Plug-Ins for Omix
Omix as Front End for 13CFLUX2
A number of plug-ins is available that extend Omix to a comprehensive
modeling front end for 13CFLUX2.
13CFLUX2 is a high-performance simulation framework for 13C-based
metabolic flux analysis developed at Forschungszentrum Jülich.
It quantifies intracellular flux rates from
given isotopic enrichment data from experimental studies.
13CFLUX2 uses an own proprietary XML-based model specification format called
FluxML. FluxML models contain the stoichiometry of the reaction network,
atom mappings, constraints, measurement data and simulation parameters.
Usually, preparing a valid FluxML model of realistic size takes several
weeks, if not months. Particularly time-consuming are:
assembling the reaction network from literature and database information.
defining consistent atom mappings for the entire reaction network.
converting available measurement data from spreadsheets to
the xml data structure of FluxML.
All these modeling steps can be done in a fraction of the time with Omix.
Atom mappings can be modeled in the
Atomic Layer Plug-In.
By equipping each metabolite with a chemical structure within the
Structural Formula Plug-In, the atom mappings base
upon real molecule information where each individual atom is well-identifyable.
The KEGG as well as the
BioCyc database plug-ins allow to download reaction
networks including their atom mappings directly from KEGG and BioCyc, respectively.
Further database plug-ins are planned.
The flux constraints are defined in the
Network Constraints Plug-In.
The measurement model and simulation parameters are edited
within the 13CFLUX2 Modeling Plug-In. The modeling
process is completely dialog-based and software-supported.
The plug-in supports importing data and parameters from various
formats into the model.
After modeling with Omix, the FluxML file can be exported
by using the 13CFLUX2 FluxML Plug-In.
Finally, results from the simulation runs can be visualized in Omix.
Therefore, the 13CFLUX2 FWDSIM Import Plug-In and the
HDF5 for OVL Plug-In allow to access simulation
data in the corresponding file formats.
The Cumovis Plug-In supports the modeling process
by providing a visual representation of the atom transport
pathways within the model including path tracing and topology
The Fluxomix3D Visualization Plug-In visualizes
the simulation results in 3D.
13CFLUX2 related plug-ins are only available for registered 13CFLUX2 licensees.