diff --git a/stable/modules/analysis/FBA/index.html b/stable/modules/analysis/FBA/index.html index cb80e0f760..714f171a11 100644 --- a/stable/modules/analysis/FBA/index.html +++ b/stable/modules/analysis/FBA/index.html @@ -335,7 +335,7 @@

The COBRA Toolbox

OPTIONAL INPUTS
-
USAGE
-
-
+

Example

+

Obtain all reactions with Glycolysis in their respective subSystems +field. +[reactionNames,rxnPos] = findRxnsFromSubSystem(model,’Glycolysis’)

@@ -1161,7 +1159,7 @@

The COBRA Toolbox

USAGE
@@ -1218,12 +1216,12 @@

The COBRA Toolbox

Determine whether a reaction is in a given subSystem.

USAGE
-

[subSystems] = getModelSubSystems (model)

+

[present] = isReactionInSubSystem (model,reactions,subSystem)

INPUT

  • model – A COBRA model struct with at least rxns and -subSystems fields

    • +subSystems or rxn2subSystem(COBRA V4) fields

  • reactions – Either a string identifying a reaction, or a cell array of strings identifying multiple reactions, or a double vector identifying the @@ -1234,12 +1232,6 @@

    The COBRA Toolbox

    OUTPUT

    present – a boolean vector for each provided reaction.

    -
    USAGE
    -
      -

    • %Get all subSystems present in the model.

      • -

    • [subSystems] = getModelSubSystems (model)

      • -
    -
diff --git a/stable/modules/analysis/index.html b/stable/modules/analysis/index.html index f8d3e97859..448a3c1ec9 100644 --- a/stable/modules/analysis/index.html +++ b/stable/modules/analysis/index.html @@ -353,6 +353,7 @@

Analysis
  • Wholebody diff --git a/stable/modules/analysis/sampling/BarrierRound/PolytopeSimplifier/index.html b/stable/modules/analysis/sampling/BarrierRound/PolytopeSimplifier/index.html index b008d25a3e..157fc850db 100644 --- a/stable/modules/analysis/sampling/BarrierRound/PolytopeSimplifier/index.html +++ b/stable/modules/analysis/sampling/BarrierRound/PolytopeSimplifier/index.html @@ -434,20 +434,30 @@

    The COBRA Toolbox

    -class TwoSidedBarrier(lb, ub)[source]
    +class TwoSidedBarrier(lb, ub, vdim)[source]

    The log barrier for the domain {lu <= x <= ub}: phi(x) = - sum log(x - lb) - sum log(ub - x).

    -TwoSidedBarrier(lb, ub)[source]
    -

    Construct a barrier with lower bound lb and upper bound ub.

    +TwoSidedBarrier(lb, ub, vdim)[source] +

    o.update(lb, ub) +Update the bounds lb and ub.

    -boundary(o, x, blocks)[source]
    -

    [idx, b] = o.boundary(x, blocks) -Output the boundary value of each block and their cooresponding indices

    +boundary(o, x)[source] +

    [A, b] = o.boundary(x) +Output the normal at the boundary around x for each barrier. +Assume: only 1 vector is given

    +
    + +
    +
    +boundary_distance(o, x)[source]
    +

    v = o.boundary_distance(x) +Output the distance of x with its closest boundary for each +coordinate

    @@ -456,28 +466,44 @@

    The COBRA Toolbox

    Some feasible point x

    +
    +
    +extraHessian[source]
    +

    Extra factor added when computing Hessian. Used to handle free constraints.

    +
    + +
    +
    +feasible(o, x)[source]
    +

    r = o.feasible(x) +Output if x is feasible.

    +
    + +
    +
    +freeIdx[source]
    +

    Indices that ub == Inf and lb == -Inf

    +
    +
    -
    -derivatives(o, x)[source]
    -

    [g, h, t] = o.derivatives(x) -Output the gradient, Hessian and the third derivative of phi(x).

    +
    +gradient(o, x)[source]
    +

    g = o.gradient(x) +Output gradient phi(x).

    -
    -distance(o, x, v)[source]
    -

    t = o.distance(x) -Output the distance of x with its closest boundary for each coordinate -Any negative entries implies infeasible

    -

    t = o.distance(x, v) -Output the maximum step from x with direction v for each coordinate

    +
    +hessian(o, x)[source]
    +

    g = o.hessian(x) +Output Hessian phi(x).

    -
    -feasible(o, x)[source]
    -

    t = o.feasible(x) -Output if x is feasible

    +
    +hessian_norm(o, x, d)[source]
    +

    v = o.hessian_norm(x, d) +Output d_i (hess phi(x))_ii d_i for each i

    @@ -486,6 +512,20 @@

    The COBRA Toolbox

    lb

    +
    +
    +logdet_gradient(o, x)[source]
    +

    v = o.logdet_gradient(x) +Output the gradient of log det (hess phi(x)) +which is (hess phi(x))^-1 (grad hess phi (x))

    +
    + +
    +
    +lowerIdx[source]
    +

    Indices that ub == Inf

    +
    +
    n[source]
    @@ -493,21 +533,37 @@

    The COBRA Toolbox

    -
    -remove(x, blocks)[source]
    -

    Remove the blocks from the barrier

    +
    +quadratic_form_gradient(o, x, u)[source]
    +

    v = o.quadratic_form_gradient(x, u) +Output the -grad of u’ (hess phi(x)) u.

    -
    -rescale(scale)[source]
    -

    Rescale lb = lb .* scale, ub = ub .* scale

    +
    +set_bound(lb, ub)[source]
    +

    Update the bounds lb and ub.

    -
    -set(lb, ub)[source]
    -

    Update the bounds lb and ub.

    +
    +set_vdim(o, vdim)[source]
    +

    o.set_bound(lb, ub) +Update the dimension dim.

    +
    + +
    +
    +step_size(o, x, v)[source]
    +

    t = o.stepsize(x, v) +Output the maximum step size from x with direction v.

    +
    + +
    +
    +tensor(o, x)[source]
    +

    g = o.tensor(x) +Output the third derivative of phi(x).

    @@ -516,6 +572,18 @@

    The COBRA Toolbox

    ub

    +
    +
    +upperIdx[source]
    +

    Indices that lb == -Inf

    +
    + +
    +
    +vdim[source]
    +

    Each point is stored along the dimension vdim

    +
    +
    diff --git a/stable/modules/analysis/thermo/inchi/old/index.html b/stable/modules/analysis/thermo/inchi/old/index.html index bb7119d315..13d0a7eeec 100644 --- a/stable/modules/analysis/thermo/inchi/old/index.html +++ b/stable/modules/analysis/thermo/inchi/old/index.html @@ -307,24 +307,16 @@

    The COBRA Toolbox

    -getFormulaAndChargeFromInChI(InChI)[source]
    -

    Extracts the chemical formula of a given compound from -the InChI string provided

    -
    -
    USAGE
    -

    [formula, protons] = getFormulaFromInChI (InChI)

    -
    -
    INPUT
    -

    InChI – The Inchi String of the chemical formula (e.g. InChI= -extract formula from InChI = 1S/C3H4O3/c1-2(4)3(5)6/h1H3, (H,5,6)/p-1 for pyruvate

    -
    -
    OUTPUTS
    -
      -

    • formula – The chemical formula (including the protonation state

      • -

    • protons – The total number of protons

      • -
    -
    -
    +getFormulaAndChargeFromInChI(inchi)[source] +

    [formula,charge] = getFormulaAndChargeFromInChI(inchi)

    +

    INPUT +inchi…….Nonstandard IUPAC InChI for a particular pseudoisomer of a

    +
    +

    metabolite

    +
    +

    OUTPUTS +formula….The chemical formula for the input pseudoisomer +charge…..The charge on the input pseudoisomer

    diff --git a/stable/modules/analysis/topology/extremeRays/lrs/lrsInterface/index.html b/stable/modules/analysis/topology/extremeRays/lrs/lrsInterface/index.html index 25d52b8dfe..f92cb57106 100644 --- a/stable/modules/analysis/topology/extremeRays/lrs/lrsInterface/index.html +++ b/stable/modules/analysis/topology/extremeRays/lrs/lrsInterface/index.html @@ -265,6 +265,58 @@

    The COBRA Toolbox

    Lrsinterface

    +
    +lrsInputHalfspace(A, D, filename, positivity, inequality, a, d, f, sh)[source]
    +

    Outputs a file for lrs to convert an H-representation (half-space) of a +polyhedron to a V-representation (vertex / ray) via vertex enumeration

    +
    +
    USAGE
    +

    lrsInputHalfspace (A, D, filename, positivity, inequality, a, d, f, sh)

    +
    +
    INPUTS
    +
      +

    • A – matrix of linear equalities \(A x =(a)\)

      • +

    • D – matrix of linear inequalities \(D x \geq (d)\)

      • +

    • filename – base name of output file

      • +
    +
    +
    OPTIONAL INPUTS
    +
      +

    • positivity – {0, (1)} if positivity == 1, then positive orthant base

      • +

    • inequality – {0, (1)} if inequality == 1, then use two inequalities rather than a single equaltiy

      • +

    • a – boundary values for matrix of linear equalities \(A x = a\)

      • +

    • d – boundary values for matrix of linear inequalities \(D x \geq d\)

      • +

    • f – linear objective for a linear optimization problem in rational arithmetic

      +

      minimise \(f^T x\), +subject to \(A x = (a)\), \(D x \geq (d)\)

      +
      • +

    • sh – {(0), 1} if sh == 1, output a shell script for submitting qsub job

      • +
    +
    +
    +
    + +
    +
    +lrsOutputReadRay(filename)[source]
    +

    Reads into matlab a vertex representation output from lrs

    +
    +
    USAGE
    +

    [R, V] = lrsOutputReadRay (filename)

    +
    +
    INPUT
    +

    filename – name of .ext file from lrs

    +
    +
    OUTPUT
    +
      +

    • R – nDim by nRay matrix of extreme rays

      • +

    • V – nDim by nVertex matrix of vertices

      • +
    +
    +
    +
    + +
    lrsReadHalfspace(modelName, param)[source]

    Read in a halfspace representation (*.ine) of a polytope derived from lrs diff --git a/stable/modules/analysis/wholeBody/Nutrition_Modelling_Toolbox/index.html b/stable/modules/analysis/wholeBody/Nutrition_Modelling_Toolbox/index.html index 2f28eb0598..006429649c 100644 --- a/stable/modules/analysis/wholeBody/Nutrition_Modelling_Toolbox/index.html +++ b/stable/modules/analysis/wholeBody/Nutrition_Modelling_Toolbox/index.html @@ -191,6 +191,7 @@

    The COBRA Toolbox

  • Rmta
  • Deletion
  • Wholebody diff --git a/stable/modules/analysis/wholeBody/PSCMToolbox/BMRcalculations/index.html b/stable/modules/analysis/wholeBody/PSCMToolbox/BMRcalculations/index.html index e2068faa2c..46b4716763 100644 --- a/stable/modules/analysis/wholeBody/PSCMToolbox/BMRcalculations/index.html +++ b/stable/modules/analysis/wholeBody/PSCMToolbox/BMRcalculations/index.html @@ -191,6 +191,7 @@

    The COBRA Toolbox

  • Rmta
  • Deletion
  • Wholebody
      +
    • Io
    • Pscmtoolbox
      • Bmrcalculations
      • Io
        • diff --git a/stable/modules/analysis/wholeBody/PSCMToolbox/hostMicrobeInteraction/index.html b/stable/modules/analysis/wholeBody/PSCMToolbox/hostMicrobeInteraction/index.html index 44db8e0032..551d230d9a 100644 --- a/stable/modules/analysis/wholeBody/PSCMToolbox/hostMicrobeInteraction/index.html +++ b/stable/modules/analysis/wholeBody/PSCMToolbox/hostMicrobeInteraction/index.html @@ -191,6 +191,7 @@

        The COBRA Toolbox

      • Rmta
      • Deletion
      • Wholebody
          +
        • Io
        • Pscmtoolbox
          • Bmrcalculations
          • Io
            • diff --git a/stable/modules/analysis/wholeBody/PSCMToolbox/index.html b/stable/modules/analysis/wholeBody/PSCMToolbox/index.html index 6c06fad6af..50fed9fd16 100644 --- a/stable/modules/analysis/wholeBody/PSCMToolbox/index.html +++ b/stable/modules/analysis/wholeBody/PSCMToolbox/index.html @@ -70,7 +70,7 @@ - + @@ -191,6 +191,7 @@

            The COBRA Toolbox

          • Rmta
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              +
            • Io
            • Pscmtoolbox
              • Bmrcalculations
              • Io
                • @@ -985,7 +986,7 @@

                The COBRA Toolbox

                - + diff --git a/stable/modules/analysis/wholeBody/PSCMToolbox/io/index.html b/stable/modules/analysis/wholeBody/PSCMToolbox/io/index.html index 70c7284f49..a3110c44bc 100644 --- a/stable/modules/analysis/wholeBody/PSCMToolbox/io/index.html +++ b/stable/modules/analysis/wholeBody/PSCMToolbox/io/index.html @@ -191,6 +191,7 @@

                The COBRA Toolbox

              • Rmta
              • Deletion
              • Wholebody
                  +
                • Io
                • Pscmtoolbox
                  • Bmrcalculations
                  • Io
                    • diff --git a/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/diets/index.html b/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/diets/index.html index c165cd9737..a888effc53 100644 --- a/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/diets/index.html +++ b/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/diets/index.html @@ -191,6 +191,7 @@

                    The COBRA Toolbox

                  • Rmta
                  • Deletion
                  • Wholebody
                      +
                    • Io
                    • Pscmtoolbox
                      • Bmrcalculations
                      • Io
                        • diff --git a/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/index.html b/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/index.html index 078183605f..f63d6a7e06 100644 --- a/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/index.html +++ b/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/index.html @@ -191,6 +191,7 @@

                        The COBRA Toolbox

                      • Rmta
                      • Deletion
                      • Wholebody
                          +
                        • Io
                        • Pscmtoolbox
                          • Bmrcalculations
                          • Io
                            • diff --git a/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/inputData/index.html b/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/inputData/index.html index 4b2d62d26a..b76fa538de 100644 --- a/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/inputData/index.html +++ b/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/inputData/index.html @@ -191,6 +191,7 @@

                            The COBRA Toolbox

                          • Rmta
                          • Deletion
                          • Wholebody
                              +
                            • Io
                            • Pscmtoolbox
                              • Bmrcalculations
                              • Io
                                • diff --git a/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/organWeight/index.html b/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/organWeight/index.html index 1cc844f888..42c812ac5f 100644 --- a/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/organWeight/index.html +++ b/stable/modules/analysis/wholeBody/PSCMToolbox/setConstraints/organWeight/index.html @@ -191,6 +191,7 @@

                                The COBRA Toolbox

                              • Rmta
                              • Deletion
                              • Wholebody
                                  +
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                                • Pscmtoolbox
                                  • Bmrcalculations
                                  • Io
                                    • diff --git a/stable/modules/analysis/wholeBody/index.html b/stable/modules/analysis/wholeBody/index.html index f060b717b1..8ac9fea848 100644 --- a/stable/modules/analysis/wholeBody/index.html +++ b/stable/modules/analysis/wholeBody/index.html @@ -69,7 +69,7 @@ - + @@ -191,6 +191,7 @@

                                    The COBRA Toolbox

                                  • Rmta
                                  • Deletion
                                  • Wholebody @@ -254,6 +255,7 @@

                                    The COBRA Toolbox

                                    Wholebody

                                      +
                                    • Io
                                    • Pscmtoolbox
                                      • Bmrcalculations
                                      • Io
                                        • @@ -281,7 +283,7 @@

                                        The COBRA Toolbox

    • OUTPUTS
    diff --git a/stable/modules/base/solvers/NLP/index.html b/stable/modules/base/solvers/NLP/index.html index 8cb97e69df..4e3d7fe959 100644 --- a/stable/modules/base/solvers/NLP/index.html +++ b/stable/modules/base/solvers/NLP/index.html @@ -162,9 +162,9 @@

    The COBRA Toolbox

  • Paths
  • Ci
  • Solvers
    • diff --git a/stable/modules/base/solvers/cardOpt/index.html b/stable/modules/base/solvers/cardOpt/index.html index 05d7458767..5558fb13c0 100644 --- a/stable/modules/base/solvers/cardOpt/index.html +++ b/stable/modules/base/solvers/cardOpt/index.html @@ -70,7 +70,7 @@ - + @@ -162,9 +162,9 @@

    The COBRA Toolbox

  • Paths
  • Ci
  • Solvers
      -
    • Msk
    • Rescale
    • Param
      • +
    • Gurobi
    • Cardopt
      • @@ -265,7 +266,7 @@

      The COBRA Toolbox

      - + diff --git a/stable/modules/base/solvers/cardOpt/smoothConcave/index.html b/stable/modules/base/solvers/cardOpt/smoothConcave/index.html index e9aee2d72b..6d2857c18b 100644 --- a/stable/modules/base/solvers/cardOpt/smoothConcave/index.html +++ b/stable/modules/base/solvers/cardOpt/smoothConcave/index.html @@ -162,9 +162,9 @@

      The COBRA Toolbox

    • Paths
    • Ci
    • Solvers
        -
      • Msk
      • Rescale
      • Param
        • +
      • Gurobi
      • Cardopt
        • diff --git a/stable/modules/base/solvers/cardOpt/sparseLP/index.html b/stable/modules/base/solvers/cardOpt/sparseLP/index.html index de80eef729..9b7f0095a2 100644 --- a/stable/modules/base/solvers/cardOpt/sparseLP/index.html +++ b/stable/modules/base/solvers/cardOpt/sparseLP/index.html @@ -162,9 +162,9 @@

        The COBRA Toolbox

      • Paths
      • Ci
      • Solvers
          -
        • Msk
        • Rescale
        • Param
          • +
        • Gurobi
        • Cardopt
          • Smoothconcave
          • Sparselp
            • diff --git a/stable/modules/base/solvers/cardOpt/sparseLP/old/index.html b/stable/modules/base/solvers/cardOpt/sparseLP/old/index.html index 783bcc3794..c819c1f5de 100644 --- a/stable/modules/base/solvers/cardOpt/sparseLP/old/index.html +++ b/stable/modules/base/solvers/cardOpt/sparseLP/old/index.html @@ -162,9 +162,9 @@

            The COBRA Toolbox

          • Paths
          • Ci
          • Solvers
              -
            • Msk
            • Rescale
            • Param
              • +
            • Gurobi
            • Cardopt
              • Smoothconcave
              • Sparselp
                • diff --git a/stable/modules/base/solvers/cplex/index.html b/stable/modules/base/solvers/cplex/index.html index c0977d8cff..5c15dc2cc5 100644 --- a/stable/modules/base/solvers/cplex/index.html +++ b/stable/modules/base/solvers/cplex/index.html @@ -162,9 +162,9 @@

                The COBRA Toolbox

              • Paths
              • Ci
              • Solvers
                • diff --git a/stable/modules/base/solvers/entropicFBA/index.html b/stable/modules/base/solvers/entropicFBA/index.html index 315c48a582..dcc9825586 100644 --- a/stable/modules/base/solvers/entropicFBA/index.html +++ b/stable/modules/base/solvers/entropicFBA/index.html @@ -162,9 +162,9 @@

                The COBRA Toolbox

              • Paths
              • Ci
              • Solvers
                • @@ -287,8 +288,10 @@

                The COBRA Toolbox

                entropicFluxBalanceAnalysis(model, param)[source]
                -

                TBC -minimize g.*vf’*(log(vf) -1) + (cf + ci)’*vf +

                Entropy maximisation of fluxes (or fluxes and concentrations) subject to +mass balance, optionally coupling constraints, optionally quadratic +penalisation of deviation from given fluxes.

                +

                minimize g.*vf’*(log(vf) -1) + (cf + ci)’*vf vf,vr,w,x,x0 + g.*vr’*(log(vr) -1) + (cr - ci)’*vr

                  @@ -393,7 +396,7 @@

                  The COBRA Toolbox

                  model.SConsistentRxnBool: n x 1 boolean indicating stoichiometrically consistent metabolites

                  param.solver: {(‘pdco’),’mosek’} -param.method: {(‘fluxes’),’fluxConc’)} maximise entropy of fluxes or also concentrations +param.entropicFBAMethod: {(‘fluxes’),’fluxConc’)} maximise entropy of fluxes or also concentrations param.printLevel: {(0),1}

                  @@ -438,20 +441,6 @@

                  The COBRA Toolbox

                  Author(s): Ronan M.T. Fleming 2021

                -
                -
                -mosekParamSetEFBA(param)[source]
                -

                creates a structure of pertinent user defined options for MOSEK -OUTPUT -param parameter structure to be passed to the MOSEK solver

                -
                - -
                -
                -mosekParamStrip(solverParams)[source]
                -

                Remove non-modek parameters to avoid crashing solver interface

                -
                -
                processConcConstraints(model, param)[source]
                @@ -483,8 +472,7 @@

                The COBRA Toolbox

                model.dcl: m x 1 real valued lower bound on difference between final and initial molecular concentrations (default -inf) model.dcu: m x 1 real valued upper bound on difference between final and initial initial molecular concentrations (default inf) model.gasConstant: scalar gas constant (default 8.31446261815324 J K^-1 mol^-1) -model.temperature: scalar temperature (default 310.15 Kelvin)

                -

                param.method: ‘fluxConc’ +model.temperature: scalar temperature (default 310.15 Kelvin) param.maxConc: (1e4) maximim micromolar concentration allowed param.maxConc: (1e-4) minimum micromolar concentration allowed param.externalNetFluxBounds: (‘original’) =

                @@ -550,7 +538,7 @@

                The COBRA Toolbox

                param.printLevel: param.solver: {‘pdco’,(‘mosek’)} param.debug: {(0),1} 1 = run in debug mode -param.method: {(‘fluxes’),’fluxesConcentrations’} maximise entropy of fluxes (default) or also concentrations +param.entropicFBAMethod: {(‘fluxes’),’fluxesConcentrations’} maximise entropy of fluxes (default) or also concentrations param.maxUnidirectionalFlux: maximum unidirectional flux (1e5 by default) param.minUnidirectionalFlux: minimum unidirectional flux (zero by default) param.internalNetFluxBounds: (‘original’) = use model.lb and model.ub to set the direction and magnitude of internal net flux bounds

                @@ -611,7 +599,7 @@

                The COBRA Toolbox

                USAGE
                -

                solution = solveCobraEP (EPproblem, varargin)

                +

                sol = solveCobraEP (EPproblem, varargin)

                INPUT

                EPproblem –

                @@ -700,43 +688,40 @@

                The COBRA Toolbox

                optTol: Optimality tolerance

                OUTPUT
                -

                solution – Structure containing the following fields describing a LP solution: -* .obj: Objective value -*.objLinear osense*c’*x; -*.objEntropy d.*x’*(log(x) -1); -*.objQuadratic (1/2)*x’*Q*x; -* .full: Primal solution vector -* .slack: bl = A*x + s = bu -* .rcost: Reduced costs, dual solution to \(lb <= x <= ub\) -* .dual: dual solution to constraints :math: A*x (‘E’ | ‘G’ | ‘L’) b

                +

                sol – Structure containing the following fields describing a LP sol: +*.obj: Objective value +*.objLinear osense*c’*x; +*.objEntropy d.*x’*(log(x) -1); +*.objQuadratic (1/2)*x’*Q*x; +*.v: n+k ×1 double +*.vf: n × 1 double +*.vr: n × 1 double +*.vt: 1’*vt + 1’*vr +*.y_N: m x 1 double dual sol to constraints :math: A*x (‘E’ | ‘G’ | ‘L’) b +*.z_dx: 0 +*.z_vf: n × 1 double dual sol to \(lb <= vr <= ub\) +*.z_vr: n × 1 double dual sol to \(lb <= vf <= ub\) +*.z_vi: n × 1 double dual sol to \(lb <= v <= ub\) +*.z_v: n + k × 1 double dual sol to \(lb <= w <= ub\) +* .stat: Solver status in standardized form

                +
                +
                  +

                • 0 - Infeasible problem

                  • +

                • 1 - Optimal sol

                  • +

                • 2 - Unbounded sol

                  • +

                • 3 - Almost optimal sol

                  • +

                • -1 - Some other problem (timelimit, numerical problem etc)

                  • +
                +
                  -

                • .solver: Solver used to solve EP problem

                  • -

                • .stat: Solver status in standardized form -* 0 - Infeasible problem -* 1 - Optimal solution -* 2 - Unbounded solution -* 3 - Almost optimal solution -* -1 - Some other problem (timelimit, numerical problem etc)

                • .origStat: Original status returned by the specific solver

                • .origStatText: Original status text returned by the specific solver

                • .time: Solve time in seconds

                  • +

                • .solver: Solver used to solve EP problem

                  • +

                • .epmethod: solver method used e.g. ‘CONIC’

                -
                -
                OPTIONAL OUTPUT (from conic optimisation with mosek):

                solution.auxPrimal: auxiliary primal variable -solution.auxRcost: dual to auxiliary primal variable -solution.coneF: affine constraint matrix -solution.coneDual: dual to affine constraints -solution.dualNorm: dual to the probability normalisation constraint

                -
                -
                OPTIONAL OUTPUT (from optimisation with pdco):

                solution.d1: primal regularisation parameter, see pdco.m -solution.d2: dual regularisation parameter, see pdco.m

                -
                -
                -

                EXAMPLE:

                -

                NOTE: This code is a draft version released for the ELIXIR Fluxomic course and is not yet published and not to be redistributed without express permission of the author.

                -

                Author(s): Ronan M.T. Fleming, 2021

    • diff --git a/stable/modules/base/solvers/gams/index.html b/stable/modules/base/solvers/gams/index.html index fa44e62479..98d854a6bf 100644 --- a/stable/modules/base/solvers/gams/index.html +++ b/stable/modules/base/solvers/gams/index.html @@ -162,9 +162,9 @@

    The COBRA Toolbox

  • Paths
  • Ci
  • Solvers
    • diff --git a/stable/modules/base/solvers/getSetSolver/index.html b/stable/modules/base/solvers/getSetSolver/index.html index 014494f23e..3a7eb2b60b 100644 --- a/stable/modules/base/solvers/getSetSolver/index.html +++ b/stable/modules/base/solvers/getSetSolver/index.html @@ -162,9 +162,9 @@

    The COBRA Toolbox

  • Paths
  • Ci
  • Solvers
    • @@ -239,19 +240,19 @@

    The COBRA Toolbox

    Getsetsolver

    -changeCobraSolver(solverName, solverType, printLevel, validationLevel)[source]
    +changeCobraSolver(solverName, problemType, printLevel, validationLevel)[source]

    Changes the Cobra Toolbox optimization solver(s)

    USAGE
    -

    solverOK = changeCobraSolver (solverName, solverType, printLevel, validationLevel)

    +

    [solverOK, solverInstalled] = changeCobraSolver (solverName, solverType, printLevel, validationLevel)

    INPUTS

    • solverName – Solver name

      • -

    • solverType – Solver type (‘LP’ by default) +

    • problemType – Problem type (‘LP’ by default) (a) One of the following: LP MILP, QP, MIQP ‘EP’, ‘CLP’ (b) ‘all’ attempts to change all applicable solvers to solverName. This is purely a shorthand convenience. -(c) Cell array of solverTypes, e.g. {‘LP’,’QP’}

      • +(c) Cell array of problemTypes, e.g. {‘LP’,’QP’}

    • printLevel – verbose level

      • if 0, warnings and errors are silenced

        • @@ -265,7 +266,7 @@

        The COBRA Toolbox

        • -1: assign only the global variable. Do not assign any path.

        • 0: adjust solver paths but don’t validate the solver

          • -

        • 1: validate but remove outputs (default)

          • +

        • 1: validate but remove outputs, silent (default)

        • 2: validate and keep any outputs

    diff --git a/stable/modules/base/solvers/gurobi/index.html b/stable/modules/base/solvers/gurobi/index.html new file mode 100644 index 0000000000..eee3761950 --- /dev/null +++ b/stable/modules/base/solvers/gurobi/index.html @@ -0,0 +1,337 @@ + + + + + + + + + + + + Gurobi — The COBRA Toolbox + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + +
    + + + + + + +
    +
    +
    + +
    +
    +
    +
    + +
    +

    Gurobi

    +
    +
    +setGurobiParam(param)[source]
    +

    The params struct contains Gurobi parameters. A full list may be +found on the Parameter page of the reference manual: +https://www.gurobi.com/documentation/current/refman/parameter_descriptions.html +Parameters must be in TimeLimit not timelimit or timeLimit format, see +below for full list that are eligible to be passed to the solver.

    +
    + +
    + + +
    +
    + +
    +
    +
    + + + + +
    + +
    +

    + © Copyright 2017-2021, The COBRA Toolbox developers. + +

    +
    + Built with Sphinx using a theme provided by Read the Docs. + +
    + +
    +
    + +
    + +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/stable/modules/base/solvers/index.html b/stable/modules/base/solvers/index.html index 9c2ff6d72c..125b102548 100644 --- a/stable/modules/base/solvers/index.html +++ b/stable/modules/base/solvers/index.html @@ -69,7 +69,7 @@ - + @@ -162,9 +162,9 @@

    The COBRA Toolbox

  • Paths
  • Ci
  • Solvers
    • @@ -238,9 +239,9 @@

    The COBRA Toolbox

    Solvers

    @@ -313,7 +315,8 @@

    The COBRA Toolbox

    * `.ub`: Upper bound vector * `.osense`: Objective sense (`-1`: maximise (default); `1`: minimise) * `.csense`: string with the constraint sense for each row in A ('E', equality, 'G' greater than, 'L' less than). - * `.F`: Positive semidefinite matrix for quadratic part of objective\end{aligned}\end{align} \] + * `.F`: Positive semidefinite matrix for quadratic part of objective +OPTIONAL OUTPUT:\end{aligned}\end{align} \]
    @@ -485,7 +488,7 @@

    The COBRA Toolbox

    * .rcost: Reduced costs, dual solution to \(lb <= v <= ub\) * .dual: dual solution to A*v (‘E’ | ‘G’ | ‘L’) b * .solver: Solver used to solve LP problem -* .method: Algorithm used by solver to solve LP problem +* .lpmethod: Algorithm used by solver to solve LP problem * .stat: Solver status in standardized form

      @@ -753,6 +756,7 @@

      The COBRA Toolbox

    • .slack: slack variable such that \(A*x + s = b\)

    • .obj: Objective value

    • .solver: Solver used to solve QP problem

      • +

    • .qpmethod: Solver qpmethod used to solve QP problem

    • .origStat: Original status returned by the specific solver

    • .time: Solve time in seconds

    • .stat: Solver status in standardized form (see below)

      • @@ -821,7 +825,7 @@

      The COBRA Toolbox

      diff --git a/stable/modules/base/solvers/lp_solve/index.html b/stable/modules/base/solvers/lp_solve/index.html index d94f7f8b99..8f7a8ffd60 100644 --- a/stable/modules/base/solvers/lp_solve/index.html +++ b/stable/modules/base/solvers/lp_solve/index.html @@ -69,7 +69,7 @@ - + @@ -162,9 +162,9 @@

      The COBRA Toolbox

    • Paths
    • Ci
    • Solvers
      • @@ -563,7 +564,7 @@

      The COBRA Toolbox

    @@ -235,11 +236,17 @@

    The COBRA Toolbox

    -
    -

    Msk

    -
    -
    -parseMskResult(res, solverOnlyParams, printLevel)[source]
    +
    +

    Mosek

    +
    +
    +mosekParamStrip(solverParams)[source]
    +

    Remove non-modek parameters to avoid crashing solver interface

    +
    + +
    +
    +parseMskResult(res)[source]

    parse the res structure returned from mosek :INPUTS: res – mosek results structure returned by mosekopt

    @@ -287,6 +294,14 @@

    The COBRA Toolbox

    Author(s): Ronan Fleming

    +
    +
    +setMosekParam(param)[source]
    +

    set mosek parameters from param fields +strip any non mosek compatible fields from param and return it as +mosekParam

    +
    +
    @@ -299,10 +314,10 @@

    The COBRA Toolbox

    diff --git a/stable/modules/base/solvers/param/index.html b/stable/modules/base/solvers/param/index.html index c2eb719c36..e747d19631 100644 --- a/stable/modules/base/solvers/param/index.html +++ b/stable/modules/base/solvers/param/index.html @@ -69,7 +69,7 @@ - + @@ -162,9 +162,9 @@

    The COBRA Toolbox

  • Paths
  • Ci
  • Solvers
    • @@ -309,7 +310,7 @@

    The COBRA Toolbox

    getCobraSolverParams(problemType, paramNames, paramStructure)[source]

    This function gets the specified paramStructure in paramNames from -paramStructure, the global cobra paramters variable or default values set within +paramStructure, the global cobra parameters variable or default values set within this script.

    It will use values with the following priority paramStructure > solver type paramStructure > default paramStructure

    @@ -359,7 +360,7 @@

    The COBRA Toolbox

    INPUT

    problemType – One of the problem types available in the COBRA -Toolbox (‘LP’,’QP’,’MILP’,’MIQP’,’NLP’)

    +Toolbox (‘LP’,’QP’,’EP’,’CLP’,’MILP’,’MIQP’,’NLP’)

    @@ -372,6 +373,12 @@

    The COBRA Toolbox

    +
    +
    +mergeCobraParams(param1, param2)[source]
    +

    Merge the structures with preference to param1 fields over param2 fields

    +
    +
    parseSolverParameters(problemType, varargin)[source]
    @@ -419,7 +426,7 @@

    The COBRA Toolbox

    -
    -
    -reformulateWBMCoupling(model, BIG, printLevel)[source]
    -

    Reformulates badly-scaled model -Transforms LPproblems with badly-scaled stoichiometric and -coupling constraints of the form: -\(max c*x\) subject to: math:Ax <= b

    -

    Eliminates the need for scaling and hence prevents infeasibilities -after unscaling. After using PREFBA to transform a badly-scaled FBA program, -please turn off scaling and reduce the aggressiveness of presolve.

    -

    Rransforms a badly-scaled LPproblem -contained in the struct FBA and returns the transformed program in the -structure FBA. reformulate assumes S and C do not contain very small entries -and transforms constraints containing very large entries (entries larger than -BIG). BIG should be set between 1000 and 10000 on double precision machines. -printLevel = 1 or 0 enables/diables printing respectively.

    -

    Reformulation techniques are described in detail in: -Y. Sun, R. M.T. Fleming, M. A. Saunders, I. Thiele, An Algorithm for Flux -Balance Analysis of Multi-scale Biochemical Networks, submitted.

    -
    -
    USAGE
    -

    [LPproblem] = reformulate (LPproblem, BIG, printLevel)

    -
    -
    INPUTS
    -

    LPproblem – Structure contain the original LP to be solved. The format of -this struct is described in the documentation for solveCobraLP.m

    -
    -
    OPTIONAL INPUTS
    -
      -

    • BIG – A parameter the controls the largest entries that appear in the -reformulated problem.

      • -

    • printLevel – 1 enables printing of problem statistics; -0 = silent

      • -
    -
    -
    OUTPUTS
    -

    LPproblem – Structure contain the reformulated LP to be solved.

    -
    -
    -
    - @@ -365,7 +380,7 @@

    The COBRA Toolbox

    - + diff --git a/stable/modules/base/solvers/varKin/BDCAmethods/index.html b/stable/modules/base/solvers/varKin/BDCAmethods/index.html index e96efb7db0..b9c3422466 100644 --- a/stable/modules/base/solvers/varKin/BDCAmethods/index.html +++ b/stable/modules/base/solvers/varKin/BDCAmethods/index.html @@ -162,9 +162,9 @@

    The COBRA Toolbox

  • Paths
  • Ci
  • Solvers
    • diff --git a/stable/modules/base/solvers/varKin/derFreeMethods/index.html b/stable/modules/base/solvers/varKin/derFreeMethods/index.html index e29028b269..30e573618d 100644 --- a/stable/modules/base/solvers/varKin/derFreeMethods/index.html +++ b/stable/modules/base/solvers/varKin/derFreeMethods/index.html @@ -162,9 +162,9 @@

    The COBRA Toolbox

  • Paths
  • Ci
  • Solvers
    • diff --git a/stable/modules/base/solvers/varKin/index.html b/stable/modules/base/solvers/varKin/index.html index 5a15beee95..ee7f520b51 100644 --- a/stable/modules/base/solvers/varKin/index.html +++ b/stable/modules/base/solvers/varKin/index.html @@ -162,9 +162,9 @@

    The COBRA Toolbox

  • Paths
  • Ci
  • Solvers
    • diff --git a/stable/modules/base/solvers/varKin/levMarMethods/index.html b/stable/modules/base/solvers/varKin/levMarMethods/index.html index 42a9d115c3..9a3d3689a3 100644 --- a/stable/modules/base/solvers/varKin/levMarMethods/index.html +++ b/stable/modules/base/solvers/varKin/levMarMethods/index.html @@ -162,9 +162,9 @@

    The COBRA Toolbox

  • Paths
  • Ci
  • Solvers
    • diff --git a/stable/modules/basefunctions.json b/stable/modules/basefunctions.json index 076b1741e1..53176094aa 100644 --- a/stable/modules/basefunctions.json +++ b/stable/modules/basefunctions.json @@ -1 +1 @@ -[{"name": "adaptMacPath", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/base/install/index.html?highlight=adaptMacPath#src.base.install.adaptMacPath", "id": "1"}, {"name": "addCOBRABinaryPathToSystemPath", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/base/install/index.html?highlight=addCOBRABinaryPathToSystemPath#src.base.install.addCOBRABinaryPathToSystemPath", "id": "2"}, {"name": "addExoMetToEFBA", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/base/solvers/entropicFBA/index.html?highlight=addExoMetToEFBA#src.base.solvers.entropicFBA.addExoMetToEFBA", "id": "3"}, {"name": "addKeyToKnownHosts", "parent_id": "-1", "url": 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"id": "8"}, {"name": "buildCplexProblemFromCOBRAStruct", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/base/solvers/cplex/index.html?highlight=buildCplexProblemFromCOBRAStruct#src.base.solvers.cplex.buildCplexProblemFromCOBRAStruct", "id": "9"}, {"name": "buildOptProblemFromModel", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/base/solvers/index.html?highlight=buildOptProblemFromModel#src.base.solvers.buildOptProblemFromModel", "id": "10"}, {"name": "buildRxnGeneMat", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/base/io/utilities/index.html?highlight=buildRxnGeneMat#src.base.io.utilities.buildRxnGeneMat", "id": "11"}, {"name": "calcDist", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/base/utilities/index.html?highlight=calcDist#src.base.utilities.calcDist", "id": "12"}, {"name": "calcGroupStats", "parent_id": "-1", "url": 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{"name": "COBRArrowSolver", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/base/cobrarrow/index.html?highlight=COBRArrowSolver#src.base.cobrarrow.COBRArrowSolver", "id": "22"}, {"name": "columnVector", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/base/utilities/index.html?highlight=columnVector#src.base.utilities.columnVector", "id": "23"}, {"name": "comparePaths", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/base/paths/index.html?highlight=comparePaths#src.base.paths.comparePaths", "id": "24"}, {"name": "computeMutualCoherence", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/base/solvers/cardOpt/sparseLP/index.html?highlight=computeMutualCoherence#src.base.solvers.cardOpt.sparseLP.computeMutualCoherence", "id": "25"}, {"name": "conda", "parent_id": "-1", "url": 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"https://opencobra.github.io/cobratoolbox/stable/modules/base/io/utilities/index.html?highlight=writePajekNet#src.base.io.utilities.writePajekNet", "id": "220"}, {"name": "writeSBML", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/base/io/utilities/index.html?highlight=writeSBML#src.base.io.utilities.writeSBML", "id": "221"}, {"name": "xls2model", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/base/io/utilities/index.html?highlight=xls2model#src.base.io.utilities.xls2model", "id": "222"}] \ No newline at end of file diff --git a/stable/modules/dataIntegration/XomicsToModel/index.html b/stable/modules/dataIntegration/XomicsToModel/index.html index fc4e8702b3..767a524a86 100644 --- a/stable/modules/dataIntegration/XomicsToModel/index.html +++ b/stable/modules/dataIntegration/XomicsToModel/index.html @@ -345,7 +345,7 @@

    The COBRA Toolbox

  • .addSinksexoMet - Logical, should sink reactions be added for metabolites detected in exometabolomic data (if no exchange or sink is already present).

  • .activeGenesApproach -String with the name of the active genes approach will be used

    ‘oneRxnPerActiveGene’ adds at least one reaction per active gene (Default) -‘deleteModelGenes’ adds all reactions corresponding to an active gene (generates a larger model)

    +‘allRxnPerActiveGene’ adds all reactions corresponding to an active gene (generates a larger model)

    • @@ -548,8 +548,8 @@

    The COBRA Toolbox

    • -
      .activeGenesApproach -The different approached to identify the active

      genes (Possible options: ‘deleteModelGenes’ and ‘oneRxnPerActiveGene’; -default: ‘deleteModelGenes’);

      +
      .activeGenesApproach -The different approached to identify the active

      genes (Possible options: ‘allRxnPerActiveGene’ and ‘oneRxnPerActiveGene’; +default: ‘oneRxnPerActiveGene’);

      • diff --git a/stable/modules/reconstruction/refinement/index.html b/stable/modules/reconstruction/refinement/index.html index a8191ad8b5..f3a79071ff 100644 --- a/stable/modules/reconstruction/refinement/index.html +++ b/stable/modules/reconstruction/refinement/index.html @@ -1024,6 +1024,38 @@

      The COBRA Toolbox

    +
    +
    +buildRxn2subSystem(model, removeSubSystems)[source]
    +

    Generates reaction-subSystem matrix for a COBRA model +This function adds two fields to the COBRA model: 1) rxnSubsystemMat and +2)subSystemsNames and removes the old subSystems field(optional and can +be set to false)

    +
    +
    USAGE
    +

    [modelOut, rxn2subSystem, subSystemNames, nestedCells] = buildRxn2subSystem (model, removeSubSystems)

    +
    +
    INPUTS
    +

    model – COBRA model structure

    +
    +
    OPTIONAL INPUTS
    +

    removeSubSystems – Binary variable, if equals to 1 (or true) subSystems +field will be removed from the model default:true

    +
    +
    OUTPUTS
    +
      +

    • modelOut – COBRA model structure containing two added fields of +“rxn2subSystem” and “subSystemsNames”

      • +

    • rxn2subSystem – Matrix of reactions vs subSystems

      • +

    • subSystemNames – Unique sub-system names in the model with order +corrosponding to the matrix

      • +

    • nestedCells – logical variable, True if sub-system field is a +nested cell vector and False if it’s not

      • +
    +
    +
    +
    +
    changeCOBRAConstraints(model, constraintID, varargin)[source]
    @@ -1701,6 +1733,9 @@

    The COBRA Toolbox

    +

    Note: Notice that this function checks if two models are the same, two +same models does not necessary mean two same structures. +use structeq.m to compare two structures

    diff --git a/stable/modules/reconstructionfunctions.json b/stable/modules/reconstructionfunctions.json index ca92988ec6..e0cf4aadb6 100644 --- a/stable/modules/reconstructionfunctions.json +++ b/stable/modules/reconstructionfunctions.json @@ -1 +1 @@ -[{"name": "adaptDraftModelID", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/demeter/src/integration/index.html?highlight=adaptDraftModelID#src.reconstruction.demeter.src.integration.adaptDraftModelID", "id": "1"}, {"name": "addCOBRAConstraints", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/refinement/index.html?highlight=addCOBRAConstraints#src.reconstruction.refinement.addCOBRAConstraints", "id": "2"}, {"name": "addCOBRAVariables", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/refinement/index.html?highlight=addCOBRAVariables#src.reconstruction.refinement.addCOBRAVariables", "id": "3"}, {"name": "addDemandReaction", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/refinement/index.html?highlight=addDemandReaction#src.reconstruction.refinement.addDemandReaction", "id": "4"}, {"name": "addExchangeRxn", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/refinement/index.html?highlight=addExchangeRxn#src.reconstruction.refinement.addExchangeRxn", "id": "5"}, {"name": "addGenes", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/refinement/index.html?highlight=addGenes#src.reconstruction.refinement.addGenes", "id": "6"}, {"name": "addMetabolite", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/refinement/index.html?highlight=addMetabolite#src.reconstruction.refinement.addMetabolite", "id": "7"}, {"name": "addmetabolites", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/rBioNet/index.html?highlight=addmetabolites#src.reconstruction.rBioNet.addmetabolites", "id": "8"}, {"name": "addMetInfo", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/comparison/modelBorgifier/index.html?highlight=addMetInfo#src.reconstruction.comparison.modelBorgifier.addMetInfo", "id": "9"}, {"name": "addMIRIAMAnnotations", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/refinement/index.html?highlight=addMIRIAMAnnotations#src.reconstruction.refinement.addMIRIAMAnnotations", "id": "10"}, {"name": "addmissing", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/rBioNet/index.html?highlight=addmissing#src.reconstruction.rBioNet.addmissing", "id": "11"}, {"name": "addMultipleMetabolites", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/refinement/index.html?highlight=addMultipleMetabolites#src.reconstruction.refinement.addMultipleMetabolites", "id": "12"}, {"name": "addMultipleReactions", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/refinement/index.html?highlight=addMultipleReactions#src.reconstruction.refinement.addMultipleReactions", "id": "13"}, {"name": "addMultipleReactionsIT", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/refinement/index.html?highlight=addMultipleReactionsIT#src.reconstruction.refinement.addMultipleReactionsIT", "id": "14"}, {"name": "addReaction", "parent_id": "-1", "url": "https://opencobra.github.io/cobratoolbox/stable/modules/reconstruction/refinement/index.html?highlight=addReaction#src.reconstruction.refinement.addReaction", "id": "15"}, {"name": "addReactionGEM", "parent_id": "-1", "url": 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