Functions_Simulation.rst

Simulation and Scoring

f_sim_score

.. toggle-header::
    :header: **Code**

       .. literalinclude:: ../Matlab/Code/Simulation/f_sim_score.m
          :linenos:
          :language: matlab

Calls the function that runs the simulations and the function that scores the output of the runs.

• Inputs
  • :ref:`stg<stg>`
  • parameters - (double) Set of parameters that we are working on
• Outputs
  • score - :ref:`rst.st<rst.st>`
  • :ref:`rst<rst>` - :ref:`rst.simd<rst.simd>`, :ref:`rst.xfinal<rst.xfinal>`, :ref:`rst.sd<rst.sd>`, :ref:`rst.se<rst.se>`, and :ref:`rst.st<rst.st>`
  • rst_not_simd - :ref:`rst.xfinal<rst.xfinal>`, :ref:`rst.sd<rst.sd>`, :ref:`rst.se<rst.se>`, and :ref:`rst.st<rst.st>`
• Calls - f_prep_sim, f_score
• Loads

f_prep_sim

.. toggle-header::
    :header: **Code**

       .. literalinclude:: ../Matlab/Code/Simulation/f_prep_sim.m
          :linenos:
          :language: matlab

Prepares the simulation making sure that an equilibration is preformed when necessary before running the main simulation.

• Inputs
  • :ref:`stg<stg>` - :ref:`stg.folder_model<stg.folder_model>`, :ref:`stg.name<stg.name>`, :ref:`stg.partest<stg.partest>`, :ref:`stg.tci<stg.tci>`, :ref:`stg.tcm<stg.tcm>`, :ref:`stg.tcd<stg.tcd>`, :ref:`stg.exprun<stg.exprun>`, :ref:`stg.simcsl<stg.simcsl>`, :ref:`stg.expn<stg.expn>`
  • parameters - (double) Set of parameters that we are working on
• Created Variables
  • rt
    • rt.ssa - (double) steady state amounts
    • rt.par - (double) All parameters of the model, takes the default ones from SBtab and then replaces the ones being worked on.
• Outputs
  • :ref:`rst<rst>` - :ref:`rst.simd<rst.simd>`
• Calls - f_sim
• Loads - :ref:`data.mat<data.mat>`, :ref:`model.mat<model.mat>`

f_sim

.. toggle-header::
    :header: **Code**

       .. literalinclude:: ../Matlab/Code/Simulation/f_sim.m
          :linenos:
          :language: matlab

Simulates the model with the provided configurations. The first time it is run it loads a representation of the model and the simulation, and compiles this information to C code.

• Inputs
  • exp_n - (double) Unique number to identify the model for each experiment or equilibrium reaction (it needs a new model object for each one)
  • :ref:`stg<stg>` - :ref:`stg.expn<stg.expn>`, :ref:`stg.folder_model<stg.folder_model>`, :ref:`stg.name<stg.name>`, :ref:`stg.sbioacc<stg.sbioacc>`
  • rt
    • rt.ssa - (double) steady state amounts
    • rt.par - (double) All parameters of the model, takes the default ones from SBtab and then replaces the ones being worked on.
  • :ref:`rst<rst>` - :ref:`rst.simd<rst.simd>`
• Outputs
  • :ref:`rst<rst>` - :ref:`rst.simd<rst.simd>`
• Calls - Sbioaccelerate, Sbiosimulate
• Loads - :ref:`Ready to run model<rr_model.mat>`, :ref:`Ready to run model equilibration<rr_model_eq.mat>`

f_score

.. toggle-header::
    :header: **Code**

       .. literalinclude:: ../Matlab/Code/Simulation/f_score.m
          :linenos:
          :language: matlab

Uses the results from the simulation of the model and the Data provided via the SBTAB to calculate a score for a given parameter set.

• Inputs
  • :ref:`rst<rst>` - :ref:`rst.simd<rst.simd>`
  • :ref:`stg<stg>` - :ref:`stg.folder_model<stg.folder_model>`, :ref:`stg.name<stg.name>`, :ref:`stg.exprun<stg.exprun>`, :ref:`stg.useLog<stg.useLog>`
• Outputs
  • :ref:`rst.st<rst.st>` - :ref:`rst.xfinal<rst.xfinal>`, :ref:`rst.sd<rst.sd>`, :ref:`rst.se<rst.se>`, :ref:`rst.st<rst.st>`
• Calls
• Loads - :ref:`data.mat<data.mat>`