View source for User:Pfitzg

== Personal Information ==

I study Computer Science and Physics as an undergraduate student at [http://www.purdue.edu/ Purdue University]. I will be a junior in the Fall of 2011. I am working this summer under [http://www.marquette.edu/mscs/facstaff.shtml 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