnosed with the disease will receive a positive final test conclusion is actually quite small - around 10% - indicating that the class' final conclusions were not very effective at predicting whether or not the disease would develop. In addition, the probability that a patient with a positive final test conclusion would develop the disease was similarly low. This, unfortunately, implies that false positives were common. Calculation 4 indicates that a patient without the disease will receive a negative final test conclusion was close to 40%, and that a patient with a negative final test conclusion will not develop the disease close to 40% of the time. Therefore, negative test conclusions also seemed to be fairly poor predictors of disease development. | |||
<!-- Instructions: Discuss three possible sources of human or machine/device error that could have occurred during the PCR & detection steps that could have affected the Bayes values in a negative way. --> | <!-- Instructions: Discuss three possible sources of human or machine/device error that could have occurred during the PCR & detection steps that could have affected the Bayes values in a negative way. --> | ||
One possible source of error in this investigation is contamination. If any groups reused pipette tips by mistake, they could have false positives in their results. Another is mislabeling tubes, which could have led to either false negatives or positives because the results would not correspond to the indicated label. In addition, if any of the groups incorrectly set up the machines, they could have followed the wrong protocol and gotten inaccurate results. | |||
==Intro to Computer-Aided Design== | ==Intro to Computer-Aided Design== | ||
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| bgcolor=#cfcfcf | Our Brand Name: | | bgcolor=#cfcfcf | Our Brand Name: | ||
| bgcolor=#ffffff | | | bgcolor=#ffffff | HALO | ||
|} | |} | ||
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| bgcolor=#cfcfcf | Place | | bgcolor=#cfcfcf | Place | ||
|- | |- | ||
| | | Finally PCR for the masses. PCR method of copying DNA molecules that now can be done at your own desk. With our new and improved fluorimeter the data collected from analysis will be more accurate. We have reconstructed the fluorimeter to reduce the variable affecting your data. With an adjustable attached camera stand that provides a more secure and accurate stand for photography. The box cover is also attached to the fluorimeter and weighed down at the base to avoid any movement that may effect the accuracy of data. || Our product will be cheaper and made of stronger material than typical PCR units. Our PCR unit will be easy to follow and will contain detailed instructions || Our target market will be for anyone that uses Open PCR machines. Our product is made to be simple to use and is very self explanatory and doesn't need a lot of teaching before use. || Our target market in high school and university students. We are providing portable and accurate PCR machine that are easy to use for all. With simple steps and procedures, any high school or college student can easily operate this. Little previous understanding is needed to operate it and it is a very economically wise investment to improve a student education. | ||
|| - PCR is used in a multitude of places, ranging from hospitals that attempt to treat infectious diseases, to areas of forensics, and many research labs that deal with DNA sequencing and cloning. | |||
|} | |} | ||
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<!-- Instructions: Under the image, describe your design. Why did you choose this design? How is it different from the original OpenPCR design? --><br> | <!-- Instructions: Under the image, describe your design. Why did you choose this design? How is it different from the original OpenPCR design? --><br> | ||
[[Image:Fluorimeter2.PNG|300px|Open PCR. No changes were made to the PCR machine]] | |||
[[Image:Fluorimeter3.PNG|300px|Open PCR. No changes were made to the PCR machine]] | |||
[[Image:Fluorimeter4.PNG|300px|Open PCR. No changes were made to the PCR machine]] | |||
[[Image:Fluorimeter5.PNG|300px|Open PCR. No changes were made to the PCR machine]] | |||
[[Image:Fluorimeter6.PNG|300px|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. The whole set up can also be disassembled and placed inside the black box for easy storage | |||
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From 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. | From 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 | However the fluorimeter that was used to analyze the the samples seemed to have far too 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 were not connected causing the high possibility of the movement of any part effecting the other moving parts position. This can affect 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. | 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. The 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 its 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. | ||
[[Image:OpenPCRbox.png|300px|Open PCR. No changes were made to the PCR machine]] | [[Image:OpenPCRbox.png|300px|Open PCR. No changes were made to the PCR machine]] | ||
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Open PCR. No changes were made to the PCR machine | Open PCR. No changes were made to the PCR machine | ||
[[Image:Fluorimeter1. | [[Image:Fluorimeter1.PNG|300px|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. | The black box, fluorimeter and camera stand were connected together to form a more secure system that reduces the variability in the data. |
Latest revision as of 00:03, 25 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.
Final Data:
Calculation 1 implies that close to 80% of patients with a positive PCR reaction will receive a positive final test conclusion, and that the reverse is also true: the probability that a patient with a positive final test conclusion has a positive PCR reaction is close to 80%. In other words, close to 80% of people for which the PCR test comes back positive will be concluded to have the SNP, and people who are concluded to have the SNP will receive positive PCR tests around 80% of the time. Similarly, calculation 2 implies that people with negative final test conclusions will receive negative PCR reaction results about 80% of the time, while patients who receive a negative PCR result will get a negative final test conclusion about 90% of the time. This slightly higher percentage may indicate that the class' results favored negative test conclusions.
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
The black box, fluorimeter and camera stand were connected together to form a more secure system that reduces the variability in the data. The whole set up can also be disassembled and placed inside the black box for easy storage
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 too 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 were not connected causing the high possibility of the movement of any part effecting the other moving parts position. This can affect 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. The 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 its 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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