Utilities¶
The command-line tools listed on this page use Myokit to perform various tasks such as model import or export and model comparison.
compare
¶
Compares two Myokit models, for example:
$ myokit compare model1.mmt model2.mmt
Example output:
Comparing:
[1] decker-2009
[2] decker-2009
[1] Missing Variable <calcium.gamma>
[x] Mismatched RHS <stimulus.amplitude>
Done
2 differences found
For the full syntax, see:
$ myokit compare --help
debug
¶
Displays the calculation of a single variable from a model.
Example:
$ 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
export
¶
Exports an mmt
file using any of the available exporters.
Syntax:
$ 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
eval
¶
Evaluates an expression.
Example:
$ myokit eval "100 / 2 / 2"
100 / 2 / 2 = 25.0
For the full syntax, see:
$ myokit eval --help
import
¶
Imports a model definition or protocol using any of the available importers.
Syntax:
$ myokit import <format> <source_file> -o <output_file>
If no output file is specified, the generated mmt file is simply printed to the screen.
Examples:
$ myokit import cellml example.cellml
$ myokit import cellml example.cellml test.mmt
For the full syntax, see:
$ myokit import --help
run
¶
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
step
¶
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
video
¶
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.
Example:
$ myokit video results.zip membrane.V -dst movie.mp4
For the full syntax, use:
$ myokit video --help