Output data for plots

[jonrkarr]

As discussed on the last day of HARMONY, in order to enable more modular execution of SED documents, tools which generate simulation data need to be able to export such data in a format (e.g., similar to the CSV format that tellurium uses for reports) that visualization tools can use to generate plots. Specifically, we discussed this in the context of runBioSimulations. But, this is generally needed to allow tools to focus on executing parts of SED-ML rather than the current status quo which emphasizes developing monolithic applications that support all of SED-ML.

• tellurium functions should return the raw data for curves and surfaces of plots (e.g., using numpy.ndarray)
• Provide capability to export this data in a similar format to that used for exporting reports
  • Rows: time
  • Columns: data generators for curves/surfaces of plots
  • Column headings: ids of the data generators

Status in BioSimulators/runBioSimulations

For runBioSimulations to work, each simulation tool has to support this. We have added the above functionality externally to tellurium so that runBioSimulations users can use tellurium to generate the data needed to interactively visualize plots in runBioSimulations.