Stoichiometric Flux Balance

Check S·v steady-state residuals against a supplied flux-balance tolerance.

Description

Steady-state flux balance checks whether a supplied flux vector leaves metabolite residuals near zero.

Steady-state flux balance checks whether a supplied flux vector leaves metabolite residuals near zero. This evaluates a proposed vector without optimizing one.^[1]

Check S·v steady-state residuals against a supplied flux-balance tolerance.

When to use Stoichiometric Flux Balance

Use this tool to check S·v steady-state residuals against a supplied flux-balance tolerance.

Prepare the measured profile, formula counts, upstream model outputs or caller-defined reference criteria requested. Keep paired entries aligned and units, sample basis and preprocessing consistent.

How to use Stoichiometric Flux Balance and understand its results

Prepare the measured profile, formula counts, upstream model outputs or caller-defined reference criteria requested. Keep paired entries aligned and units, sample basis and preprocessing consistent.
Enter stoichiometry, fluxes, residualTolerance using the field table and calculation rules, then run the tool.
Read reactionCount, metaboliteCount, residuals, balanced. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
stoichiometry	Stoichiometry	list of list of number	Required
fluxes	Fluxes	list of number	Required
residualTolerance	Residual tolerance	number	Required

Enter a nonempty stoichiometric matrix whose row widths match a nonempty signed flux vector and nonnegative tolerance. Return reaction/metabolite counts, row residuals and inclusive balance flag.

residual=S×flux; balanced=all |residual_i|≤tolerance

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
reactionCount	Reaction count	number
metaboliteCount	Metabolite count	number
residuals	Residuals	list of number
balanced	Balanced	boolean

json

{
  "input": {
    "stoichiometry": [
      [
        1,
        -1
      ],
      [
        2,
        -2
      ]
    ],
    "fluxes": [
      1,
      1
    ],
    "residualTolerance": 0
  },
  "output": {
    "reactionCount": 2,
    "metaboliteCount": 2,
    "residuals": [
      0,
      0
    ],
    "balanced": true
  }
}

Limitations and assumptions

No reaction bounds, thermodynamic constraints, flux fitting or objective optimization is performed.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Matrices are limited to 128 rows and 128 entries per row; other lists are limited to 100,000 entries. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use Flux Objective Score: Evaluate a caller-supplied flux-balance objective function. For a complementary task, use Anaplerosis Flux Split: Partition two measured anaplerosis-associated fluxes by caller-defined branches.

References

Stoichiometric Flux Balance — tool.io

Similar or alternative tools

Flux Objective Score
Evaluate a caller-supplied flux-balance objective function.
Anaplerosis Flux Split
Partition two measured anaplerosis-associated fluxes by caller-defined branches.