13CFLUX2 FWDSIM Import Plug-In

The simulation framework 13CFLUX2 uses the FWDSIM file format for simulation results. The 13CFLUX2 FWDSIM Import Plug-In allows to load these simulation results for visualization and post-processing into into the Data Manager of Omix. From there, the content of the FEDSIM files is accessible in Quick Visualizer and in OVL by standard API (see here).

We strictly recommend to only use the new API to access FWDSIM files from inside OVL.

As a deprecated feature, you can also use FWDSIM loader class to handle FWDSIM files in OVL:

The FWDSIM files can be loaded by importing the package net.x3cflux.fwdsim:
import net.x3cflux.fwdsim.*;

Just create an object of the class FWDFile with the target file:
FWDFile fwddata = new FWDFile(new File("results.fwd"));

Inspect the class in Omix in the Class Inspector and you see, it has the same structure as the FWDSIM files.
The FWDFile object has an element called stoichiometry which contains the flux values.

You can, for instance, write:
for(Reaction reaction : reactions()){
    Flux flux = fwddata.stiochiometry.getFluxValueById(reaction.getName());

Mapping of Identifiers

The net.x3cflux.fwdsim.Flux class contains the fields net and exchange.
So, flux.net.value is the actual net flux value that you can visualize, flux.exchange.value the exchange flux, respectively.
This works as long as the reaction names correspond to the identifiers in the FWDSIM file. The identifiers in the FWDSIM file correspond to the identifiers in the FluxML file.

When the FluxML file was created with Omix, reaction names could possibly be converted into a valid form. For instance the name "123-aldolase" would be changed to "_123_aldolase" in the exported model file because leading numbers and dashes are not allowed here.
If a FWDSIM file is based on an Omix model, the class

helps to assign flux values to the reactions in the model.

The file FWDSIM-Visualization.ovl is a well-documented visualization example using the FluxMLMapper interface.

Instead of visualizing 13CFLUX2 results within the Omix diagram, you can use the Fluxomix3D visualization plug-in. Start the plug-in from the Extras menu and load the FWDSIM file.
The plug-in shows the net and exchanged fluxes as well as the sensitivities of the network in a 3D environment.


The content in an FWDSIM file can be inspected in the dialog window shown in the next image:

FWDSIM content view
FWDSIM content view

The dialog appears when you edit an item property of type FWDFile, for instance, as network property:
extend MetabolicNetwork{
    FWDFile fwddata;

From here, you can also change the loaded FWDSIM file. Therefore, click the button "Open File" and select the preferred data file.