agos

Cellml to code converter

Compile

cmake .

make

Run

./bin/agos -i cellml/model.cellml -o model -s -l python

This will generate a single cell solver for the model. To run the solver:

python model_single_cell_solver.py [simulation_time]

Ex:

python model.py 1000

will run a simulation of 1000 milliseconds.

It is also possible to generate a C solver that uses CVODE.

./bin/agos -i cellml/model.cellml -o model -s -l c

to compile the solver:

gcc model_single_cell_solver.c -o model -lm -lsundials_cvode

to run the solver:

./model [simulation_time]

Results

The model state variables will be saved in a file named out.txt

You can use gnuplot to plot the results:

gnuplot

gnuplot> plot 'out.txt' u 1:2 w lines

How to cite:

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Ciro B. Barbosa, Rodrigo W. dos Santos, Ronan M. Amorim, Leandro N. Ciuffo, Fairus Manfroi, Rafael S. Oliveira, Fernando O. Campos. A Transformation Tool for ODE Based Models. Part of the Lecture Notes in Computer Science book series (LNCS, volume 3991). https://doi.org/10.1007/11758501_14