Command line interface#

When you install goss you will also get access to a command line interface that can be used to solve ODEs and to list information. You can get the help text by typing

$ goss --help

 Usage: goss [OPTIONS] COMMAND [ARGS]...

 goss - General ODE System Solver
 goss is a library for solving ODEs using the gotran ode format. It is
 written in C++ but contains python bindings.

╭─ Options ──────────────────────────────────────────────────────────────╮
│ --version      Show the version and exit.                              │
│ --help         Show this message and exit.                             │
╰────────────────────────────────────────────────────────────────────────╯
╭─ Commands ─────────────────────────────────────────────────────────────╮
│ code-params      List available parameters to codegeneration           │
│ gotran2goss      Convert .ode file to goss file                        │
│ list-solvers     List available solvers and info about them            │
│ run              Solve an ODE                                          │
╰────────────────────────────────────────────────────────────────────────╯

The CLI is built on click, rich and pydantic

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Use command line interface for solving the Ten Tusscher model#

To solve an ODE from the command line, we can use the goss run commend. You can see all the available options by typing goss run --help

$ goss run --help

 Usage: goss run [OPTIONS] FILENAME

 Solve an ODE

╭─ Options ──────────────────────────────────────────────────────────────╮
│ --end-time  -T   FLOAT                      End time                   │
│ --solver         [ExplicitEuler|RK2|RK4|RL  Which solver to use        │
│                  1|RL2|GRL1|GRL2|ImplicitE                             │
│                  uler|ThetaSolver|RKF32|ES                             │
│                  DIRK23a]                                              │
│ --dt        -dt  FLOAT                      Time step                  │
│ --plot-y    -y   TEXT                       States or monitored to     │
│                                             plot on the y axis         │
│ --plot-x    -x   TEXT                       Values used for the x      │
│                                             axis. Can be time and any  │
│                                             valid plot_y variable.     │
│ --help                                      Show this message and      │
│                                             exit.                      │
╰────────────────────────────────────────────────────────────────────────╯

Assume that we have the Ten Tusscher model defined in the file tentusscher_panfilov_2006_M_cell.ode. To get this file you could do the following

  1. The model is available at CellML

  2. Download model and convert

    git clone https://models.physiomeproject.org/workspace/tentusscher_panfilov_2006
cd tentusscher_panfilov_2006

  3. Convert .cellml file to .ode

    gotran cellml2gotran ten_tusscher_model_2006_IK1Ko_M_units.cellml

Now, to solve the model we could for example do

goss run -T 1000 --solver GRL1 -dt 0.01 --plot-y V --plot-y Ca_i tentusscher_panfilov_2006_M_cell.ode

Here we have specified the we want to solve for 1000ms using the GRL1 solver and an internal time step of 0.01. We have also specified that we want plot the voltage (V) and the intracellular calcium concentration (Ca_i)

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