Fig. 4
From: Visualizing metabolic network dynamics through time-series metabolomic data
Creation of an animated video from an SBML file, a pathway map, and a time-course metabolomic data set. EscherConverter converts the manually drawn pathway map in Escher’s JSON format [6] to SBML [33] with Layout extension [32]. The resulting SBML file is merged with the corresponding GEM (in SBML Level 3 Version 1 format, e.g., using the Java code from Additional file 14). After opening the merged SBML file in SBMLsimulator [48], a time-course metabolomic data set in CSV format (character-separated values) is also loaded to SBMLsimulator. An export function is provided in SBMLsimulator to generate a dynamic time-course animation