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).
Table of contents
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:
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:
A=0.1 B<=4.8 C>D+E D>=2*F
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.
- = equals
- != not equals
- >= geater or equals
- <= less or equals
- > greater than
- < less than
- .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:
- 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:
- 'citrate synthase'
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.
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.
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.