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. 2018 Jun 15;14(6):e1006220. doi: 10.1371/journal.pcbi.1006220

Fig 1. A demonstration of Tellurium’s SBO syntax.

Fig 1

This figure shows a model of mitotic exit in budding yeast [38] available via the Biomodels repository entry BIOMD0000000370 [39]. When the SBML for this model is imported, Tellurium automatically extracts SBO identifiers for species, reactions, compartments, etc. and embeds the identifiers in the Antimony code. These identifiers point to specific physical, biological, or mathematical entities recorded in the ontology. For example, the first identifier, SBO:0000290, refers to a compartment in physical space [40]. Other identifiers refer to polypeptide chains (SBO:0000252) and protein complexes (SBO:0000297). These identifiers appear inline in the notebook cell and can be edited by the user. The right panel shows the transient response for this model from 0 to 120 minutes. This example is included with the Tellurium notebook viewer version 2.0.14 and later (File→Open Example Notebook→Mitotic Exit (Vinod)).