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Latest revision as of 06:25, 12 June 2015
Contents
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 99mTcHMPAO 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
 Reran 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