Fig 1.
Combining SBML and SED-ML to generate simulation results.
Table 1.
Reproducibility levels.
Fig 2.
SED-ML and wrappers that allow researchers to replicate results across multiple simulators.
See Shaikh et al. [24] for more details about the biosimulation engine wrapper architecture.
Fig 3.
BioModels 001 simulated with Copasi (A), an older version of Tellurium (B), and the latest version of Tellurium (C).
Fig 4.
The revised BioModels curation protocol.
Adapted from Malik-Sheriff, et al., 2020 [7] with permission.
Table 2.
Successful runs for each simulator of the 1055 currently curated ODE-based BioModels.
Fig 5.
Template (A) and Full SED-ML (B) replication across five wrapped simulators.
Table 3.
Example software fixes and enhancements.
Fig 6.
Simulation results from BioModel 19 (A) [35] and from BioModel 117 (B) [36], from all five wrapped simulators. The two graphs in C show a zoomed-in subset of the data from BioModel 117: all five simulator results on a single graph for y (top) and z (bottom).
No pair of simulator results passed our ’match’ threshold, for reasons that are obvious to the eye for Biomodel 19, but for reasons that can only be seen at larger scales for BioModel 117.