Network Constraints Plug-In

The Network Constraints Plug-In allows to define linear stoichiometric constraints within metabolic networks. Network constraints in this context are related to reaction velocities (fluxes) and metabolite concentrations (pools).
Flux constraints are furthermore divided into net and exchange flux constraints (read more).

Using the Plug-In

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

Activating network constraints
Activating network constraints

Extended property list
Extended property list

After activation, the list of network properties is extended by the entry "Constraints" (see property editor).
By clicking on "Edit..." the following text editor dialog appears:

Code suggestions while editing constraints
Code suggestions while editing constraints

Network constraints editor dialog
Network constraints editor dialog

Here, constraints can be entered in textual manner line by line for the "Net Fluxes", "Exchange Fluxes" and "Pool Sizes" depending on the active tab. Each line in the text editor contains a single constraint expression as linear (in)equation. Typical Examples are:

Optionally, global constraints for all fluxes and pools can be defined as upper and lower bounds. The upper and lower bounds editor accepts decimal numbers in scientific notation.

1.1.1. Constraint Expression Syntax

The following operators can be used to declare (in)equality:
  • = equals
  • != not equals
  • >= geater or equals
  • <= less or equals
  • > greater than
  • < less than
Each side of the (in)equation may contain an arbitrary linear combination of constants and/or variables. Here, constants can be any numbers given in scientific notation:
  • 1.0
  • .032 (meaning 0.032)
  • 3.6e-6 (meaning 3.6 times 10 to the power of -6)

It is also possible to use parantheses and additive and multiplicative operators:
  • (2+2)
  • 3*4
  • 3/5
  • 4^3 (meaning 4 to the power of 3)

Furthermore, you can use a set of mathematical functions in constraint expressions:
  • min(a,b) the minimum of a or b
  • max(a,b) the maximum of a or b
  • abs(a) the absolute value of a
  • exp(a) the exponent of a
  • sqrt(a) square root
  • sqr(a) square
  • log(a) natural logarithm
  • log2(a) logarithm to base 2
  • log10(a) logarithm to base 10

Variables correspond to the reaction names (flux contraints) or metabolite names (pool size constraints) in the network. If a reaction/metabolite name contains non-alphanumeric characters (not a-z or A-Z or 0-9 or _) or if the name starts with a number, use single quotes for the variable name:
  • '2fra'
  • 'citrate synthase'

1.1.2. Code Suggestions and Error Check

While writing, a completer menu appears providing code suggestions. E.g. by writing an 'r' all reactions are displayed whose name starts with 'r' etc.

The entered constraint expressions are continually checked for possible errors and occurring errors are displayed in the message area bottom of the editor dialog window.

1.1.3. Network Changes

Network constraints are internally stored with reference to the actual reaction and metabolite, respectively. When the network components are change, the constraints expressions remain in line with the network. For instance, when you rename a reaction whose name is used in a constraint expression, the expression is later displayed with the new reaction name.

When you delete a network component that is used in a constraint expression, the non-availability of the component is displayed as error message in the constraints editor.

1.1.4. Model Output

The Flux Balance Analysis Plug-In requires network constraints as model input.
Furthermore, the Network Constraints Plug-In plays an important role in the plug-in collection of the Fluxomix Suite for Metabolic Flux Analysis.
Here, the network constraints can be exported to FluxML, the model specification of 13CFLUX2, and serve as basis for the simulation of carbon labeling experiments.
Additionally, you can export constraints to SBML and to stoichiometry matrixes in CSV.

If you require a way to import or export network constraints that is currently not yet supported (file formats, databases etc.) please contact us.