Introduced preprocessing wrapper function

jchitpin · Nov 12, 2024 · 1f1ec3a · 1f1ec3a
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diff --git a/docs/build/.documenter-siteinfo.json b/docs/build/.documenter-siteinfo.json
@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-11-12T11:05:44","documenter_version":"1.7.0"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-11-12T14:39:50","documenter_version":"1.7.0"}}
diff --git a/docs/build/index.html b/docs/build/index.html
diff --git a/docs/build/installation/installation/index.html b/docs/build/installation/installation/index.html
diff --git a/docs/build/installation/python-dependencies/index.html b/docs/build/installation/python-dependencies/index.html
diff --git a/docs/build/library/chmc-atomic/index.html b/docs/build/library/chmc-atomic/index.html
diff --git a/docs/build/library/chmc-plots-atomic/index.html b/docs/build/library/chmc-plots-atomic/index.html
diff --git a/docs/build/library/chmc-plots-standard/index.html b/docs/build/library/chmc-plots-standard/index.html
diff --git a/docs/build/library/chmc-standard/index.html b/docs/build/library/chmc-standard/index.html
diff --git a/docs/build/objects.inv b/docs/build/objects.inv
diff --git a/docs/build/search_index.js b/docs/build/search_index.js
diff --git a/docs/build/tutorials/boilerplate-for-bigg-gems/index.html b/docs/build/tutorials/boilerplate-for-bigg-gems/index.html
diff --git a/docs/build/tutorials/chmc-atomic-glucose-under-the-hood/index.html b/docs/build/tutorials/chmc-atomic-glucose-under-the-hood/index.html
diff --git a/docs/build/tutorials/chmc-atomic-glucose/index.html b/docs/build/tutorials/chmc-atomic-glucose/index.html
diff --git a/docs/build/tutorials/chmc-standard-ion-channels/index.html b/docs/build/tutorials/chmc-standard-ion-channels/index.html
diff --git a/docs/build/tutorials/chmc-standard-metabolic-networks/index.html b/docs/build/tutorials/chmc-standard-metabolic-networks/index.html
diff --git a/docs/make.jl b/docs/make.jl
@@ -21,6 +21,7 @@ makedocs(#
             "tutorials/chmc-standard-metabolic-networks.md",
             "tutorials/chmc-standard-ion-channels.md",
             "tutorials/chmc-atomic-glucose.md",
+            "tutorials/chmc-atomic-glucose-under-the-hood.md",
             "tutorials/boilerplate-for-bigg-gems.md",
         ],
         "Library" => Any[#

diff --git a/docs/src/tutorials/boilerplate-for-bigg-gems.md b/docs/src/tutorials/boilerplate-for-bigg-gems.md
@@ -1,14 +1,17 @@
 # Boilerplate code for ACHMC analysis of BiGG models
 
-The following code is provided to quickly construct ACHMC models of BiGG
-metabolic models and others stored in the SBML file format. Each code
-block is designed to be standalone with calculations saved to file and
-re-loaded in a subsequent code block. Unfortunately, BiGG does not store
-SMILES strings so these will need to be manually compiled by the user.
+The following code is provided to construct ACHMC models of BiGG metabolic
+models (and others) stored in the SBML file format. Each code block is
+designed to be standalone with calculations saved to file and re-loaded in
+a subsequent code block. Since metabolic models can be quite complex,
+individual pre-processesing functions are used rather than the wrapper
+function `preprocess_all_for_atomic_chmc`. Unfortunately, BiGG does not
+store SMILES strings so these will need to be manually compiled by the
+user.
 
 Note we recommend starting with relatively small networks (<500
-metabolites and reactions in the original metabolic model) for
-computational feasibility.
+metabolites and reactions in the original metabolic model) for computational
+feasibility before scaling to larger ones.
 
 ## Inputs (from BiGG)