start rba

.gitignore

@@ -25,3 +25,4 @@ Manifest.toml
 *.xml
 *.json
 *.mat
+*.tsv

docs/src/examples/0x-resource-balance.jl

@@ -0,0 +1,57 @@
+
+# Copyright (c) 2021-2024, University of Luxembourg                         #src
+# Copyright (c) 2021-2024, Heinrich-Heine University Duesseldorf            #src
+#                                                                           #src
+# Licensed under the Apache License, Version 2.0 (the "License");           #src
+# you may not use this file except in compliance with the License.          #src
+# You may obtain a copy of the License at                                   #src
+#                                                                           #src
+#     http://www.apache.org/licenses/LICENSE-2.0                            #src
+#                                                                           #src
+# Unless required by applicable law or agreed to in writing, software       #src
+# distributed under the License is distributed on an "AS IS" BASIS,         #src
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.  #src
+# See the License for the specific language governing permissions and       #src
+# limitations under the License.                                            #src
+
+# # Resource balance analysis
+
+using COBREXA
+using SBtabFBCModels
+
+import Downloads: download
+
+!isfile("bsubtilis_rba_model.tsv") &&
+    download("https://rba.inrae.fr/models/Bacillus-subtilis-168-WT/data/rba-sbtab_model.tsv", "bsubtilis_rba_model.tsv")
+
+!isfile("bsubtilis_rba_parameters.tsv") &&
+    download("https://rba.inrae.fr/models/Bacillus-subtilis-168-WT/data/rba-sbtab_parameters.tsv", "bsubtilis_rba_parameters.tsv")
+
+md, tabs = SBtabFBCModels.load_tables("bsubtilis_rba_model.tsv");
+p_md, p_tabs = SBtabFBCModels.load_tables("bsubtilis_rba_parameters.tsv");
+
+using DataFrames
+using ConstraintTrees
+
+
+summary = DataFrame(tabs[2]) # summary
+mets = DataFrame(tabs[3])
+rxns = DataFrame(tabs[4])
+enzs = DataFrame(tabs[5])
+prots = DataFrame(tabs[6])
+macro_mols = DataFrame(tabs[7])
+compartments = DataFrame(tabs[8])
+cell_modules = DataFrame(tabs[9]) # empty
+processes = DataFrame(tabs[10])
+cell_targets = DataFrame(tabs[11])
+met_cons = DataFrame(tabs[12])
+dens_cons = DataFrame(tabs[13])
+machine_cap_con = DataFrame(tabs[14])
+enz_cap_con = DataFrame(tabs[15])
+
+medium_comp = DataFrame(p_tabs[1]) # mmol/l
+enz_cap_f = DataFrame(p_tabs[2]) # 1/h
+enz_cap_b = DataFrame(p_tabs[3]) # 1/h
+machine_cap = DataFrame(p_tabs[4]) # 1/h
+comp_cap = DataFrame(p_tabs[5]) # mmol/gDW
+target_vals = DataFrame(p_tabs[6]) # no unit