13CFLUX2 FluxML Plug-In

The 13CFLUX2 FluxML Plug-In allows to import and export files in FluxML, the model format for 13CFLUX2.

After installation, the plug-in functionality is available during opening files as well as when importing or exporting the network model. The corresponding file dialogs allow to select FluxML files (file name suffix *.fml).
Aspects of a 13CFLUX2 Model
The plug-in only provides the sole import and export feature. The entire 13CFLUX2 model consists of different model parts that are realized by a number of additional plug-ins:
  • network stoichiometry - the stoichiometry of the network model is a built-in feature of Omix. Read about how to setup the network stoichiometry here.
  • atom mappings - the Atomic Layer Plug-In provides modeling features to define carbon atom mappings for each reaction of the network. Optionally the Chemical Structure Plug-In allows to equip the network with chemical structures that make the atom mappings unique and well interpretable. If a metabolite provides a structural formula its InChi code is exported as annotation of the pool in FluxML.
  • network constraints - the Network Constraints Plug-In equips the Omix document with the capability to define linear stoichiometric constraints for net and exchange fluxes as well as pool sizes. (The global bounds parameter available in the Network Constraints Plug-In is skipped in FluxML.)
  • model configuration - the 13CFLUX2 Modeling Plug-In provides extended modeling features for the 13CFLUX2 model prepared in Omix. This includes:
    • isotope enrichment of the network's input substrates
    • measurement data e.g. MS or NMR measured isotope enrichments of the network's intermediates
    • model variables and properties
    • simulation settings
Model Export
After preparing the 13CFLUX2 model in all its aspects, the FluxML Plug-In exports the model to a FluxML file that can subsequently be simulated with 13CFLUX2. Before exporting, the model is checked for validity (cf. 13CFLUX2 Modeling Plug-In, Atomic Layer Plug-In). If network inconsistencies are found, the you can decide to break or continue the export procedure.

During export, three cases can occur, where you have to decide how to continue with metabolites and reactions:
  • non-positioned items - if the diagram contains metabolites or reactions that are not placed in the diagram but only available in the component view, you can decide if they should be exported as well or skipped completely.
  • hidden items - the same option is given in combination with hidden items
  • variants - if your atom mappings contain different variants (see Atomic Layer Plug-In) you can decide to use the FluxML variant notation or to export individual reactions for each variant.
The user can decide how to export atom mapping variants
The user can decide how to export atom mapping variants

If you check "don't ask me again" your choice is take each time you export a network. However, can change the export behavior in the Omix configuration window:

Configuring FluxML plug-in
Configuring FluxML plug-in

Model Import
Likewise, the 13CFLUX2 FluxML Plug-In can load FluxML files to Omix (Open File, Import File).
After loading the network from FluxML all reactions and metabolites are not drawn on the drawing area but listed in the component view (highlighted red) because, no positioning information is available for the components. You can place the individual items on the drawing area by drag and drop, you can use the layout pattern and motif stamp feature of Omix (see User Manual) and/or you can use the AutoLayout Plug-In in order to arrange the network on the drawing area.

Non-positioned network nodes available in the component view
Non-positioned network nodes available in the component view