GlobalFit-package: Bi-Level Optimization of Metabolic Network Models
In GlobalFit: Bi-Level Optimization of Metabolic Network Models
Description
Details
Author(s)
Examples
Description
Initial metabolic networks often inaccurately predict in-silico growth or non-growth if compared to in-vivo data. This package refines metabolic network models by making networks changes (i.e., removing, adding, changing reversibility of reactions; adding and removing biomass metabolites) and simultaneously matching sets of experimental growth and non-growth data (e.g., KO-mutants, mutants grown under different media conditions,...). Three versions of GlobalFit are provided; an old(algorithm=2), a newer (faster) version (algorithm=1) and a third version (algortithm=3) which can be used to remove thermodynamically infeasible cyles.
Details
Package: GlobalFit
Type: Package
Version: 1.2
Date: 2016-08-12
License: GPL-3
Author(s)
Daniel Hartleb
daniel.hartleb@hhu.de
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## Not run:
library(sybil)
library(GlobalFit)
library("cplexAPI")
SYBIL_SETTINGS("SOLVER", "cplexAPI")
#SYBIL_SETTINGS("SOLVER", "sybilGUROBI")
###################
##EXAMPLE1: RECONCILATION OF TWO FALSE PREDICTIONS
data(example_net1)
# names of reactions, which are not allowed to be removed
not_delete_for=c(react_id(findExchReact(example_net1)),"Biomass")
not_delete_back=c(react_id(findExchReact(example_net1)),"Biomass")
#set biomass object function
obj_coef(example_net1)[which(react_id(example_net1)=="Biomass")]=1
#create list of influxes
influxes=list()
influxes[[1]]=list(exRea="A[e]_import",value=-10)
#set influxes
lowbnd(example_net1)[pos=which(react_id(example_net1)=="A[e]_import")]=-10
#growth cases
on=list()
on[[1]]=list(on=influxes,name="LIVE!",ko_react=c("AtoB"),forced=TRUE,viability_threshold=1,
gene_copy_number=1)
on[[2]]=list(on=influxes,name="LIVE!",ko_react=c("AtoB"),forced=TRUE,viability_threshold=1,
gene_copy_number=1)
#non-growth cases
off=list()
off[[1]]=list(on=influxes,name="DIE!",ko_react=c("AtoR"),forced=FALSE,viability_threshold=1,
gene_copy_number=1)
off[[2]]=list(on=influxes,name="DIE!",ko_react=c("AtoR"),forced=FALSE,viability_threshold=1,
gene_copy_number=1)
#optional parameter list for solver, in this example for cplex
p_list=list(CPX_PARAM_THREADS=as.integer(1),CPX_PARAM_EPRHS=as.double(1e-9),
CPX_PARAM_NETEPRHS=as.double(1e-11),CPX_PARAM_EPINT=as.double(1e-09),
CPX_PARAM_TILIM=1e5,CPX_PARAM_PARALLELMODE=CPX_PARALLEL_OPPORTUNISTIC)
#create list of reactions, that are allowed to be reversed
reverse_reaction_list=list()
reverse_reaction_list[[1]]=list(reaction="AtoC",pen=1)
reverse_reaction_list[[2]]=list(reaction="TtoB",pen=1)
#create list of additional reactions
additional_reactions_list=list()
additional_reactions_list[[1]]=list(id="KtoB",name="KtoB reaction",eq="(2.1) K[e] => B[e]",pen=7)
additional_reactions_list[[2]]=list(id="TtoR",name="TtoR reaction",eq="T[e] <=> R[e] + Q[e]",pen=3)
additional_reactions_list[[3]]=list(id="CtoB",name="TtoQ reaction",eq="C[e] => B[e]",pen=5)
#create list of additional biomass metabolites
additional_biomass_mets=list()
additional_biomass_mets[[1]]=list(met="Q[e]",pen=0.1,factor=-1)
additional_biomass_mets[[2]]=list(met="R[e]",pen=0.1,factor=-1)
additional_biomass_mets[[3]]=list(met="B[e]",pen=0.1,factor=-1)
#create list of biomass metabolites, that are allowed to be removed
remove_biomass_mets=list()
remove_biomass_mets[[1]]=list(met="S[e]",pen=40.1)
remove_biomass_mets[[2]]=list(met="T[e]",pen=0.1)
remove_biomass_mets[[3]]=list(met="Z[e]",pen=0.1)
#set penalties for removing reactions (network contains nine reactions, so we have to set 9 values)
remove_penalties_hin=c(1,2.5,3,4,5,6,7,8,9)
remove_penalties_back=c(1,2.5,3,4,5,6,7,8,9)
opt_net=bilevel_optimize(network=example_net1,on=on,off=off,algorithm=1,
additional_reactions=additional_reactions_list,not_delete_for=not_delete_for,
not_delete_back=not_delete_back,minimize=FALSE,simple=FALSE,verboseMode=1,
param_list=p_list,cancel_case_penalty=NULL,use_indicator_constraints=FALSE,
stat_file=NULL,react_file=NULL,remove_penalties_hin=remove_penalties_hin,
remove_penalties_back=remove_penalties_back,reverse_reaction_list=reverse_reaction_list,
alternatives=0,MaxPenalty=NULL,additional_biomass_metabolites=additional_biomass_mets,
remove_biomass_metabolites=remove_biomass_mets,variable_lower_bound=NULL,forced_modifications=0)
##############
##EXAMPLE2: NETWORK CONTAINS THERMODYNAMIC INFEASIBLE CYCLES
# (CYC1 AND CYC2 CAN CARRY FLUX WITHOUT ANY INFLUX);
# WE USE GLOBALFIT AND DIFFERENT BIOMASS OBEJCTIVE FUNCTIONS
# FOR THE GROWTH AND NON-GROWTH CASE
data(example_net2)
#set wild type biomass object function
obj_coef(example_net2)[which(react_id(example_net2)=="Biomass")]=1
#create 2 lists of influxes (one list is empty)
influxes=list()
influxes[[1]]=list(exRea="T[e]_import",value=-10)
influxes2=list()
#set influxes for wild type
lowbnd(example_net2)[pos=which(react_id(example_net2)=="T[e]_import")]=-10
#growth cases with wild type biomass
on=list()
on[[1]]=list(on=influxes,name="LIVE!",ko_react=c(),forced=TRUE,viability_threshold=1,
gene_copy_number=1,biomass="Biomass")
#non-growth cases with different biomass ("CYC1","CYC2")
off=list()
off[[1]]=list(on=influxes,name="DIE!",ko_react=c(),forced=FALSE,viability_threshold=1,
gene_copy_number=1,biomass=c("CYC1","CYC2"))
# no alternative modifications allowed
reverse_reaction_list=list()
additional_reactions_list=list()
additional_biomass_mets=list()
remove_biomass_mets=list()
# names of reactions, which are not allowed to be removed, including the cycle reactions
not_delete_for=c(react_id(findExchReact(example_net2)),"Biomass","CYC1","CYC2")
not_delete_back=c(react_id(findExchReact(example_net2)),"Biomass","CYC1","CYC2")
opt_net=bilevel_optimize(network=example_net2,on=on,off=off,algorithm=3,
additional_reactions=additional_reactions_list,not_delete_for=not_delete_for,
not_delete_back=not_delete_back,minimize=FALSE,simple=FALSE,verboseMode=1,
param_list=p_list,cancel_case_penalty=NULL,use_indicator_constraints=FALSE,
stat_file=NULL,react_file=NULL,reverse_reaction_list=reverse_reaction_list,
alternatives=0,MaxPenalty=NULL,additional_biomass_metabolites=additional_biomass_mets,
remove_biomass_metabolites=remove_biomass_mets,
variable_lower_bound=NULL,forced_modifications=0)
##########################
##EXAMPLE3: NON-GROWTH CASE CAN ONLY BE RESOLVED BY CHANGING THE LOWER BOUND OF AN INFLUX
#(ONLY WORKS WITH THE SLOWER IMPLEMENTATION OF GLOBALFIT; ALGORITHM=2).
#THIS CAN BE USED TO FIND SUITABLE QUALITATIVE MEDIA COMPOSITIONS.
#NOTE IN THIS SIMPLE EXAMPLE THE VIABILITY THRESHOLD
#OF THE NON-GROWTH CASE IS HIGHER THAN THE GROWTH CASE
data(example_net3)
# names of reactions, which are not allowed to be removed
not_delete_for=c(react_id(findExchReact(example_net3)),"Biomass")
not_delete_back=c(react_id(findExchReact(example_net3)),"Biomass")
#set wild type biomass object function
obj_coef(example_net3)[which(react_id(example_net3)=="Biomass")]=1
#create 2 lists of influxes (one list is empty)
influxes=list()
influxes[[1]]=list(exRea="T[e]_import",value=-100)
influxes2=list()
#set influxes for wild type
lowbnd(example_net3)[pos=which(react_id(example_net3)=="T[e]_import")]=-100
#growth cases with wild type biomass
on=list()
on[[1]]=list(on=influxes,name="LIVE!",ko_react=c(),forced=TRUE,viability_threshold=1,
gene_copy_number=1)
#non-growth cases with different biomass(A[e]_imoprt)
off=list()
off[[1]]=list(on=influxes,name="DIE!",ko_react=c(),forced=FALSE,viability_threshold=2,
gene_copy_number=1)
## set varying_lower_bound; T[e]_import is allowed to vary between 0 and -20.
# Because the viability threshold of the non-growth case is 2
# and the viability threshold of the growth case is 1;
# the optimized value should be between -2 and -1
varying_lower_bound_list=list()
varying_lower_bound_list[[1]]=list(reaction="T[e]_import",min=-20,max=-0,penalty=0.1)
# no alternative modifications allowed
reverse_reaction_list=list()
additional_reactions_list=list()
additional_biomass_mets=list()
remove_biomass_mets=list()
opt_net=bilevel_optimize(network=example_net3,on=on,off=off,algorithm=2,
additional_reactions=additional_reactions_list,not_delete_for=not_delete_for,
not_delete_back=not_delete_back,minimize=FALSE,simple=FALSE,verboseMode=1,
param_list=p_list,cancel_case_penalty=NULL,use_indicator_constraints=FALSE,
stat_file=NULL,react_file=NULL,reverse_reaction_list=reverse_reaction_list,
alternatives=0,MaxPenalty=NULL,additional_biomass_metabolites=additional_biomass_mets,
remove_biomass_metabolites=remove_biomass_mets,variable_lower_bound=varying_lower_bound_list,
forced_modifications=0)
## End(Not run)
GlobalFit documentation built on May 2, 2019, 5:07 a.m.
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Description Details Author(s) Examples
Description
Initial metabolic networks often inaccurately predict in-silico growth or non-growth if compared to in-vivo data. This package refines metabolic network models by making networks changes (i.e., removing, adding, changing reversibility of reactions; adding and removing biomass metabolites) and simultaneously matching sets of experimental growth and non-growth data (e.g., KO-mutants, mutants grown under different media conditions,...). Three versions of GlobalFit are provided; an old(algorithm=2), a newer (faster) version (algorithm=1) and a third version (algortithm=3) which can be used to remove thermodynamically infeasible cyles.
Details
| Package: | GlobalFit |
| Type: | Package |
| Version: | 1.2 |
| Date: | 2016-08-12 |
| License: | GPL-3 |
Author(s)
Daniel Hartleb
daniel.hartleb@hhu.de
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 | ## Not run:
library(sybil)
library(GlobalFit)
library("cplexAPI")
SYBIL_SETTINGS("SOLVER", "cplexAPI")
#SYBIL_SETTINGS("SOLVER", "sybilGUROBI")
###################
##EXAMPLE1: RECONCILATION OF TWO FALSE PREDICTIONS
data(example_net1)
# names of reactions, which are not allowed to be removed
not_delete_for=c(react_id(findExchReact(example_net1)),"Biomass")
not_delete_back=c(react_id(findExchReact(example_net1)),"Biomass")
#set biomass object function
obj_coef(example_net1)[which(react_id(example_net1)=="Biomass")]=1
#create list of influxes
influxes=list()
influxes[[1]]=list(exRea="A[e]_import",value=-10)
#set influxes
lowbnd(example_net1)[pos=which(react_id(example_net1)=="A[e]_import")]=-10
#growth cases
on=list()
on[[1]]=list(on=influxes,name="LIVE!",ko_react=c("AtoB"),forced=TRUE,viability_threshold=1,
gene_copy_number=1)
on[[2]]=list(on=influxes,name="LIVE!",ko_react=c("AtoB"),forced=TRUE,viability_threshold=1,
gene_copy_number=1)
#non-growth cases
off=list()
off[[1]]=list(on=influxes,name="DIE!",ko_react=c("AtoR"),forced=FALSE,viability_threshold=1,
gene_copy_number=1)
off[[2]]=list(on=influxes,name="DIE!",ko_react=c("AtoR"),forced=FALSE,viability_threshold=1,
gene_copy_number=1)
#optional parameter list for solver, in this example for cplex
p_list=list(CPX_PARAM_THREADS=as.integer(1),CPX_PARAM_EPRHS=as.double(1e-9),
CPX_PARAM_NETEPRHS=as.double(1e-11),CPX_PARAM_EPINT=as.double(1e-09),
CPX_PARAM_TILIM=1e5,CPX_PARAM_PARALLELMODE=CPX_PARALLEL_OPPORTUNISTIC)
#create list of reactions, that are allowed to be reversed
reverse_reaction_list=list()
reverse_reaction_list[[1]]=list(reaction="AtoC",pen=1)
reverse_reaction_list[[2]]=list(reaction="TtoB",pen=1)
#create list of additional reactions
additional_reactions_list=list()
additional_reactions_list[[1]]=list(id="KtoB",name="KtoB reaction",eq="(2.1) K[e] => B[e]",pen=7)
additional_reactions_list[[2]]=list(id="TtoR",name="TtoR reaction",eq="T[e] <=> R[e] + Q[e]",pen=3)
additional_reactions_list[[3]]=list(id="CtoB",name="TtoQ reaction",eq="C[e] => B[e]",pen=5)
#create list of additional biomass metabolites
additional_biomass_mets=list()
additional_biomass_mets[[1]]=list(met="Q[e]",pen=0.1,factor=-1)
additional_biomass_mets[[2]]=list(met="R[e]",pen=0.1,factor=-1)
additional_biomass_mets[[3]]=list(met="B[e]",pen=0.1,factor=-1)
#create list of biomass metabolites, that are allowed to be removed
remove_biomass_mets=list()
remove_biomass_mets[[1]]=list(met="S[e]",pen=40.1)
remove_biomass_mets[[2]]=list(met="T[e]",pen=0.1)
remove_biomass_mets[[3]]=list(met="Z[e]",pen=0.1)
#set penalties for removing reactions (network contains nine reactions, so we have to set 9 values)
remove_penalties_hin=c(1,2.5,3,4,5,6,7,8,9)
remove_penalties_back=c(1,2.5,3,4,5,6,7,8,9)
opt_net=bilevel_optimize(network=example_net1,on=on,off=off,algorithm=1,
additional_reactions=additional_reactions_list,not_delete_for=not_delete_for,
not_delete_back=not_delete_back,minimize=FALSE,simple=FALSE,verboseMode=1,
param_list=p_list,cancel_case_penalty=NULL,use_indicator_constraints=FALSE,
stat_file=NULL,react_file=NULL,remove_penalties_hin=remove_penalties_hin,
remove_penalties_back=remove_penalties_back,reverse_reaction_list=reverse_reaction_list,
alternatives=0,MaxPenalty=NULL,additional_biomass_metabolites=additional_biomass_mets,
remove_biomass_metabolites=remove_biomass_mets,variable_lower_bound=NULL,forced_modifications=0)
##############
##EXAMPLE2: NETWORK CONTAINS THERMODYNAMIC INFEASIBLE CYCLES
# (CYC1 AND CYC2 CAN CARRY FLUX WITHOUT ANY INFLUX);
# WE USE GLOBALFIT AND DIFFERENT BIOMASS OBEJCTIVE FUNCTIONS
# FOR THE GROWTH AND NON-GROWTH CASE
data(example_net2)
#set wild type biomass object function
obj_coef(example_net2)[which(react_id(example_net2)=="Biomass")]=1
#create 2 lists of influxes (one list is empty)
influxes=list()
influxes[[1]]=list(exRea="T[e]_import",value=-10)
influxes2=list()
#set influxes for wild type
lowbnd(example_net2)[pos=which(react_id(example_net2)=="T[e]_import")]=-10
#growth cases with wild type biomass
on=list()
on[[1]]=list(on=influxes,name="LIVE!",ko_react=c(),forced=TRUE,viability_threshold=1,
gene_copy_number=1,biomass="Biomass")
#non-growth cases with different biomass ("CYC1","CYC2")
off=list()
off[[1]]=list(on=influxes,name="DIE!",ko_react=c(),forced=FALSE,viability_threshold=1,
gene_copy_number=1,biomass=c("CYC1","CYC2"))
# no alternative modifications allowed
reverse_reaction_list=list()
additional_reactions_list=list()
additional_biomass_mets=list()
remove_biomass_mets=list()
# names of reactions, which are not allowed to be removed, including the cycle reactions
not_delete_for=c(react_id(findExchReact(example_net2)),"Biomass","CYC1","CYC2")
not_delete_back=c(react_id(findExchReact(example_net2)),"Biomass","CYC1","CYC2")
opt_net=bilevel_optimize(network=example_net2,on=on,off=off,algorithm=3,
additional_reactions=additional_reactions_list,not_delete_for=not_delete_for,
not_delete_back=not_delete_back,minimize=FALSE,simple=FALSE,verboseMode=1,
param_list=p_list,cancel_case_penalty=NULL,use_indicator_constraints=FALSE,
stat_file=NULL,react_file=NULL,reverse_reaction_list=reverse_reaction_list,
alternatives=0,MaxPenalty=NULL,additional_biomass_metabolites=additional_biomass_mets,
remove_biomass_metabolites=remove_biomass_mets,
variable_lower_bound=NULL,forced_modifications=0)
##########################
##EXAMPLE3: NON-GROWTH CASE CAN ONLY BE RESOLVED BY CHANGING THE LOWER BOUND OF AN INFLUX
#(ONLY WORKS WITH THE SLOWER IMPLEMENTATION OF GLOBALFIT; ALGORITHM=2).
#THIS CAN BE USED TO FIND SUITABLE QUALITATIVE MEDIA COMPOSITIONS.
#NOTE IN THIS SIMPLE EXAMPLE THE VIABILITY THRESHOLD
#OF THE NON-GROWTH CASE IS HIGHER THAN THE GROWTH CASE
data(example_net3)
# names of reactions, which are not allowed to be removed
not_delete_for=c(react_id(findExchReact(example_net3)),"Biomass")
not_delete_back=c(react_id(findExchReact(example_net3)),"Biomass")
#set wild type biomass object function
obj_coef(example_net3)[which(react_id(example_net3)=="Biomass")]=1
#create 2 lists of influxes (one list is empty)
influxes=list()
influxes[[1]]=list(exRea="T[e]_import",value=-100)
influxes2=list()
#set influxes for wild type
lowbnd(example_net3)[pos=which(react_id(example_net3)=="T[e]_import")]=-100
#growth cases with wild type biomass
on=list()
on[[1]]=list(on=influxes,name="LIVE!",ko_react=c(),forced=TRUE,viability_threshold=1,
gene_copy_number=1)
#non-growth cases with different biomass(A[e]_imoprt)
off=list()
off[[1]]=list(on=influxes,name="DIE!",ko_react=c(),forced=FALSE,viability_threshold=2,
gene_copy_number=1)
## set varying_lower_bound; T[e]_import is allowed to vary between 0 and -20.
# Because the viability threshold of the non-growth case is 2
# and the viability threshold of the growth case is 1;
# the optimized value should be between -2 and -1
varying_lower_bound_list=list()
varying_lower_bound_list[[1]]=list(reaction="T[e]_import",min=-20,max=-0,penalty=0.1)
# no alternative modifications allowed
reverse_reaction_list=list()
additional_reactions_list=list()
additional_biomass_mets=list()
remove_biomass_mets=list()
opt_net=bilevel_optimize(network=example_net3,on=on,off=off,algorithm=2,
additional_reactions=additional_reactions_list,not_delete_for=not_delete_for,
not_delete_back=not_delete_back,minimize=FALSE,simple=FALSE,verboseMode=1,
param_list=p_list,cancel_case_penalty=NULL,use_indicator_constraints=FALSE,
stat_file=NULL,react_file=NULL,reverse_reaction_list=reverse_reaction_list,
alternatives=0,MaxPenalty=NULL,additional_biomass_metabolites=additional_biomass_mets,
remove_biomass_metabolites=remove_biomass_mets,variable_lower_bound=varying_lower_bound_list,
forced_modifications=0)
## End(Not run)
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