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Network Biomass WormPaths
FBA PEAPathway Enrichment Analysis
You can have a look at this tool which is introduced below. However, the SUBMIT button will not give you any results, because you are not signed in. Please sign in first to use this tool.


Perform constraint-based flux balance analysis (FBA) in the worm by setting reaction constraints and an objective function. To change reaction constraints and to define the objective function, you can use one or more of the four options below.

Each option includes an easy way of setting lower and upper limits of reaction fluxes (i.e., constraints; the default is based on reversibility, except for exchange reactions, which are set at zero lower boundary to block the uptake of nutrients freely) and the coefficients (weights) of reactions in the linear objective function (default is zero for all, so no objective function is set).

Usually, one reaction is selected as the objective function and its coefficient changed to 1 for the maximization of its flux or to -1 for minimization.

If you have inconsistent edits in different options, the latest edit in Options 1-3 will overwrite all other edits in these three options, and edits in Option 4 will overwrite all others. The table in Option 3 shows all edits in Options 1-3.

To run FBA when you are done editing the constraints and coefficients, simply click the SUBMIT button at the end of this page.

To restart the entries, use the RESTART button below rather than reloading in your browser, as browsers sometimes maintain the existing edits upon reloading.

Use brief instructions (?) provided for each method to figure out what to do, or see details in the help section in the menu above.

OPTION 1: Choose a classical run (?) Chose one of the most commonly used FBA runs that include the maximization of a biomass prodution or an energy generation flux. The input is the bacterial diet in all cases. You can directly run FBA, or edit the default parameters set in the related reactions using tables in Option 2 (Exchange, energy, or biomass reaction tables) or Option 3. You can add any other constraints or even change the objective function using any Option.
Select your objective
OPTION 2: Define input and output (?) Use the tables below to determine the dietary input (bacteria and/or supplementary nutrients), output (biomass, storage, energy), or the by-products (secreted metabolites) of C. elegans metabolism.
► | Exchange reactions (click to view)▼ | Exchange reactions (click to hide)

EXC0050 Bacteria
► | Biomass reactions (click to view)▼ | Biomass reactions (click to hide)
► | Demand and sink reactions (click to view)▼ | Demand and sink reactions (click to hide)

SNK0012 Glycogen
► | Energetics (click to view)▼ | Energetics (click to hide)
OPTION 3: Find and edit (?) Bring the reactions you want to edit using the select menu (below, left) or using the search tool (below, right; opens a pop-up window). Reactions will appear in the master table below and then you can edit the constraints and objective function coefficients.

Note that this table also shows all edits from the first two options so that you can see what you have done and re-edit if necessary.
Bring reaction (?) Bring the reaction you want to edit to the top of the table below. If you do not know the ID of the reaction you are looking for, either surf in WormFlux to find it and then come back here to bring it, or use the search engine on the right instead.
ID (?) Click to see the details about a reaction (enzyme, compounds etc. with links as well as the general overview) in another window. Enzyme Reaction Genes Pathway Lower (?) Sets the lower limit of flux in the selected reaction. Negative values indicate a flux in the reverse direction with respect to the way reaction is written. To impose a particular flux in a reaction, enter that value in both Lower and Upper fields.

Double click on an edited box to go back to the default value.
Upper (?) Sets the upper limit of flux in the selected reaction. To impose a particular flux in a reaction, enter that value in both Lower and Upper fields.

Double click on an edited box to go back to the default value.
Obj (?) Sets the coefficient (i.e., weight) of the selected reaction in the objective function. A positive value indicates maximization and a negative value indicates minimization of flux in the selected reaction. Typically, the flux of one reaction is maximized or minimized, by setting the objective function coefficient of that reaction to 1 or -1, respectively.

Double click on an edited box to go back to the default value.