HOME DOWNLOAD CITATION HELP
Umass Logo PSB Logo
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.

Instructions

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)
Exchange reactions (?) Use exchange reactions to constrain the uptake and secretion of metabolites. By convention, uptake is defined by a negative flux and secretion by a positive flux, therefore, uptake of nutrients is allowed by setting a negative lower limit and secretion is limited by an upper limit. To block the exhcange of a metabolite, set both the upper and lower limits to zero flux.
Bring metabolite (?) Bring the exchange reaction of a selected metabolite to the top of the table below, to be able to edit the uptake and secretion constraints for that metabolite. If you cannot find the metabolite in the list because of naming, or if you are not sure it is in the network, use Option 3 below to search for all reactions associated with the metabolite name (exchange reactions are included in Option 3 as well).

ID Metabolite Lower (?) Sets the lower limit of flux in the reaction that exchanges the indicated metabolite with the environment. A negative value indicates flux in the reverse direction, which corresponds to uptake, as the forward direction of an exchange reaction defines secretion to the environment. To block the exchange of a metabolite altogether, set both lower and upper limits to 0.

Double click on an edited box to go back to the default value. 		Upper (?) Sets the upper limit of flux in the reaction that exchanges the indicated metabolite with the environment. A positive value indicates flux in the forward direction, which corresponds to secretion. To block the exchange of a metabolite altogether, set both lower and upper limits to 0. To enforce uptake, set both the lower and upper limits to a negative value, as a negative flux in an exchange reaction indicates uptake.

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.
EXC0050 Bacteria
► | Biomass reactions (click to view)▼ | Biomass reactions (click to hide)
Biomass reactions (?) Edit the parameters of biomass assembly reactions used in the C. elegans model to perform growth simulations. For example, set the objective function coefficient of a reaction to 1 to maximize the growth in the mode represented by that reaction (click on the reaction IDs for further information), or impose a particular growth rate by entering this value in both Lower and Upper limit fields of a biomass reaction.
ID Biomass type Lower (?) Sets the lower limit of flux in the biomass assembly reaction. Negative values are not meaningful. 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 biomass assembly 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.

To maximize the growth rate based on a particular biomass assembly reaction, simply set the coefficient for that reaction at 1.

Double click on an edited box to go back to the default value.
BIO0100 Body (including storage)
BIO0101 Body (excluding storage)
BIO0102 Embryo (biosynthesis in germline)
BIO0103 Embryo (growth in eggs)
BIO0010 Any mixture
► | Demand and sink reactions (click to view)▼ | Demand and sink reactions (click to hide)
Demand and sink reactions (?) Describe storage, accumulation, or utilization of certain metabolites using demand reactions (irreversible, designated by DMN in reaction ID) or sink reactions (reversible, SNK) below. For example, allow utilization of stored triglycerides by setting a negative lower limit (means reaction can proceed in the reverse direction; forward direction is towards accumulation/storage) in TAG sink reaction, or impose accumulation of iron by bringing Fe3+ from the selection menu below and then setting a positive flux in both the lower and upper limit in the demand reaction brought forward.
Bring metabolite (?) Bring the demand or sink reaction of a selected metabolite to the top of the table below, to be able to edit the utilization and storage/accumulation constraints for that metabolite. If you cannot find the metabolite in the list because of naming, or if you are not sure it is in the network, use Option 3 below to search for all reactions associated with the metabolite name (demand and sink reactions are included in Option 3 as well). Note that another option to bring metabolites in and out of the metabolic network is to use exchange reactions (see above).

ID Metabolite Lower (?) Sets the lower limit of flux in the reaction that drains or provides the indicated metabolite. A negative value indicates flux in the reverse direction, which corresponds to utilization, as the forward direction of each reaction defines storage/accumulation. We recommend negative flux to be used only in reversible sink reactions. To enforce utilization, set both upper and lower limits to a negative value.

Double click on an edited box to go back to the default value. 		Upper (?) Sets the upper limit of flux in the reaction that drains or provides the indicated metabolite. A positive value indicates flux in the forward direction, which corresponds to storage/accumulation. To enforce storage/accumulation, set both upper and lower limits to a positive value.

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.
SNK0012 Glycogen
SNK0014 TAG
► | Energetics (click to view)▼ | Energetics (click to hide)
Generation of energy (?) Edit parameters of reactions related to maintenance cost and ATP synthesis to manipulate energy generation. For example, to maximize energy generation, set the objective function coefficient of ATP maintenance reaction (RCC0005) to 1, or to manipulate the energetic yield during ATP generation, use one of the two alternative ATP synthase reactions by setting its upper flux limit to a positive value while restraining the other reaction to a zero flux. Click on reaction IDs for further information on reaction stoichiometry etc.
ID Definition Lower (?) Sets the lower limit of flux in the selected reaction. Negative values are not meaningful. 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.
RCC0005 Non-growth associated maintenance
RMC0004 ATPase (default)
RMC0005 ATPase (alternative)
Growth associated maintenance cost (GAM) (?) ATP requirement (mmol/gDW/h, with gDW indicating dry worm biomass in grams) for maintenance during growth, in excess of polymerization costs for biomass assembly.

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

Cost (mmol/gDW/h)
GAM
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.

All edits from Options 1-3 appear in this table

OPTION 4: Enter as text (?) You can paste your constraints and objective function coefficients in this textbox with the format shown with examples (reaction ID, lower flux limit, upper flux limit, objective function coefficient). Each line should represent one reaction. The only entry that may not be a reaction is GAM (see the example in the box; also see Energetics table in Option 2).

Further details on the three fields of entry:
  1. Lower limit: 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.
  2. Upper limit: Sets the upper limit of flux in the selected reaction.
  3. Objective function coefficient: 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.
To impose a particular flux in a reaction, enter that value in both Lower and Upper flux limit fields.

Note that entries in this Option will overwrite others in case of overlaps.
Text input
(?) Opens up a pop-up window. If you do not see any new windows, this may be because a pop-up window have already been opened by this button recently and the results are being updated there.
The information and tools provided in this website are to be used for academic purposes only. Potential users of the flux analysis tools (grey buttons in the vertical menu) are asked to show proof of working at an academic institution during the creation of their accounts. These mathematical tools are powered by the commercial software Gurobi.