0001 classdef KEY_CLASSNAME < ModelAdapter 0002 methods 0003 function obj = KEY_CLASSNAME() 0004 % Set initial values of the obj.params - they can be changed by the user 0005 0006 % Directory where all model-specific files and scripts are kept. 0007 % Is assumed to follow the GECKO-defined folder structure. 0008 obj.params.path = fullfile('KEY_PATH', 'KEY_NAME'); 0009 0010 % Path to the conventional GEM that this ecModel will be based on. 0011 obj.params.convGEM = fullfile(obj.params.path,'models','yourModel.xml'); 0012 0013 % Average enzyme saturation factor 0014 obj.params.sigma = 0.5; 0015 0016 % Total protein content in the cell [g protein/gDw] 0017 obj.params.Ptot = 0.5; 0018 0019 % Fraction of enzymes in the model [g enzyme/g protein] 0020 obj.params.f = 0.5; 0021 0022 % Growth rate the model should be able to reach when not 0023 % constraint by nutrient uptake (e.g. max growth rate) [1/h] 0024 obj.params.gR_exp = 0.41; 0025 0026 % Provide your organism scientific name 0027 obj.params.org_name = 'genus species'; 0028 0029 % Taxonomic identifier for Complex Portal 0030 obj.params.complex.taxonomicID = []; 0031 0032 % Provide your organism KEGG ID, selected at 0033 % https://www.genome.jp/kegg/catalog/org_list.html 0034 obj.params.kegg.ID = 'sce'; 0035 % Field for KEGG gene identifier; should match the gene 0036 % identifiers used in the model. With 'kegg', it takes the 0037 % default KEGG Entry identifier (for example YER023W here: 0038 % https://www.genome.jp/dbget-bin/www_bget?sce:YER023W). 0039 % Alternatively, gene identifiers from the "Other DBs" section 0040 % of the KEGG page can be selected. For example "NCBI-GeneID", 0041 % "UniProt", or "Ensembl". Not all DB entries are available for 0042 % all organisms and/or genes. 0043 obj.params.kegg.geneID = 'kegg'; 0044 0045 % Provide what identifier should be used to query UniProt. 0046 % Select proteome IDs at https://www.uniprot.org/proteomes/ 0047 % or taxonomy IDs at https://www.uniprot.org/taxonomy. 0048 obj.params.uniprot.type = 'taxonomy'; % 'proteome' or 'taxonomy' 0049 obj.params.uniprot.ID = '559292'; % should match the ID type 0050 % Field for Uniprot gene ID - should match the gene ids used in the 0051 % model. It should be one of the "Returned Field" entries under 0052 % "Names & Taxonomy" at this page: https://www.uniprot.org/help/return_fields 0053 obj.params.uniprot.geneIDfield = 'gene_oln'; 0054 % Whether only reviewed data from UniProt should be considered. 0055 % Reviewed data has highest confidence, but coverage might be (very) 0056 % low for non-model organisms 0057 obj.params.uniprot.reviewed = false; 0058 0059 % Reaction ID for glucose exchange reaction (or other preferred carbon source) 0060 obj.params.c_source = 'r_1714'; 0061 0062 % Reaction ID for biomass pseudoreaction 0063 obj.params.bioRxn = 'r_4041'; 0064 0065 % Name of the compartment where the protein pseudometabolites 0066 % should be located (all be located in the same compartment, 0067 % this does not interfere with them catalyzing reactions in 0068 % different compartments). Typically, cytoplasm is chosen. 0069 obj.params.enzyme_comp = 'cytoplasm'; 0070 end 0071 0072 function [spont,spontRxnNames] = getSpontaneousReactions(obj,model) 0073 % Indicates how spontaneous reactions are identified. Here it 0074 % is done by the reaction have 'spontaneous' in its name. 0075 spont = contains(model.rxnNames,'spontaneous'); 0076 spontRxnNames = model.rxnNames(spont); 0077 end 0078 end 0079 end