bilevel_optimize: pre und post-processing of optimization
In GlobalFit: Bi-Level Optimization of Metabolic Network Models
Description
Usage
Arguments
Value
Author(s)
References
Examples
View source: R/GlobalFit_methods.R
Description
pre und post-processing of optimization. Adds reaction to network, creates output, creates optimization object, interprets solution, applies modification to network.
Usage
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bilevel_optimize(network, on = c(), off = c(), algorithm = 1,
additional_reactions = NULL, minimize = TRUE, simple = FALSE,
verboseMode = 1, cancel_case_penalty = NULL, not_delete_for = c(),
not_delete_back = c(), param_list = NULL, use_indicator_constraints = FALSE,
remove_penalties_hin = c(), remove_penalties_back = c(), stat_file = NULL,
react_file = NULL, reverse_reaction_list = NULL, MaxPenalty = NULL,
alternatives = 0, bio_stoich = 1e-05, additional_biomass_metabolites = NULL,
remove_biomass_metabolites = NULL, variable_lower_bound = NULL,
forced_modifications = 0)
Arguments
network
metabolic network model of type modelorg
on
each entry must contain:
on: list of influxes
name: character, name of growth case
ko_react: vector of reaction, which are knocked out (i.e.,lower und upper bound = 0)
forced: logical, FALSE (growth case can be ignored with according penalty) or TRUE (case cannot be ignored)
viability_threshold: numerical>0 threshold, which is considered as growth
gene_copy_number: integer >0, multiplies the penalty for ignoring this growth case
biomass: specifies the biomass objective function of this growth case
Example:
on=list()
on[[1]]=list(on=influxes,name="LIVE!",ko_react=c(),forced=TRUE,
viability_threshold=1,gene_copy_number=1,biomass="Biomass")
default: NULL
off
list of non-growth cases
each entry must contain:
on: list of influxes
name: character, name of non-growth case
ko_react: vector of reactions, which are knocked out (i.e.,lower und upper bound = 0)
forced: logical, FALSE (growth case can be ignored with according penalty) or TRUE (case cannot be ignored)
viability_threshold: numerical>0 threshold, which is considered as growth
gene_copy_number=:integer >0, multiplies the penalty for ignoring this non-growth case
biomass: specifies the biomass objective function of this growth case (or vector of reactions if algorithm 3 is choosen)
Example:
off=list()
off[[1]]=list(on=influxes,name="DIE!",ko_react=c(),forced=FALSE,
viability_threshold=1,gene_copy_number=1,biomass="A[e]_import")
default: NULL
algorithm
integer, specifies which version of GlobalFit should be used:
1: fast version
2: old version, but allows to use variable_lower_bound
3: fast version, used for removing thermodynamically infeasible cycles
default: 1
additional_reactions
list containing additional reaction. Each entry must contain the following attributes.
id: character, id of reaction
name: character, name of reaction
eq: character, equation of reaction.
pen: numeric >0, penalty for adding this reaction to the network
Example:
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]",pen=3)
additional_reactions_list[[3]]=list(id="TtoQ",name="TtoQ reaction",eq="T[e] => Q[e]",pen=5)
default: NULL
\
minimize
logical, specifies if blocked reaction should be removed from network before optimizing. May decrease solving time, but it takes time to calculate blocked reactions
default: FALSE
simple
logical, if run in simple mode (TRUE) only the number of contradicting cases are minimized, network changes are not penalized
default: FALSE
verboseMode
numeric, should output be printed (1 => yes; !1 => no)
default: 1
cancel_case_penalty
numerical>0, penalty for ignoring (case is violating viability threshold) a single growth case
default: NULL, penalty is higher than all network changes combined
not_delete_for
vector of reaction names; forward reactions that are not allowed to be removed (e.g., biomass objective function, exchange reactions)
default: NULL
not_delete_back
vector of reaction names; backward reactions that are not allowed to be removed (e.g., biomass objective function, exchange reactions)
default: NULL
param_list
list of specific paramaters, that will be passed on to the solver
default: NULL
use_indicator_constraints
logical,indicator constraints may prevent trickle flow, only usable if cplex (cplexAPI) is used as solver
default:FALSE
remove_penalties_hin
Vector of penalties for removing each forward reaction. Must have the same length as the number of reactions in the network.
If not specified the penalty for removing each reaction will be set to 1.
default: NULL
remove_penalties_back
Vector of penalties for removing each forward reaction. Must have the same length as the number of reactions in the network.
If not specified the penalty for removing each reaction will be set to 1.
default: NULL
stat_file
path for stat file
default: NULL
react_file
path of react file, contains all network modifications (subset of stat file)
default: NULL
reverse_reaction_list
list containing reaction, that are allowed to be reversed and according penalty. The following attributes must be defined for each entry:
reaction, character: name of reaction
pen, numeric>0, penalty for reversing reaction
Example:
reverse_reaction_list=list()
reverse_reaction_list[[1]]=list(reaction="KtoT",pen=1)
reverse_reaction_list[[2]]=list(reaction="TtoB",pen=1)
default: NULL
MaxPenalty
integer >=0, amount of alternative solution that should be calculated
default: 0
alternatives
integer >=0, amount of alternative solution that should be calculated
default: 0
bio_stoich
numeric>0, stoichiometric coefficient for additional biomass metabolites
default: 1e-5
additional_biomass_metabolites
list of additional biomass metabolites
met specifies the metabolite, which can be added to the biomass objective function (note metabolites, which are already in the biomass objective function can not be added).
pen specifies the corresponding penalty for adding this metabolite.
factor: -1 or 1; -1 metabolite can be added as substrate; 1 metabolite can be added as product
Example:
additional_biomass_mets=list()
additional_biomass_mets[[1]]=list(met="K[e]",pen=0.1,factor=1)
default: NULL
remove_biomass_metabolites
list of metabolites that can be removed from the biomass objective function
met specifies the metabolite, which can be removed from the biomass objective function
pen specifies the corresponding penalty
Example:
remove_biomass_mets=list()
remove_biomass_mets[[1]]=list(met="Z[e]",pen=0.01)
default: NULL
variable_lower_bound
list containing reactions, which lowerbound can be optimized.
This can be used to calculate an qualitatively optimized media formulation
Can only be used if algorithm=2
reaction specifies the name of the reaction
min specifies the minimal possible value
max specifies the maximal possible value
penalty specifies the penalty for changing the lowerbound
Example:
varying_lower_bound_list=list()
varying_lower_bound_list[[1]]=list(reaction="T[e]_import",min=-20,max=-0,penalty=0.1)
default: NULL
forced_modifications
integer>=0,number of minimal modification; may reduce computation time if set >=1
default: 0
Value
optimized metabolic network model of type modelorg
Author(s)
Daniel Hartleb
References
Hartleb D, Jarre F, Lercher MJ. Improved Metabolic Models for E. coli and
Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches
Growth and Non-Growth Data Sets. PLoS Comput Biol. 2016 Aug 2;12(8):e1005036.
doi: 10.1371/journal.pcbi.1005036. eCollection 2016 Aug. PubMed PMID: 27482704.
Examples
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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 Usage Arguments Value Author(s) References Examples
View source: R/GlobalFit_methods.R
Description
pre und post-processing of optimization. Adds reaction to network, creates output, creates optimization object, interprets solution, applies modification to network.
Usage
1 2 3 4 5 6 7 8 9 | bilevel_optimize(network, on = c(), off = c(), algorithm = 1,
additional_reactions = NULL, minimize = TRUE, simple = FALSE,
verboseMode = 1, cancel_case_penalty = NULL, not_delete_for = c(),
not_delete_back = c(), param_list = NULL, use_indicator_constraints = FALSE,
remove_penalties_hin = c(), remove_penalties_back = c(), stat_file = NULL,
react_file = NULL, reverse_reaction_list = NULL, MaxPenalty = NULL,
alternatives = 0, bio_stoich = 1e-05, additional_biomass_metabolites = NULL,
remove_biomass_metabolites = NULL, variable_lower_bound = NULL,
forced_modifications = 0)
|
Arguments
network |
metabolic network model of type |
on |
each entry must contain:
on: list of influxes default: NULL |
off |
list of non-growth cases
each entry must contain:
on: list of influxes Example: default: NULL |
algorithm |
integer, specifies which version of GlobalFit should be used: default: 1 |
additional_reactions |
list containing additional reaction. Each entry must contain the following attributes. Example: default: NULL |
\
minimize |
logical, specifies if blocked reaction should be removed from network before optimizing. May decrease solving time, but it takes time to calculate blocked reactions |
simple |
logical, if run in simple mode (TRUE) only the number of contradicting cases are minimized, network changes are not penalized |
verboseMode |
numeric, should output be printed (1 => yes; !1 => no) |
cancel_case_penalty |
numerical>0, penalty for ignoring (case is violating viability threshold) a single growth case |
not_delete_for |
vector of reaction names; forward reactions that are not allowed to be removed (e.g., biomass objective function, exchange reactions) |
not_delete_back |
vector of reaction names; backward reactions that are not allowed to be removed (e.g., biomass objective function, exchange reactions) |
param_list |
list of specific paramaters, that will be passed on to the solver |
use_indicator_constraints |
logical,indicator constraints may prevent trickle flow, only usable if cplex (cplexAPI) is used as solver |
remove_penalties_hin |
Vector of penalties for removing each forward reaction. Must have the same length as the number of reactions in the network. |
remove_penalties_back |
Vector of penalties for removing each forward reaction. Must have the same length as the number of reactions in the network. |
stat_file |
path for stat file |
react_file |
path of react file, contains all network modifications (subset of stat file) |
reverse_reaction_list |
list containing reaction, that are allowed to be reversed and according penalty. The following attributes must be defined for each entry: Example: default: NULL |
MaxPenalty |
integer >=0, amount of alternative solution that should be calculated |
alternatives |
integer >=0, amount of alternative solution that should be calculated |
bio_stoich |
numeric>0, stoichiometric coefficient for additional biomass metabolites |
additional_biomass_metabolites |
list of additional biomass metabolites default: NULL |
remove_biomass_metabolites |
list of metabolites that can be removed from the biomass objective function Example: default: NULL |
variable_lower_bound |
list containing reactions, which lowerbound can be optimized. reaction specifies the name of the reaction Example: default: NULL |
forced_modifications |
integer>=0,number of minimal modification; may reduce computation time if set >=1 |
Value
optimized metabolic network model of type modelorg
Author(s)
Daniel Hartleb
References
Hartleb D, Jarre F, Lercher MJ. Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets. PLoS Comput Biol. 2016 Aug 2;12(8):e1005036. doi: 10.1371/journal.pcbi.1005036. eCollection 2016 Aug. PubMed PMID: 27482704.
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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