embedding_example_2_make_model

0001 function [model_name, kinetic_models,network,network_CoHid,me_options] = embedding_example_2_make_model(position_file,matlab_file)
0002 
0003 eval(default('matlab_file','[]'));
0004 
0005 model_name = 'embedding_example_2';
0006 
0007 % --------------------------------------------------------------------------------
0008 % Two kinetic models (both with kinetics of type 'numeric') are combined
0009 %
0010 % The models contain overlapping (but non-lumped) metabolites and reactions
0011 % The surrounding network is left undefined and will be constructed automatically
0012 %  upon insertion of the submodels
0013 % --------------------------------------------------------------------------------
0014 
0015 
0016 % --------------------------------------------------------------------------------
0017 % make small pathway model 'kinetic_model_2a' with kinetics of type 'numeric'
0018 
0019 N            = [-1 0 0; 1 -1 0; 0 1 -1; 0 0 1]; 
0020 reversible   = [1 1 1]';
0021 ind_external = [1 4]';
0022 metabolites  = {'X1','A1','B1','C1'}'; 
0023 actions      = {'R0','R1','R2'}'; 
0024 
0025 kinetic_model_a = network_construct(N,reversible,ind_external,metabolites,actions);
0026 kinetic_model_a.metabolite_id = {'id_X1','id_A1','id_B1','id_C1'}'; 
0027 kinetic_model_a.reaction_id   = {'id_R0','id_R1','id_R2'}'; 
0028 
0029 kinetic_model_a.kinetics.type = 'numeric';
0030 kinetic_model_a.kinetics.velocity_function = @embedding_example_2a_velocities;
0031 kinetic_model_a.kinetics.parameters = struct;
0032 kinetic_model_a.s_init = [8 5 4 3]';
0033 
0034 
0035 % --------------------------------------------------------------------------------
0036 % make small pathway model 'kinetic_model_2b' with kinetics of type 'numeric'
0037 
0038 N            = [-1 0; 1 -1; 0 1]; 
0039 reversible   = [1 1]';
0040 ind_external = [1 3]';
0041 metabolites  = {'C1','D1','E1'}'; 
0042 actions      = {'R3','R4'}'; 
0043 
0044 kinetic_model_b = network_construct(N,reversible,ind_external,metabolites,actions);
0045 kinetic_model_b.metabolite_id = {'id_C1','id_D1','id_E1'}'; 
0046 kinetic_model_b.reaction_id   = {'id_R3','id_R4'}'; 
0047 
0048 kinetic_model_b.kinetics.type = 'numeric';
0049 kinetic_model_b.kinetics.velocity_function = @embedding_example_2b_velocities;
0050 kinetic_model_b.kinetics.parameters = struct;
0051 kinetic_model_b.kinetics.concentrations = [2 1.5 1]';
0052 kinetic_model_b.s_init = kinetic_model_b.kinetics.concentrations;
0053 
0054 % --------------------------------------------------------------------------------
0055 % make an empty network model 'network'
0056 
0057 N            = []; 
0058 reversible   = [];
0059 ind_external = [];
0060 metabolites  = {}; 
0061 actions      = {}; 
0062 
0063 network               = network_construct(N,reversible,ind_external,metabolites,actions);
0064 network.metabolite_id = {};
0065 network.reaction_id   = {}';    
0066 
0067 
0068 % --------------------------------------------------------------------------------
0069 % ids for mapping the models
0070 % which name fields should be used for mapping the elements?
0071 
0072 id.metabolites_network        = 'metabolite_id';
0073 id.metabolites_kinetic_models = {'metabolite_id','metabolite_id'};
0074 id.reactions_network          = 'reaction_id';
0075 id.reactions_kinetic_models   = {'reaction_id','reaction_id'};
0076 
0077 % --------------------------------------------------------------------------------
0078 %
0079 % fba_constraints = fba_default_options(network);
0080 % fba_constraints.zv    = [0 0 1 1 0]';
0081 % fba_constraints.v_fix = nan * ones(5,1);
0082 % fba_constraints.v_min = nan * ones(5,1);
0083 % fba_constraints.v_max = nan * ones(5,1);
0084 % fba_constraints.v_sign= nan * ones(5,1);
0085 % fba_constraints.ext_sign= nan * ones(3,1);
0086 
0087 % --------------------------------------------------------------------------------
0088 
0089 % netgraph_edit_positions(network,position_file,0);
0090 
0091 % --------------------------------------------------------------------------------
0092 % save
0093 
0094 kinetic_models = {kinetic_model_a,kinetic_model_b};
0095 
0096 network_CoHid = network;
0097 
0098 % --------------------------------------------------------------------------------
0099 
0100 
0101     me_options.set_internal         = {'id_X1'};
0102     me_options.id                   = id;
0103     me_options.enforce_stationarity = 0;
0104     me_options.arrowsize            = 0.1;
0105     me_options.squaresize           = 0.1;
0106     me_options.text_offset          = [0.05,0.02];
0107     me_options.arrowvaluesmax       = 1.2;
0108     me_options.legendFontsize       = 8;
0109     me_options.position_file        = position_file;
0110 
0111     me_options.c_init               = [1 0 0 0 0 0]';
0112     me_options.Tmax                 = 5; 
0113 
0114 if length(matlab_file),
0115   save(matlab_file,'kinetic_models','network','network_CoHid','me_options');
0116 end