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Free Flux Plug-In

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The Free Flux Plug-In allows to interactively determine free fluxes in Omix.

Background

In a metabolic network all fluxes (i.e. reaction velocities) can be computed when a certain number of fluxes are known. These known fluxes are called free fluxes while all others are called dependent (cf. Weitzel et al. 2007). The dependency results from the network stoichiometry and constraints. In the Free Flux Plug-In you can interactively select free fluxes while dependent fluxes are determined automatically and excluded from choice. This can be done for both, net and exchange fluxes (read more).

1.2. Using the Plug-In

After installation, the Free Flux Plug-In is available in the list of active plug-ins. Activate the plug-in within a network document.

Activating Free Fluxes
Activating Free Fluxes

1.2.1. Setting Free Fluxes

After activation, each reaction is equipped with two yellow squared buttons. The upper one represents the net flux, the lower one the exchange flux (a). While mouse hovering, the button expands (b, c):

Interactive element showing 'free' state of net and exchange flux
Interactive element showing 'free' state of net and exchange flux


By clicking on a button, you define the corresponding net or exchange flux to be free flux. The button of a free flux is colored green as shown in the next image series (b). Consequently, all dependent fluxes can no longer be selected as free flux. Thus, their "free" button is being disabled and colored red (b). When the full set of free fluxes has been selected no yellow buttons remain (c).

a) FreeFluxes3.png b) FreeFluxes4.png c) FreeFluxes5.png

1.2.2. Alternatives

Instead of using the button beside the reaction items in the diagram, there are two alternative ways to define free fluxes:

1.2.2.1. Context Menu

The context menu of reaction items wether in the scene or in the component view contains a checkbox entry for free fluxes (net/exchange) as shown in the following image:

Context menu of a reaction item in the component view
Context menu of a reaction item in the component view

1.2.2.2. Free Fluxes Dialog

The selection of free fluxes can also be done in a dialog window. Therefore, click on the "Set" entry in the menu bar to be found in Extras -> Free Fluxes (cf. image a). Alternatively, you can find the functionality on the free fluxes toolbar (b).

a) FreeFluxes7.png b) FreeFluxes6.png c) FreeFluxes8.png

1.2.3. Constraints

Exchange fluxes do not depend on the network stoichiometry but can be selected as free fluxes independent from each other. In order to model further dependencies between certain nett as well as exchange fluxes the Network Constraints Plug-In can be used. After defining network constraints, all equality constraints can be taken into account while computing flux dependencies. Therefore, select "Include Constraints" button from the toolbar or Extras menu.

1.2.4. Reset

The "Reset" button available on the toolbar, in the menu or on the free fluxes dialog resets the free fluxes selection including all included equality constraints.

1.2.5. Hiding Free Fluxes Buttons

In order to hide the free fluxes buttons in the network diagram go to "View" menu -> "Hide Item Accessories" -> "Reaction" -> "Hide 'Free Fluxes Button Panel'".

1.3. Further Reading

  • Weitzel, M., Wiechert, W., and Nöh, K. 2007. The topology of metabolic isotope labeling networks. BMC Bioinformatics, 8 (1), 315.