ModelSEED · freiburgermsu · Jul 17, 2022 · Jul 18, 2022 · Jul 18, 2022 · Jul 18, 2022
diff --git a/.gitignore b/.gitignore
@@ -101,6 +101,10 @@ celerybeat.pid
 # SageMath parsed files
 *.sage.py
 
+# GROW genomes
+grow/OWC_MAGS/*
+grow/renamed_gffs/*
+
 # Environments
 .env
 .venv
@@ -118,12 +122,27 @@ venv.bak/
 .ropeproject
 
 # mkdocs documentation
+*DS_Store
+*/*.DS_Store
 /site
 
+# MSCommfitting
+*.zip
+*.lp
+**/mscommfitting.json
+*/C:/*
+CommunityModeling/CommFitting/simple_kinetics_loop/*
+
 # mypy
 .mypy_cache/
 .dmypy.json
 dmypy.json
 
 # Pyre type checker
 .pyre/
+
+
+# raw paragraph files
+reaction_paragraphs.txt
+compound_paragraphs.txt
+*.gz
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "CommunityModeling/CommFitting/data/becketal-syntheticconsortia"]
+	path = CommunityModeling/CommFitting/data/becketal-syntheticconsortia
+	url = https://github.com/rosspcarlson/becketal-syntheticconsortia
diff --git a/.idea/.gitignore b/.idea/.gitignore
diff --git a/.idea/ProjectNotebooks.iml b/.idea/ProjectNotebooks.iml
diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
diff --git a/.idea/misc.xml b/.idea/misc.xml
diff --git a/.idea/modules.xml b/.idea/modules.xml
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
diff --git a/SABIORK/sabio_reagents.txt → 0 b/SABIORK/sabio_reagents.txt → 0
diff --git a/AuroraGPT/CreateCentralCarbonPathways.ipynb b/AuroraGPT/CreateCentralCarbonPathways.ipynb
diff --git a/CommunityModeling/.idea/.gitignore b/CommunityModeling/.idea/.gitignore
diff --git a/CommunityModeling/.idea/CommunityModeling.iml b/CommunityModeling/.idea/CommunityModeling.iml
diff --git a/CommunityModeling/.idea/inspectionProfiles/profiles_settings.xml b/CommunityModeling/.idea/inspectionProfiles/profiles_settings.xml
diff --git a/CommunityModeling/.idea/misc.xml b/CommunityModeling/.idea/misc.xml
diff --git a/CommunityModeling/.idea/modules.xml b/CommunityModeling/.idea/modules.xml
diff --git a/CommunityModeling/.idea/vcs.xml b/CommunityModeling/.idea/vcs.xml