Interactive Flux Visualization Tool Help Page

Relative vs. Absolute Fluxes

The choice between relative and absolute fluxes refers to whether the user would like to visualize the mutant flux distribution as is, or as the difference from the wildtype predictions under the same conditions. Note that only absolute can be selected when looking at the wildtype flux, as otherwise the result would be visualizing zero flux through the network!

ORF ID for gene deletion

Here the user is to enter the ORF ID of the deletion mutant whose predicted flux distribution would like to be viewed. If the user selects an ORF which is not present in the model, then an error will be displayed. If no ORF ID is given then the wildtype flux distribution for the selected condition will be displayed.

Growth media condition

Here the user selects the media condition under which the predicted fluxes would like to be viewed.

Network layout

Here the user selects how much of the network they would like displayed. If only central energy metabolism is selected then only reactions and metabolites participating in those processes will be displayed. If the layout in which "other processes available" is selected, then in addition to reaction and metabolites in central energy metabolism being displayed all other reactions and metabolites will be present in "metanodes" corresponsing to their process. Briefly, a metanode is a special type of node in VisANT which contains other nodes. In the implementation of this visualization tool we created a metanode for each process and assigned as member nodes all reactions and metabolites assigned to that process. Note that because metabolites can participate in many processes, a single process was assigned to each metabolite in a way which allowed for the most parsimonious view of central energy metabolic processes.