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   AUTHORS:
        
        Taewon Cho, Department of Mathematics, Virginia Tech

        Julianne Chung, Department of Mathematics, Virginia Tech
       
        Hodjat Pendar, Department of Biomedical Engineering and Mechanics, Virginia Tech
   
   REFERENCE:

       "Computational Tools for Inversion and Uncertainty Estimation in Respirometry". 
            2021.

   SOFTWARE LANGUAGE:

       MATLAB 9.6 (R2019a)


=====================================================================
SOFTWARE
=====================================================================
The MainDrivers require the following packages:

   (1) RestoreTools by James Nagy, Katrina Palmer, and Lisa Perrone
	http://www.mathcs.emory.edu/~nagy/RestoreTools/index.html

   (2) IRTools by James Nagy, Sivia Gazzola, and Per Christian Hansen
	https://github.com/silviagazzola/IRtools

   (3) genHyBR by by Julianne Chung and Arvind Saibaba
	https://github.com/juliannechung/genHyBR

   (4) Codes from the SIAM Book by Johnathan M. Bardsley
      "Computational Uncertainty Quantification for Inverse Problems"
        https://github.com/bardsleyj/SIAMBookCodes  

   (5) FISTA, a MATLAB implementation by Tiep Vu
	https://github.com/tiepvupsu/FISTA

First run startup_Respirometry.m for setting paths.

MainDrivers for each numerical experiments of inverse problems

  EX_1_MainDriver_sim.m           Sets up and runs a linear inverse
                                  problem corresponding to Sections  
                                  "Linear Respirometry Reconstruction"
                                  and "Nonlinear Respirometry
                                  Reconstruction" with simulations.
                                  Generates Figures 1-10

  EX_2_MainDriver_real.m          Sets up and runs real blind
                                  deconvolution corresponding to
                                  "Nonlinear case study: Abdominal
                                  pumping and CO2 emission in a darkling
                                  beetle" and generating Figures 13, 14

  Ex_3_MainDriver_real_true.m     Sets up and runs real linear case study
                                  generating Figures 11, 12