Difference between revisions of "User:Asisk"

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(→‎Relative 'Cleanability' from Geometry)
(→‎Goals for the Summer)
 
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=Predicting Relative 'Cleanability' from Geometry=
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=[[Validating a CFD Model for Predicting Relative ‘Cleanability’ of Reusable Medical Devices]]=
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Mentors: Dr. Stephen Merrill and Casey O'Brien  
+
Mentors: [http://www.mscs.mu.edu/~stevem/ Dr. Stephen Merrill] and Casey O'Brien  
  
 
==Personal Info==
 
==Personal Info==
  
−
My name is Anna Sisk I am going into my senior year at Marquette University.  I am majoring in Mathematics and minoring in Biological Sciences.
+
My name is Anna Sisk and I am going into my senior year at Marquette University.  I am majoring in Mathematics and minoring in Biological Sciences.
  
−
==Research Topic==
+
==Goals for the Summer==
  
−
I am researching the 'cleanability' of surgical equipment, specifically arthroscopic shaver handles.  Due to the geometry of these tools cleaning and sterilizing them is not possible with the reprocessing procedures given by the manufacturers.  This can lead to the shavers retaining tissues, such as bone, blood, and other fluids, between surgeries causing infections and, in some cases, death.  After an outbreak of surgical site infections (SSI) following orthopedic operations at a Texan hospital attention was drawn to the dirty surgical equipment.  The Food and Drug Administration (FDA) issued a safety warning concerning the shavers and proper reprocessing techniques.  The project I am working on is looking at CT scans of plastic models of the shavers and developing a mathematical models to show where particles are retained.  Our goal is to validate these models.
+
*Characterize the data the micro-CT scans of the plastic models
  
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==Goals==
+
*Find scaling factor to fit plastic data to the simulation data
  
−
*Characterize the distribution from from the CT scans of the plastic models
+
*Determination of simulation time between plastic and simulation models
−
 
+
−
*Determination of simulation time between plastic and mathematical models  
+
  
 
==Weekly Accomplishments==
 
==Weekly Accomplishments==
 
===Week 1===
 
===Week 1===
 
*Orientation to the REU  
 
*Orientation to the REU  
−
*Lunch with Dr. Merrill and Casey to determine project and develop a preliminary outline for the summer
+
*Lunch with Dr. Merrill and Casey to determine project and develop a preliminary outline for the summer (Tuesday)
−
*Two additional meeting with Casey to discuss the different tools and programs we will use, receive background references and information, and work on using Matlab  
+
*Two additional meeting with Casey to discuss the different tools and programs we will use, receive background references and information, and work on using Matlab (Wednesday and Friday)
 
* Research and reading on background information: what the problem is, why it is important, how attention was brought to it, what is being done, ect.
 
* Research and reading on background information: what the problem is, why it is important, how attention was brought to it, what is being done, ect.
 
*Practicing different tools on Matlab
 
*Practicing different tools on Matlab
 
* Setting up this wiki page
 
* Setting up this wiki page
 +
===Week 2===
 +
*Meeting with Casey (Monday)
 +
**received PDF and CT scan data
 +
*Continuing Matlab practice
 +
*Meeting with Casey and Dr. Merrill (Tuesday)
 +
*Graphed and plotted the PDFs for model D
 +
**Calculated average of the 5 runs and graphed it
 +
*Read about One-Dimensional Search Methods in ''Introduction to Methods of Optimization''
 +
*Looked into sequential and dichotomous search methods
 +
*Meeting with Casey and Dr. Merrill (Thursday)
 +
**Discussed what to work on and how to make a poster
 +
*Attended Dr. Brylow's Talk on Good Research Talks and Papers (Thursday)
 +
**I am now terrified of grad school
 +
*Rescale graphs, so they accurately reflect PDFs
 +
*Calculated and graphed standard deviation and variance of PDFs
 +
*Started testing for a Poisson distribution
 +
 +
===Week 3===
 +
*Finished the test for a [[Media:poissontest.jpg|Poisson distribution]]
 +
**The data does not appear to fit this distribution
 +
*Working on developing a conceptual model (traffic flow)
 +
*Meeting with Dr. Merrill and Casey (Tuesday)
 +
**Taking the data from Casey's model and matching the mean and variance to the data from the plastic model
 +
**Find out how long Casey's model needs to run so it matches the plastic model data
 +
**Continue working on the conceptual model
 +
*Wrote up a summary for the [[Media:ConceptualModelSummary.pdf|conceptual model]]
 +
*Dr. George Corliss' talk on using LaTeX (Thursday)
 +
*Meeting with Dr. Merrill and Casey (Thursday)
 +
**Continued to outline poster and paper
 +
***Talked about different titles
 +
**Discussed conceptual model and how it can inform our thoughts on this project
 +
**Need to come up with a definition of 'cleanability'
 +
**Decided on goals for the next week and and outline for the rest of the summer
 +
*Drafted a preliminary outline for poster
 +
*Next steps:
 +
**Receive data from Casey's model and determine the correct run time for his model
 +
**Compute the sum of squares and plot it vs time
 +
**Calculate the minimum for the function
 +
**Fit the variance and mean of the two models
 +
**If we are able to validate this specific model, we can then try to apply this method to other plastic models with different geometries
 +
 +
===Week 4===
 +
*Continued working on poster outline
 +
*Received the simulated data from Casey
 +
**Plotted the data
 +
*Meeting with Casey (Tuesday)
 +
**Talked about mini presentation
 +
**Looked and the data from the simulation and the plastic models
 +
**Talked about interpolating the data so we can calculate the sum of squared differences (SSD)
 +
*Leaned how to interpolate data on MATLAB
 +
*Figured out how to calculate SSD (taking into consideration the plastic and simulated data have different slice sizes)
 +
**Plotted the SSD and fitted a spline curve to it
 +
*Meeting with Casey(Thursday)
 +
**Went over results from SSD
 +
**Simulation parameters may need to be adjusted so the simulation data fits the plastic model data better
 +
**Continued to talked about mini-presentation
 +
**Explained how to create a function on MATLAB
 +
*Worked on slides and outline for mini presentation
 +
*Created a MATLAB function for computing SSD
 +
 +
===Week 5===
 +
*Worked on powerpoint and talk for mini presentation
 +
*Meeting with Dr. Merrill and Casey (Tuesday)
 +
**Talked about how to give a short research talk
 +
**Gave update on what happened last week
 +
**Discussed ways to get the SSD work
 +
*Finished writing mini-presentation talk and slides
 +
*Received new simulation data
 +
*Mini-Presentation
 +
*Meeting with Dr. Merrill and Casey(Thursday)
 +
**Talked about presentation tips
 +
**Brief update on what I've accomplished this week
 +
*Figured out how to work with new data
 +
*Interpolated simulation data
 +
*Calculated SSD between new simulation data and plastic data average
 +
*Discussed results of SSD with Casey
 +
**Still not looking correct
 +
 +
===Week 6===
 +
*Happy Fourth of July
 +
*Meeting with Dr. Merrill and Casey (Tuesday)
 +
**Looked at SSD and data calculated last week
 +
**Talked about using scaling to fit the data
 +
**Discussed ways to improve delivering talks
 +
*Worked on scaling plastic data
 +
**scaled in by 10, 15, 20
 +
*Showed results to Casey
 +
**Data looks much better
 +
*Wrote a function to determine where the SSD stop the decreasing trend
 +
*Looked at the data scaled by 16, 17, 18, 19
 +
*Meeting with Casey and Dr. Merrill (Friday)
 +
**Reviewed scaled data
 +
**Decided to pick scaling factor by matching the area under the curve for the plastic to the area under the curve for the simulation
 +
**Looked at picking a run time (maybe 15 seconds?)
 +
**Talked about writing the research paper
 +
*Looked at area under the curve for the plastic and simulation curves
 +
**Area under the curve for simulation: 20.07
 +
**Area under the curve for plastic: 1 (since its a PDF)
 +
**Thus a scaling factor of 20 best fits the data
 +
 +
===Week 7===
 +
*Researched writing a research paper and abstract
 +
*Created a simple outline of paper
 +
*Meeting with Dr. Merrill and Casey (Tuesday)
 +
**Actual research is mostly finished
 +
**Talked about how to write a research paper
 +
**Discussed proper documentation
 +
*Began working on research paper
 +
**Drafted the Introduction and History/Related Works section
 +
*Meeting with Dr. Merrill and Casey (Thursday)
 +
**Showed and discussed draft Introduction and History/Related Works section
 +
**Discussed what needs to be fixed and the rest of the paper
 +
*Dr. Factor's talk on posters (Thursday)
 +
**Began to panic about the poster
 +
*Continued writing
 +
**Wrote draft sections on Conceptual Model and Plastic Model Data
 +
 +
===Week 8===
 +
*Began working on poster
 +
*Meeting with Dr. Merrill and Casey (Tuesday)
 +
**Showed them a draft of the poster
 +
**Discussed how to finish the poster
 +
*Finished first draft of the poster
 +
*Showed Dr. Merrill and Casey the Poster
 +
**Made corrections
 +
*Finished and submitted poster
 +
===Week 9===
 +
*Worked on poster presentation
 +
*Continued to work on paper
 +
*Started to work on final presentation
 +
*Poster Presentation (Friday)
 +
*Wrote research talk abstract
 +
 +
===Week 10===
 +
*Worked on final presentation slides
 +
*Wrote final presentation talk
 +
*Wrote paper abstract
 +
*Attended research talks (Wednesday)
 +
*Gave my research talk (Thursday)
 +
*Last meeting with Dr. Merrill (Thursday)
 +
*REU Post Survey
 +
*Sent in paper (Friday)
 +
*Final updates on wiki page

Latest revision as of 04:09, 6 August 2016

Validating a CFD Model for Predicting Relative ‘Cleanability’ of Reusable Medical Devices

Mentors: Dr. Stephen Merrill and Casey O'Brien

Personal Info

My name is Anna Sisk and I am going into my senior year at Marquette University. I am majoring in Mathematics and minoring in Biological Sciences.

Goals for the Summer

  • Characterize the data the micro-CT scans of the plastic models
  • Find scaling factor to fit plastic data to the simulation data
  • Determination of simulation time between plastic and simulation models

Weekly Accomplishments

Week 1

  • Orientation to the REU
  • Lunch with Dr. Merrill and Casey to determine project and develop a preliminary outline for the summer (Tuesday)
  • Two additional meeting with Casey to discuss the different tools and programs we will use, receive background references and information, and work on using Matlab (Wednesday and Friday)
  • Research and reading on background information: what the problem is, why it is important, how attention was brought to it, what is being done, ect.
  • Practicing different tools on Matlab
  • Setting up this wiki page

Week 2

  • Meeting with Casey (Monday)
    • received PDF and CT scan data
  • Continuing Matlab practice
  • Meeting with Casey and Dr. Merrill (Tuesday)
  • Graphed and plotted the PDFs for model D
    • Calculated average of the 5 runs and graphed it
  • Read about One-Dimensional Search Methods in Introduction to Methods of Optimization
  • Looked into sequential and dichotomous search methods
  • Meeting with Casey and Dr. Merrill (Thursday)
    • Discussed what to work on and how to make a poster
  • Attended Dr. Brylow's Talk on Good Research Talks and Papers (Thursday)
    • I am now terrified of grad school
  • Rescale graphs, so they accurately reflect PDFs
  • Calculated and graphed standard deviation and variance of PDFs
  • Started testing for a Poisson distribution

Week 3

  • Finished the test for a Poisson distribution
    • The data does not appear to fit this distribution
  • Working on developing a conceptual model (traffic flow)
  • Meeting with Dr. Merrill and Casey (Tuesday)
    • Taking the data from Casey's model and matching the mean and variance to the data from the plastic model
    • Find out how long Casey's model needs to run so it matches the plastic model data
    • Continue working on the conceptual model
  • Wrote up a summary for the conceptual model
  • Dr. George Corliss' talk on using LaTeX (Thursday)
  • Meeting with Dr. Merrill and Casey (Thursday)
    • Continued to outline poster and paper
      • Talked about different titles
    • Discussed conceptual model and how it can inform our thoughts on this project
    • Need to come up with a definition of 'cleanability'
    • Decided on goals for the next week and and outline for the rest of the summer
  • Drafted a preliminary outline for poster
  • Next steps:
    • Receive data from Casey's model and determine the correct run time for his model
    • Compute the sum of squares and plot it vs time
    • Calculate the minimum for the function
    • Fit the variance and mean of the two models
    • If we are able to validate this specific model, we can then try to apply this method to other plastic models with different geometries

Week 4

  • Continued working on poster outline
  • Received the simulated data from Casey
    • Plotted the data
  • Meeting with Casey (Tuesday)
    • Talked about mini presentation
    • Looked and the data from the simulation and the plastic models
    • Talked about interpolating the data so we can calculate the sum of squared differences (SSD)
  • Leaned how to interpolate data on MATLAB
  • Figured out how to calculate SSD (taking into consideration the plastic and simulated data have different slice sizes)
    • Plotted the SSD and fitted a spline curve to it
  • Meeting with Casey(Thursday)
    • Went over results from SSD
    • Simulation parameters may need to be adjusted so the simulation data fits the plastic model data better
    • Continued to talked about mini-presentation
    • Explained how to create a function on MATLAB
  • Worked on slides and outline for mini presentation
  • Created a MATLAB function for computing SSD

Week 5

  • Worked on powerpoint and talk for mini presentation
  • Meeting with Dr. Merrill and Casey (Tuesday)
    • Talked about how to give a short research talk
    • Gave update on what happened last week
    • Discussed ways to get the SSD work
  • Finished writing mini-presentation talk and slides
  • Received new simulation data
  • Mini-Presentation
  • Meeting with Dr. Merrill and Casey(Thursday)
    • Talked about presentation tips
    • Brief update on what I've accomplished this week
  • Figured out how to work with new data
  • Interpolated simulation data
  • Calculated SSD between new simulation data and plastic data average
  • Discussed results of SSD with Casey
    • Still not looking correct

Week 6

  • Happy Fourth of July
  • Meeting with Dr. Merrill and Casey (Tuesday)
    • Looked at SSD and data calculated last week
    • Talked about using scaling to fit the data
    • Discussed ways to improve delivering talks
  • Worked on scaling plastic data
    • scaled in by 10, 15, 20
  • Showed results to Casey
    • Data looks much better
  • Wrote a function to determine where the SSD stop the decreasing trend
  • Looked at the data scaled by 16, 17, 18, 19
  • Meeting with Casey and Dr. Merrill (Friday)
    • Reviewed scaled data
    • Decided to pick scaling factor by matching the area under the curve for the plastic to the area under the curve for the simulation
    • Looked at picking a run time (maybe 15 seconds?)
    • Talked about writing the research paper
  • Looked at area under the curve for the plastic and simulation curves
    • Area under the curve for simulation: 20.07
    • Area under the curve for plastic: 1 (since its a PDF)
    • Thus a scaling factor of 20 best fits the data

Week 7

  • Researched writing a research paper and abstract
  • Created a simple outline of paper
  • Meeting with Dr. Merrill and Casey (Tuesday)
    • Actual research is mostly finished
    • Talked about how to write a research paper
    • Discussed proper documentation
  • Began working on research paper
    • Drafted the Introduction and History/Related Works section
  • Meeting with Dr. Merrill and Casey (Thursday)
    • Showed and discussed draft Introduction and History/Related Works section
    • Discussed what needs to be fixed and the rest of the paper
  • Dr. Factor's talk on posters (Thursday)
    • Began to panic about the poster
  • Continued writing
    • Wrote draft sections on Conceptual Model and Plastic Model Data

Week 8

  • Began working on poster
  • Meeting with Dr. Merrill and Casey (Tuesday)
    • Showed them a draft of the poster
    • Discussed how to finish the poster
  • Finished first draft of the poster
  • Showed Dr. Merrill and Casey the Poster
    • Made corrections
  • Finished and submitted poster

Week 9

  • Worked on poster presentation
  • Continued to work on paper
  • Started to work on final presentation
  • Poster Presentation (Friday)
  • Wrote research talk abstract

Week 10

  • Worked on final presentation slides
  • Wrote final presentation talk
  • Wrote paper abstract
  • Attended research talks (Wednesday)
  • Gave my research talk (Thursday)
  • Last meeting with Dr. Merrill (Thursday)
  • REU Post Survey
  • Sent in paper (Friday)
  • Final updates on wiki page
Retrieved from "https://reu.cs.mu.edu/index.php?title=User:Asisk&oldid=1571"