Tellurium interface

Static network visualizations:

• sp_view(model)

• sp_rxns_view(model)

Visualization of the species network clustered with different algorithms:

• sp_comm_louvain_view(model)

• sp_comm_greedy_view(model)

• sp_comm_asyn_lpa_view(model)

• sp_comm_label_propagation_view(model)

• sp_comm_girvan_newman_view(model)

• sp_comm_asyn_fluidc_view(model)

Dynamic visualization:

• sp_dyn_view(simulation)

In the future, we plan to add more visualizations of Tellurium models

import tellurium as te
import pyvipr.tellurium_viz as tviz

r = te.loada("""
    J1:S1 -> S2; k1*S1;
    J2:S2 -> S3; k2*S2;
    J3:S4 -> S3; k2*S4;

    k1= 0.1; k2 = 0.2;
    S1 = 10; S2 = 0; S3 = 0; S4 = 20;
""")

Species view

tviz.sp_view(r)

Species reactions view

tviz.sp_rxns_view(r)

Communities view

tviz.sp_comm_louvain_view(r)

Dynamic visualization of a Tellurium model

To obtain the dynamic visualization of a Tellurium model users have to pass an specific selection to the simulate function. This selection has to contain the time variable, and all the species and reactions defined in the model.

# Obtaining species and reactions defined in a model
selections = ['time'] + r.getFloatingSpeciesIds() + r.getReactionIds()

r.simulate(0, 40, selections=selections)
tviz.sp_dyn_view(r)