sybil

Efficient Constrained Based Modelling

This Systems Biology Package (Gelius-Dietrich et. al. (2012) <doi:10.1186/1752-0509-7-125>) implements algorithms for constraint based analyses of metabolic networks, e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis. The package is easily extendable for additional algorithms. Most of the current LP/MILP solvers are supported via additional packages.

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Description file content

Package
sybil
Type
Package
Title
Efficient Constrained Based Modelling
Version
2.1.2
Date
2018-07-20
Maintainer
Mayo Roettger
Depends
R (>= 3.2.0), Matrix, lattice
Imports
methods
Suggests
glpkAPI (>= 1.2.8), cplexAPI (>= 1.2.4), clpAPI (>= 1.2.4), lpSolveAPI (>= 5.5.2.0), parallel, grid
URL
Description
This Systems Biology Package (Gelius-Dietrich et. al. (2012) ) implements algorithms for constraint based analyses of metabolic networks, e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis. The package is easily extendable for additional algorithms. Most of the current LP/MILP solvers are supported via additional packages.
LazyLoad
yes
License
GPL-3 | file LICENSE
Collate
generics.R validmodelorg.R validoptsol.R validreactId.R validreact.R reactClass.R validreactId_Exch.R validsysBiolAlg.R addAlgorithm.R addExchReact.R addReact.R addSolver.R blockedReact.R bracket_pairs.R ceilValues.R changeBounds.R changeGPR.R changeObjFunc.R checkAlgorithm.R checkDefaultMethod.R checkEmptyField.R checkReactId.R check_brackets.R createReactionString.R deadEndMetabolite.R doInRound.R doubleFluxDel.R doubleGeneDel.R doubleReact.R editEnvir.R findExchReact.R floorValues.R fluxVar.R geneDel.R geneDeletion.R generateFluxdels.R generateModKey.R generateWT.R getsybilenv.R makeLPcompatible.R mod2irrev.R modelorg2ExPA.R modelorg2text.R modelorg2tsv.R multiDel.R oneFluxDel.R oneGeneDel.R onlyChangeGPR.R onlyCheckGPR.R optObj_basicfunc.R optObj_lpSolveAPIcompat.R optimizer.R parseBoolean.R phpp.R ppProcessing.R prepareSubSysMatrix.R printLogComment.R printNamedList.R progress.R promptSysBiolAlg.R recodeMatrix.R readTEXTmod.R readTSVmod.R reassignFwBwMatch.R rmReact.R robAna.R settings.R singletonMetabolite.R sybilStack.R ypd.R zzz.R modelorgClass.R modelorg_irrevClass.R optObj_pointer.R optObjClass.R optObj_clpAPIClass.R optObj_cplexAPIClass.R optObj_glpkAPIClass.R optObj_lpSolveAPIClass.R sybilErrorClass.R ppProcClass.R netFluxClass.R fluxDistributionClass.R reactIdClass.R reactId_ExchClass.R optsolClass.R optsol_blockedReactClass.R optsol_optimizeProbClass.R optsol_fluxVarClass.R optsol_fluxdelClass.R optsol_robAnaClass.R optsol_phppClass.R optsol_genedelClass.R checksolClass.R summaryOptsolClass.R sysBiolAlgClass.R sysBiolAlg_fbaClass.R sysBiolAlg_fbaEasyConstraintClass.R sysBiolAlg_fvClass.R sysBiolAlg_lmomaClass.R sysBiolAlg_momaClass.R sysBiolAlg_mtfClass.R sysBiolAlg_mtfEasyConstraintClass.R sysBiolAlg_roomClass.R sybilLogClass.R upgradeModelorg.R mergeReact2Modelorg.R
Packaged
2018-07-20 12:53:28 UTC; roettger
Author
Mayo Roettger [cre], Gabriel Gelius-Dietrich [aut], C. Jonathan Fritzemeier [ctb], Rajen Piernikarczyk [ctb], Marc Andre Daxer [ctb], Benjamin Braasch [ctb], Abdelmoneim Desouki [ctb], Martin J. Lercher [ctb]
NeedsCompilation
no
Repository
CRAN
Date/Publication
2018-08-15 16:40:03 UTC

install.packages('sybil')

2.1.2

a month ago

Mayo Roettger

GPL-3 | file LICENSE

Depends on

R (>= 3.2.0), Matrix, lattice

Imports

methods

Suggests

glpkAPI (>= 1.2.8), cplexAPI (>= 1.2.4), clpAPI (>= 1.2.4), lpSolveAPI (>= 5.5.2.0), parallel, grid

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