embedding_threonine_make_model

0001 function [model_name,kinetic_models,network,network_CoHid,me_options] = embedding_threonine_make_model(position_file,matlab_file)
0002 
0003 eval(default('matlab_file','[]'));
0004 
0005 model_name = 'threonine';
0006 
0007 % -----------------------------------------------------------
0008 % load threonine pathway model (from threonine_chassagnole_make_model
0009 
0010 load([me_BASEDIR '../resources/models/threonine/threonine_chassagnole_network']);
0011 
0012 % -----------------------------------------------------------
0013 % omit balancing reactions ATP -> ADP + P and NADH -> NAD+
0014 % -> 'kinetic_model'
0015 
0016 kinetic_model          = network_subnetwork(network, 1:11, 1:5);
0017 kinetic_model.kinetics = network.kinetics;
0018 kinetic_model.kinetics.reactions = kinetic_model.kinetics.reactions(1:5);
0019 
0020 [c_steady, v_steady]   = network_steady_state(kinetic_model,network.s_init,500);
0021 
0022 kinetic_model.s_init   = c_steady; 
0023 
0024 
0025 % -----------------------------------------------------------
0026 % load E coli network model
0027 
0028 %[network,ind_biomass_reaction]  = ecoli_iAF1260_make_model;
0029 
0030 [network,network_CoHid,flux,cofactors] = ecoli_core;
0031 
0032 network.compartments      = kinetic_model.compartments;
0033 network.compartment_sizes = kinetic_model.compartment_sizes;
0034 
0035 v = flux; % weighting -> smaller influence of threonine pathway flux
0036 
0037 
0038 % -----------------------------------------------------------
0039 % map metabolite names
0040 
0041 T = sbtab_table_load([me_BASEDIR '../resources/models/threonine/threonine_metabolite_matching.tsv']);
0042 
0043 met_names_threonine = sbtab_table_get_column(T,'ThreonineModelName');
0044 met_names_network   = sbtab_table_get_column(T,'NetworkCoreName');
0045 
0046 ll = label_names(kinetic_model.metabolites,met_names_threonine);
0047 
0048 kinetic_model.metabolite_id = met_names_network(ll);
0049 
0050 
0051 % --------------------------------------------------------------------------------
0052 % ids for mapping the models
0053 % which name fields should be used for mapping the elements?
0054 
0055 id.metabolites_network        = 'metabolites';
0056 id.metabolites_kinetic_models = {'metabolite_id'};
0057 id.reactions_network          = 'actions';
0058 id.reactions_kinetic_models   = {'actions'};
0059 
0060 fba_constraints    = fba_default_options(network);
0061 
0062 % ------------------------------------------------------------------
0063 % Save files
0064 
0065 kinetic_models = {kinetic_model};
0066 
0067 % ---------------------------------------------------
0068 
0069 me_options.id                   = id;
0070 me_options.fba_constraints      = fba_constraints;
0071 me_options.enforce_stationarity = 1;
0072 me_options.cofactors            = cofactors;
0073 me_options.position_file        = position_file;
0074 me_options.v_network            = v;
0075 me_options.text_offset          = [0.02,0.01];
0076 me_options.fontsize             = 6;
0077 me_options.position_file        = position_file;
0078 me_options.omitreactions        = {'Biomass_Ecoli_core_w_GAM'};
0079 
0080 me_options.c_init                          = [];
0081 me_options.Tmax                            = 5;
0082 
0083 if length(matlab_file),
0084   save(matlab_file,'kinetic_models','network','network_CoHid','me_options');
0085 end
0086 
0087 % ---------------------------------------------------
0088 % graphics
0089 
0090 if 0,
0091 
0092 ca;
0093 
0094 gp = struct('actstyle','none','arrowsize',0.1,'arrowvaluesmax',max(abs(v_steady)));
0095 
0096 figure(1); netgraph_concentrations(kinetic_model,c_steady,v_steady,1,gp);
0097 
0098 gp = struct('actstyle','none','arrowsize',0.1,'arrowvaluesmax',max(abs(v)));
0099 
0100 figure(2); netgraph_concentrations(network_CoHid,[],v,1,gp);
0101 
0102 end