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.

Total

20,213

Last month

484

Last week

130

Average per day

16

Daily downloads

Total downloads

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

3 months 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

Discussions