The command-line tools listed on this page use Myokit to perform various tasks such as model import or export and model comparison.


Compares two Myokit models, for example:

$ myokit compare model1.mmt model2.mmt

Example output:

  [1] decker-2009
  [2] decker-2009
[1] Missing Variable <calcium.gamma>
[x] Mismatched RHS <stimulus.amplitude>
  2 differences found

For the full syntax, see:

$ myokit compare --help


Displays the calculation of a single variable from a model.


$ myokit debug example.mmt v
Variable not found, assuming "membrane.V"
Showing membrane.V  (State variable)
unit: mV
desc: The membrane potential
Initial value = -84.5286
ica.ICa         = -5.69307557845840514e-05
membrane.i_stim = 0.0
ib.Ib           = -9.66863706000000045e-01
ikp.IKp         = 1.27313823914652343e-08
ik1.IK1         = 1.03172820596243020e+00
ik.IK           = -7.99485510998167170e-03
ina.INa         = -1.19264480675140328e-05
dot(membrane.V) = membrane.i_stim - (ina.INa + ik.IK + ib.Ib + ikp.IKp
                    + ik1.IK1 + ica.ICa)
                = -5.68008003799787276e-02

For the full syntax, see:

$ myokit debug --help


Exports an mmt file using any of the available exporters.


$ myokit export <exporter_name> <source_file> <output_directory>

For example, to convert a model to cellml:

$ myokit export cellml example.mmt example.cellml

Or to create runnable code in the directory example_in_c:

$ myokit export ansic example.mmt example_in_c

For the full syntax, see:

$ myokit export --help


Evaluates an expression.


$ myokit eval "100 / 2 / 2"
100 / 2 / 2 = 25.0

For the full syntax, see:

$ myokit eval --help


Imports a model definition or protocol using any of the available importers.


$ myokit import <format> <source_file> -o <output_file>

If no output file is specified, the generated mmt file is simply printed to the screen.


$ myokit import cellml example.cellml

$ myokit import cellml example.cellml test.mmt

For the full syntax, see:

$ myokit import --help


Loads an mmt file and runs the embedded script. If no script is available, a default script is run using the file’s model and/or protocol.

Typical use:

$ myokit run lr1991.mmt

For the full syntax, see:

$ myokit run --help


Loads a model and evaluates the derivatives of the state variables at the initial time:

$ myokit step example.mmt
Single test step
Reading model from example.mmt...
Model LR1991 read successfully
Evaluating state vector derivatives...
Name        Initial value             Derivative at t=0
membrane.V  -8.45285999999999973e+01  -5.68008003799787276e-02
ina.m        1.69999999999999991e-03  -4.94961486033834719e-03
ina.h        9.83199999999999963e-01   9.02025299127830887e-06
ina.j        9.95484000000000036e-01  -3.70409866928434243e-04
ica.d        3.00000000000000008e-06   3.68067721821794798e-04
ica.f        1.00000000000000000e+00  -3.55010150519739432e-07
ik.x         5.70000000000000021e-03  -2.04613933160084307e-07
ica.Ca_i     2.00000000000000010e-04  -6.99430692442154227e-06

The results can be compared to a file containing reference values using

$ myokit step example.mmt -ref ref_step.txt

To test with different initial values, another file can be included:

$ myokit step example.mmt -ref ref_step.txt -ini ref_init.txt

For the full syntax, see:

$ myokit step --help


If you have moviepy (http://zulko.github.io/moviepy/) installed, this script can be used to generate movies from DataBlock1d or DataBlock2d files.

The syntax is

$ myokit video <inputfile> <variable> -dst <outputfile>

Here, <inputfile> should be the name of a DataBlock1d or 2d file. The variable to visualized should be given as <variable> and the output file should be given as <outputfile>. Supported outut formats are flv, gif, mp4, mpeg and wmv.


$ myokit video results.zip membrane.V -dst movie.mp4

For the full syntax, use:

$ myokit video --help