Package: sybil
Type: Package
Title: Efficient Constrained Based Modelling
Version: 2.1.5
Date: 2019-03-07
Authors@R: c(
         person("Mayo", "Roettger", role = c("cre"), email = "mayo.roettger@hhu.de"),
	     person("Gabriel", "Gelius-Dietrich", role = "aut"),
             person(c("C.", "Jonathan"), "Fritzemeier", role = "ctb", email = "clausjonathan.fritzemeier@uni-duesseldorf.de"),
             person("Rajen", "Piernikarczyk", role = "ctb"),
             person(c("Marc", "Andre"), "Daxer", role = "ctb"),
             person("Benjamin", "Braasch", role = "ctb"),
             person("Abdelmoneim", "Desouki", role = "ctb"),
             person(c("Martin", "J."), "Lercher", role = "ctb"))
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
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:
        http://www.cs.hhu.de/lehrstuehle-und-arbeitsgruppen/computational-cell-biology/software/sybil.html
Description: 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.
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: 2019-03-07 10:11:26 UTC; root
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: 2019-03-07 14:10:03 UTC
Built: R 4.1.0; ; 2020-08-03 06:16:53 UTC; windows
