diff --git a/DESCRIPTION b/DESCRIPTION index 6ac300ea2c54e2f3d6eb7ea65efe21c1c66e45f8..26272a2cb2d38e9560f5f26ec23482cee69b1ca4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,10 +1,11 @@ Package: sybil Type: Package -Title: sybil - Efficient Constrained Based Modelling in R +Title: Efficient Constrained Based Modelling in R Version: 1.3.0 -Date: 2015-03-30 -Authors@R: c(person("Gabriel", "Gelius-Dietrich", role = c("aut")), - person(c("C.", "Jonathan"), "Fritzemeier", role = c("ctb", "cre"), email = "clausjonathan.fritzemeier@uni-duesseldorf.de"), +Date: 2015-06-17 +Authors@R: c( + person(c("C.", "Jonathan"), "Fritzemeier", role = c("cre", "ctb"), email = "clausjonathan.fritzemeier@uni-duesseldorf.de"), + person("Gabriel", "Gelius-Dietrich", role = c("aut")), person("Rajen", "Piernikarczyk", role = "ctb"), person(c("Marc", "Andre"), "Daxer", role = "ctb"), person("Benjamin", "Braasch", role = "ctb"), @@ -17,9 +18,9 @@ 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/en/research-groups/bioinformatics/software/sybil.html -Description: The package sybil is a Systems Biology Library for R, implementing 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). +Description: This Systems Biology Library for R 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). Most of the current LP/MILP solvers are supported via additional packages. LazyLoad: yes -License: GPL-3 +License: GPL-3 | file LICENSE Collate: generics.R validmodelorg.R validoptsol.R validreactId.R validreactId_Exch.R validsysBiolAlg.R addAlgorithm.R addExchReact.R addReact.R addSolver.R blockedReact.R diff --git a/man/addReact.Rd b/man/addReact.Rd index 5e10126c735b9d0daa2a63687b3162484e6a4d61..2470300238be767f106697b71ef271d54d8a27dc 100644 --- a/man/addReact.Rd +++ b/man/addReact.Rd @@ -118,7 +118,9 @@ data(Ec_core) # add reaction A + 2 B <-> C to the model -modelNew <- addReact(Ec_core, id="newReact", met=c("A", "B", "C"), Scoef=c(-1, -2, 1), reversible=TRUE, lb=-1000, ub=1000, obj=0) +modelNew <- addReact(Ec_core, id="newReact", met=c("A", "B", "C"), + Scoef=c(-1, -2, 1), reversible=TRUE, + lb=-1000, ub=1000, obj=0) # view the new reaction shrinkMatrix(modelNew, j="newReact") diff --git a/man/readProb-methods.Rd b/man/readProb-methods.Rd index d1751961430497946cc133d4516c1f6e8efc6cd6..b33a0af46049c156b5a9b260c67b8c26e23cceba 100644 --- a/man/readProb-methods.Rd +++ b/man/readProb-methods.Rd @@ -88,9 +88,15 @@ library(sybil) data(Ec_core) - prob <- sysBiolAlg(Ec_core, algorithm = "fba", solver="glpkAPI") # create a sysBiolAlg object (we use here GLPK (!)) - save(file="prob.RData",prob) # write the R-object to disc - writeProb(prob@problem, fname="prob.lp", ff="lp") # now write the linear program part (managed by the solver) to disc + + # create a sysBiolAlg object (we use here GLPK (!)) + prob <- sysBiolAlg(Ec_core, algorithm = "fba", solver="glpkAPI") + + # write the R-object to disc + save(file="prob.RData",prob) + + # now write the linear program part (managed by the solver) to disc + writeProb(prob@problem, fname="prob.lp", ff="lp") # start new R session diff --git a/man/writeProb-methods.Rd b/man/writeProb-methods.Rd index bcb82d33246780fb249bd954d9ac19deaa66ddc0..214ebf94d092448ee188a30a81093489235b55ab 100644 --- a/man/writeProb-methods.Rd +++ b/man/writeProb-methods.Rd @@ -87,9 +87,14 @@ library(sybil) data(Ec_core) - prob <- sysBiolAlg(Ec_core, algorithm = "fba", solver="glpkAPI") # create a sysBiolAlg object (we use here GLPK (!)) - save(file="prob.RData",prob) # write the R-object to disc - writeProb(prob@problem, fname="prob.lp", ff="lp") # now write the linear program part (managed by the solver) to disc + # create a sysBiolAlg object (we use here GLPK (!)) + prob <- sysBiolAlg(Ec_core, algorithm = "fba", solver="glpkAPI") + + # write the R-object to disc + save(file="prob.RData",prob) + + # now write the linear program part (managed by the solver) to disc + writeProb(prob@problem, fname="prob.lp", ff="lp") # start new R session