sip-sensai

SIP_SENSAI code for measure-theoretic inverse sensitivity problems by Simon Tavener

How to recreate the results in Aidan's paper

Logistic

1. Using matlab, open the file

   sip-sensai/SENSAI_MuPad/Examples/ODE_examples/Logistic/Logistic.mn

   And set the correct paths at the top (set the last one to wherever you'd like the SIP stuff to go)

   From the menu, select

   Notebook > Evaluate all

   to generate "input" .m files

2. In matlab, browse to

   sip-sensai/SENSAI_MuPad

   And generate further m files using:

   run_MuPAD('Examples/ODE_examples/Logistic')

   Ignore the warning

Figure 1

3. After generating the files, run

   run_gtype('Examples/ODE_examples/Logistic', 0)

   Figures 15200, 15300 and 15301 are the ones in the paper

Hodgkin-Huxley 1, Symbolic-differentiation based stuff

Figure 4

1. Do the same as for Logistic, but with HodgkinHuxley/HodgkinHuxley.mn

   Figures 15200, 15300 and 15301 are the ones in the paper, but with different scalings for the x-axis (0-12). The y-axis of the black dotted graph should also be set to approx. -84, 34

Remaining figures

1. Generate input m files as before using MuPAD and Evaluate all

2. Now MANUALLY MODIFY the generated file

   sip-sensai/SENSAI_MuPad/Examples/ODE_examples/HodgkinHuxley/user_inputs.m

   and change

   qtype = 1;
   stype = 3;
   

   to

   qtype = 0;
   stype = 1;
   

3. Generate m-files using

   run_MuPAD('Examples/ODE_examples/Logistic')

   Ignore the warning

4. Check user_SIP.m and see if the grid size (ngrid) is set to something small

   ngrid = [10 10 10]

5. Now run an analysis using

   run_gtype('Examples/ODE_examples/HodgkinHuxley', 15)

   This should generate a bunch of files in the location specified way back in the MuPAD file.

6. Analyse the results by changing matlab's working directory to

   sip-sensai/SIP

   and running

   SIP_SENSAI('/home/michael/sensai', '/home/michael/sensai', 'HodgkinHuxley','HH-SpringBreak', 2, 2)

   where home/michael/sensai should be whatever you specified as OUTPUT_DIRECTORY way back in the MuPAD file.