Achr

ACBSampler(model, warmupPoints, fileName, nFiles, pointsPerFile, nMixPts, nWarmupNeeded, saveMatFlag, biasOpt)

Artificial centering boundary sampler

USAGE

ACBSampler (model, warmupPoints, fileName, nFiles, pointsPerFile, nMixPts, nWarmupNeeded, saveMatFlag, biasOpt)

INPUTS

• model – Model structure

• warmupPoints – Warmup points

• fileName – Base fileName for saving results

• nFiles – Number of sample point files created

• pointsPerFile – Number of points per file saved

• nMixPts – Number of steps initially used for mixing (not saved)

OPTIONAL INPUTS

• nWarmupNeeded – Number of warmup points needed (Default = 20000)

• saveMatFlag – Save points in mat format vs txt format (Default = true)

• biasOpt – Options for biasing sampler (Default = no bias)

ACHRSampler(model, warmupPoints, fileName, nFiles, pointsPerFile, stepsPerPoint, initPoint, fileBaseNo, maxTime, printLevel, minFlux, maxFlux)

Artificial Centering Hit-and-Run sampler

USAGE

ACHRSampler (model, warmupPoints, fileName, nFiles, pointsPerFile, stepsPerPoint, initPoint, fileBaseNo, maxTime)

INPUTS

• model – Model structure

• warmupPoints – Warmup points

• fileName – Base fileName for saving results

• nFiles – Number of files created

• pointsPerFile – Number of points per file saved

• stepsPerPoint – Number of sampler steps per point saved

• printLevel – 0 silent / 1 active

OPTIONAL INPUTS

• initPoint – Initial point (Default = centerPoint)

• fileBaseNo – Base file number for continuing previous sampler run (Default = 0)

• maxTime – Maximum time limit (Default = 36000 s)

• minFlux – Lower bound of the solution space given by FVA

• maxFlux – Upper bound of the solution space given by FVA

ACHRSamplerParallelGeneral(sampleStruct, nLoops, stepsPerPoint, maxtime, proc, fdirectory)

Artificial Centering Hit-and-Run sampler with in place (memory) point management

USAGE

sampleStruct = ACHRSamplerParallelGeneral (sampleStruct, nLoops, stepsPerPoint, maxtime, proc, fdirectory)

INPUTS

• sampleStruct – Sampling structure

• nLoops – Number of iterations

• stepsPerPoint – Number of sampler steps per point saved

• maxtime – Amount of time to spend on calculation (in seconds)

OPTIONAL INPUTS

• proc – Number of processes if > 0. Otherwise, the proces #.

• fdirectory – Do not use this parameter when calling function directly.

OUTPUT

sampleStruct – Sampling structure with sample points

convRevSamples(model, samples)

Converts signs for reactions that are only running in reverse direction

USAGE

[model, samples] = convRevSamples (model, samples)

INPUT

model – Constraint-based model

OPTIONAL INPUT

samples – Sample set

OUTPUTS

• model – COBRA model structure with negative-direction fluxes reversed

• samples – Sample set with negative-direction fluxes reversed

createHRWarmup(model, nPoints, verbFlag, bias, nPointsCheck)

Creates a warmup point set for hit-and-run sampling by combining orthogonal and random points

USAGE

warmupPts = createHRWarmup (model, nPoints, verbFlag, bias, nPointsCheck)

INPUTS

model – Model structure

OPTIONAL INPUTS

• nPoints – Number of warmup points (Default = 5000);

• verbFlag – Verbose flag (Default = false)

• bias – Structure with fields:

  • method - Biasing distribution: ‘uniform’, ‘normal’

  • index - The reaction indexes which to bias (nBias total)

  • param - nBias x 2 matrix of parameters (for uniform it’s min max, for normal it’s mu, sigma).

OUTPUT

warmupPts – Set of warmup points

gpSampler(sampleStruct, nPoints, bias, maxTime, maxSteps, threads, nPointsCheck)

Samples an arbitrary linearly constrained space using a fixed number of points that are moved in parallel The space is defined by

\[\begin{split}A x \leq, =, \geq b \\ lb \leq x \leq ub\end{split}\]

USAGE

[sampleStructOut, mixedFraction] = gpSampler (sampleStruct, nPoints, bias, maxTime, maxSteps, threads, nPointsCheck)

INPUTS

sampleStruct – Structure describing the space to be sampled and previous point sets:

• A - LHS matrix (optionally, if not A script checks for S)

• b - RHS vector

• lb - Lower bound

• ub - Upper bound

• csense - Constraint type for each row in A (‘G’, ‘L’, ‘E’)

• warmupPoints - Set of warmup points (optional, generated by default)

• points - Currently sampled points (optional)

OPTIONAL INPUTS

• nPoints – Number of points used in sampling (default = 2 * nRxns or 5000 whichever is greater)

• bias – Structure with fields:

  • method - Biasing distribution: ‘uniform’, ‘normal’

  • index - The reaction indexes which to bias (nBias total)

  • param - nBias x 2 matrix of parameters (for uniform it’s min max, for normal it’s mu, sigma).

• maxTime – Maximum time alloted for the sampling in seconds (default 600 s, pass an empty number [] to set maxSteps instead)

• maxSteps – Maximum number of steps to take (default 1e10). Sampler will run until either maxStep or maxTime is reached. Set maxStep or maxTime to 0 and no sampling will occur (only warmup points generated).

• threads – number of threads the sampler will use. If you have a dual core machine, you can set it to 2 etc. The speed up is almost linear w/ the number of cores. If using this feature and 2009a or newer, a futher speedup can be obtained by starting matlab from the command line by “typing matlab -singleCompThread” New feature: if threads < 0, use distributed toolbox.

• nPointsCheck – Checks that minimum number of points (2 * nRxns) are used. (Default = true).

OUTPUTS

• sampleStructOut – The sampling structure with some extra fields.

• mixedFract – The fraction mixed (relative to the warmupPts). A value of 1 means not mixed at all. A value of .5 means completely mixed.

mixFraction(sample1, sample2, fixed)

Compares two sets of sampled points and determines how mixed they are.

USAGE

mix = mixFraction (sample1, sample2, fixed)

INPUTS

sample1, sample2 – Ordered set of points. The points must be in the same order otherwise it does not make sense.

OPTIONAL INPUT

fixed – The indexes of sampled reactions which are fixed and are not expected to mix. They are ignored.

OUTPUT

mix – The mix fraction. Goes from 0 to 1 with 1 being completely unmixed and .5 being essentially perfectly mixed.

Example

example 1: mix = mixFraction(sample1, sample2) example 2: fixed = findRxnIDs({R1, R2, …, Rx}) mix = mixFraction(sample1, sample2, fixed)

removeCorrelRxns(model, R, correlCutoff)

Removes fully or almost fully correlated reactions

USAGE

[selRxns, rxnSets, rxnList, Rfilt] = removeCorrelRxns (model, R, correlCutoff)

INPUTS

• model – COBRA model structure

• R – Correl coefficient matrix

OPTIONAL INPUT

correlCutoff – Cutoff level for fully correlated rxns (Default 0.99999)

OUTPUTS

• selRxns – true/false vector that allow selecting non-redundant data

• rxnSets – Correlated reaction sets

• rxnList – Reaction list with correlated reactions concatenated

• Rfilt – Filtered R

verifyPoints(sampleStruct)

Verify that a set of points are in the solutoin space of sampleStruct. Typically, this method would be called to check a set of warmup points or points generated via gpSampler. Also verifies if points moved from warmup points.

USAGE

[errorsA, errorsLUB, stuckPoints] = verifyPoints (sampleStruct)

INPUT

sampleStruct – LPProblem containing points and warmup points

OUTPUTS

• errorsA – Row index of the constraint in sampleStruct that is not consistent with the given points

• errorsLUB – Upper and lower bounds of the constraint + tolerance

• stuckPoints – Index of points which did not move.