RunBioSimulations recommends that investigators use Vega to describe visualizations of simulation results. Vega is a powerful and flexible format which can capture a wide range of interactive 2D data visualizations, including common charts such as histograms, heatmaps, and line plots and domain-specific diagrams such as metabolic maps, activity flow digrams, and genome tracks. RunBioSimulations supports Vega as outlined in the BioSimulators conventions . These guidelines describe how to connect the outputs of SED-ML reports to the inputs of Vega data sets.

BioSimulators-utils provides a command-line program and Python API for converting diagrams in multiple formats into Vega data visualizations.

• Escher metabolic maps: Example – Escherichia coli core metabolism (COBRApy Team) – SBML-fbc
• GINsim activity flow diagrams: Example – Yeast cell cycle (Irons et al., J Theor Biol, 2009) – SBML-qual
• Systems Biology Graphical Notation (SBGN) process description maps: Example – Represillator (Elowitz & Leibler, Nature, 2000) – CellML , SBML