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# zzz.R
# FBA and friends with R.
#
# Copyright (C) 2010-2014 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
# Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
# All right reserved.
# Email: geliudie@uni-duesseldorf.de
#
# This file is part of sybil.
#
# Sybil is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Sybil is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with sybil. If not, see <http://www.gnu.org/licenses/>.
.SYBILenv <- new.env()
.onLoad <- function(lib, pkg) {
# -------------------------------------------------------------- #
# stacks and queues in sybil
.SYBILenv$sybilStack <- vector(mode = "list", length = 0)
# -------------------------------------------------------------- #
# settings in sybil
.SYBILenv$settings <- list(
MODELORG_VERSION = "2.0",
SOLVER = "glpkAPI",
METHOD = "simplex",
TOLERANCE = 1E-6,
MAXIMUM = 1000,
ALGORITHM = "fba",
OPT_DIRECTION = "max",
USE_NAMES = FALSE,
PATH_TO_MODEL = ".",
SOLVER_CTRL_PARM = as.data.frame(NA)
)
# -------------------------------------------------------------- #
# available solvers and methods
# The first method in each vector is the default one, the default
# alternate method is NA.
# solvers
.SYBILenv$solvers <- c("glpkAPI", "clpAPI", "lpSolveAPI", "cplexAPI")
# methods
.SYBILenv$solverMethods <- list(
glpkAPI = c("simplex", "interior", "exact", "mip"),
clpAPI = c("general_solve", "inidual", "iniprimal", "inibarrier",
"inibarriernoc", "idiot", "dual", "primal"),
lpSolveAPI = c("lp_solve"),
cplexAPI = c("lpopt", "primopt", "dualopt", "baropt", "hybbaropt",
"hybnetopt", "siftopt", "mipopt", "qpopt")
)
# default parameters
.SYBILenv$solverCtrlParm <- list(
glpkAPI = list(simplex = as.data.frame(NA),
interior = as.data.frame(NA),
exact = as.data.frame(NA),
mip = as.data.frame(NA)
),
clpAPI = list(general_solve = as.data.frame(NA),
inidual = as.data.frame(NA),
iniprimal = as.data.frame(NA),
inibarrier = as.data.frame(NA),
inibarriernoc = as.data.frame(NA),
dual = as.data.frame(NA),
primal = as.data.frame(NA)
),
lpSolveAPI = list(lp_solve = as.data.frame(NA)),
cplexAPI = list(lpopt = as.data.frame(NA),
primopt = as.data.frame(NA),
#primopt = data.frame(
# #CPX_PARAM_REDUCE = as.integer(1),
# CPX_PARAM_DATACHECK = as.integer(1)
#),
dualopt = as.data.frame(NA),
baropt = as.data.frame(NA),
hybbaropt = as.data.frame(NA),
hybnetopt = as.data.frame(NA),
siftopt = as.data.frame(NA),
mipopt = as.data.frame(NA),
qpopt = as.data.frame(NA)
)
)
# -------------------------------------------------------------- #
# algorithms simulation genetic perturbations
.SYBILenv$algorithm[["pert"]] <- c("fba", "mtf", "moma", "lmoma", "room")
# -------------------------------------------------------------- #
# methods problem types
.SYBILenv$ptype[["mip"]] <- list(
glpkAPI = c("mip"),
lpSolveAPI = c("lp_solve"),
cplexAPI = c("mipopt")
)
.SYBILenv$ptype[["qp"]] <- list(
cplexAPI = c("qpopt", "baropt")
)
}
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