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Latest revision as of 06:25, 12 June 2015

Personal Information

I study Computer Science and Physics as an undergraduate student at Purdue University. I will be a junior in the Fall of 2011. I am working this summer under Dr. Anne Clough on a project to model the kinetics of 99mTc-HMPAO in the lungs of rats.

Goals and Milestones

Week 1

  • Become familiar with the project

Week 2

  • Modify the input function to the model to be a Random Walk Function
  • Add subroutines to the MATLAB code
  • Add recirculation to the model
  • Modify the distribution of transit times
  • Complete a first draft of the Materials and Methods section of the final paper
  • Forward model should be mostly completed

Week 3

  • Complete a first version of the new program for the inverse problem
  • Complete a first draft of the Introduction section of the paper

Week 4

  • Complete an updated version of the program for the inverse problem
  • Complete a second draft of the Introduction section of the paper

Week 5

  • Complete a second draft of the Materials and Methods section of the paper with the inverse problem included

Week 7

  • Conduct simulations of control and hyperoxia data
  • Complete a first draft of the Results section of the paper

Week 8

  • Apply the model to real data
  • Complete the Results section of the paper

Week 9

  • Complete the discussion section of the paper

Week 10

  • Final edit of the paper
  • Presentations

Progress Log

Week 1

Monday, May 30

  • Moved in

Tuesday, May 31

  • Orientation Day
  • Had lunch with mentors
  • Paper work

Wednesday, June 1

  • Discussed project overview and goals for the week with mentor
  • Obtained the MATLAB code and became familiar with its workings
  • Read Lesson 37 in Partial Differential Equations for Scientists and Engineers to understand the method used to solve a system of PDEs

Thursday, June 2

  • Performed a literature search for papers relating to the project
  • Talk by Dr. Factor on good research practices
  • Had a tour of the library

Friday, June 3

  • Met with mentor to discuss goals and milestones for the ten week project
  • Added these goals and milestones to the wiki
  • Read MATLAB: An Introduction With Applications in preparation to begin editing the MATLAB code

Week 2

Monday, June 6

  • Read papers about modeling the distribution of capillary transit times and input functions
  • Read a chapter on ordinary differential equations
  • Began implementing subroutines in the MATLAB code

Tuesday, June 7

  • Changed the input function in the MATLAB code from a Normal Distribution to a Random Walk Function
  • Continued adding subroutines to the MATLAB code
  • Discussed numerical methods for approximating differential equations
  • Met with mentor to discuss progress and the inverse problem

Wednesday, June 8

  • Changed the distribution of transit times function in the MATLAB code to a Random Walk function
  • Documented the new MATLAB code
  • Forward model is now mostly complete
  • Began work on the first draft of the Materials and Methods section of the paper

Thursday, June 9

  • Working lunch with other REU students
  • Finished a project description
  • Continued work on the first draft of the Materials and Methods section of the paper.

Friday, June 10

  • Began reading on the use of a nonlinear least squares regression
  • Finished a first draft of the materials and methods section of the paper.

Week 3

Monday, June 13

  • Met with mentor to look over the forward model
  • Began fixing a few bugs in the MATLAB code for the forward model

Tuesday, June 14

  • Continued working on bugs in the MATLAB code for the forward model
  • Talk on research papers/presentations by Dr. Brylow

Wednesday, June 15

  • Began working on the first version of the inverse program
  • Successfully added noise to the simulated data

Thursday, June 16

  • Met with mentor to review bugs in the code and discuss the inverse model
  • Working lunch with REU students and mentors
  • Responsible conduct of research training
  • Finished the first working version of the Inverse program

Friday, June 17

  • Developed a MATLAB GUI for the forward and inverse programs
  • Worked on the Introduction section of the final paper

Week 4

Monday, June 20

  • Continued debugging of the forward model.
  • Added rate constant labels to the graphs for the forward model.
  • Read papers and continued writing the Introduction

Tuesday, June 21

  • Met with mentor to discuss progress on the inverse model
  • Modified the inverse GUI to allow for variable numbers of rate constants
  • Modified the inverse program to display graphs of forward model simulation

Wednesday, June 22

  • Ran tests on the forward model to determine the effect of each rate constant on the output
  • Documented the new code

Thursday, June 23

  • Working lunch with other REU students
  • Continued running tests to determine the effect of each rate constant
  • Read papers to try to get an idea as to which rate constants can be assumed to be zero or fixed at some other value.

Friday, June 24

  • Met with mentor to discuss changes to the inverse model
  • Continued reading papers for the Introduction section of the final paper

Week 5

Monday, June 27

  • Wrote a MATLAB script to test the sensitivity of R, Hb, Ht, Lb, and Lt to the six rate constants.
  • Worked on slides for the midway presentation.

Tuesday, June 28

  • Continued work on the sensitivity analysis MATLAB script
  • Finished the slides for the midway presentation

Wednesday, June 29

  • Met with mentor the discuss the sensitivity analysis and review the presentation slides.
  • Finished a final revision of the slides for the midway presentation.
  • Practiced the presentation

Thursday, June 30

  • Midway presentations
  • Completed a MATLAB script to varying the rate constants by 1% to test sensitivity of R, Lt, Lb, Ht, Hb.

Friday, July 1

  • Worked on a journal of progress I have made up until this point.
  • Created an annotated bibliography of the papers I have read thus far.
  • Edited the sensitivity script so k2 will permanently be held at 0

Week 6

Monday, July 4

  • Added the Inverse Model to the Materials and Methods draft
  • Ran the sensitivity script with N=150, T=20, and k2=0
  • Ran the One_percent script with N=200, T=20, and k2=0
  • Continued work on the progress journal
  • Continued work on the annotated bibliography

Tuesday, July 5

  • Continued work on the annotated bibliography
  • Ran the One_percent script with N=300, T=20, and k2=0
  • Attended a talk on good poster presentations
  • Met with mentor to discuss the sensitivity analysis

Wednesday, July 6

  • Created a MATLAB script to fit the parameters of the input function to the simulated mass (R) curve.

Thursday, July 7

  • Went to the Zablocki VA Medical Center with Dr. Clough to observe the experiments on rats.
  • Attended the weekly working lunch and a talk by Dr. Struble on his work with Tandem.
  • Obtained the experimental data and began working with it in the MATLAB models.

Friday, July 8

  • Documented new MATLAB code
  • Completed the progress journal up to the present
  • Re-ran the sensitivity analysis with an incorrect absolute value operation removed and k2=0

Week 7

Monday, July 11

  • Read papers dealing with the previous uses of HMPAO in the lungs
  • Updated the Introduction of the final paper to include a review of the lung literature

Tuesday, July 12

  • Worked on a few bugs in the function that determines the input function given the mass curve (R).

Wednesday, July 13

  • Met with Dr. Audi and Dr. Clough to discuss problems and progress so far
  • Dr. Audi recommended that I exchange velocity for a flow parameter and run sensitivity tests on the input curve and the flow parameter.
  • Made a trip to the library to find a few papers

Thursday, July 14

  • Finished an annotated bibliography
  • Began writing a MATLAB script to estimate model parameters after computing the input function using the experimental data
  • Began thinking about how to incorporate a flow parameter into the model.

Friday, July 15

  • Continued a new version of the program that combines all three scripts (Forward, Inverse, and the Input Function Calculation).
  • Learned how to use the MATLAB function interp1() to interpolate the experimental data so it can be used in this new version.

Week 8

Monday, July 18

  • Removed repetitive code from the latest version of the combined Forward/Inverse program
  • Debugged the combined Forward/Inverse program

Tuesday, July 19

  • Searched the literature for papers on the relationship between HMPAO and glutathione.
  • Finished debugging the combined Forward/Inverse program

Wednesday, July 20

  • Wrote a MATLAB script to test the sensitivities of the outputs to the input function.
  • Met with mentor and discussed improvements to the inverse model
  • Modified the code that generates an input function and tested and integrated it into the main program

Thursday, July 21

  • Working lunch with REU students
  • Created a script to perform a sensitivity analysis on the volumes
  • Continued working on bugs in the input curve fitting program
  • Began work on the poster

Friday, July 22

  • Continued working on the poster
  • Continued working on bugs in the inverse model
  • Met with mentor to discuss these bugs and discuss the poster

Week 9

Monday, July 25

  • Continued work on the input function generation algorithm
  • Fixed a scaling issue in the inverse model. The model now produces reasonable output.
  • Met with mentor to discuss the poster and input function problems
  • Finished a draft of the poster

Tuesday, July 26

  • Sent a draft of the poster to mentor for review
  • Met with mentor to review the poster
  • Began creating a version of the program with K5=K6

Wednesday, July 27

  • Finished a final draft of the poster
  • Completed a version of the program where K5 is always equal to K6
  • Met with mentor for the final time. Discussed poster, presentation slides and things to complete before leaving.
  • Worked on documenting and cleaning up code.

Thursday, July 28

  • Final lunch with other REU students
  • Worked on documenting and cleaning up code.

Friday, July 29

  • Continued documenting code.

Saturday, July 30

  • Created readme files for the MATLAB code.
  • Continued working on the final paper.

Sunday, July 31

  • Created slides for the final presentation.

Week 10

Monday, August 1

  • Finished slides
  • Worked on the final paper

Tuesday, August 2

  • Poster Session
  • Worked on the final paper

Wednesday, August 3

  • Attended the first half of the final presentations
  • Worked on the final paper.
  • Practiced presentation.

Thursday, August 4

  • Formal Presentation

Friday, August 5

  • Paper Due
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