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