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 analysis functionality.
• The Fluxomix3D Visualization Plug-In visualizes the simulation results in 3D.

13CFLUX2 related plug-ins are only available for registered 13CFLUX2 licensees.