Merge pull request #3 from PNNL-CompBio/add_missing_rxns

Adding reactions from ims837

.github/workflows/memote.yml

@@ -2,7 +2,7 @@ name: SYN memote tracking
 
 on:
   push:
-    branches: [ "main"]
+    branches: [ "main", "add_missing_rxns"]
 jobs:
   memote-history:
     runs-on: ubuntu-latest

syn_elong/__init__.py

@@ -8,6 +8,8 @@
 model = cobra.io.read_sbml_model(
     path.joinpath('syn_elong.xml').__str__()
 )
+ijb792 = cobra.io.load_json_model(path.joinpath('iJB792.json').__str__())
+ims837 =cobra.io.load_json_model(path.joinpath('iMS837.json').__str__())
 
 exp_file_path = path.joinpath('data', 'experiments.yml').__str__()
 expected_metab = pd.read_csv(

syn_elong/data/experiments.yml

@@ -5,11 +5,15 @@ medium:
     model_min_media:
       filename: "syn_min_media.csv"
       label: "Minimal"
+    no_carbon:
+      filename: "min_media_all_wavelength.csv"
+      label: "No Carbon"
 essentiality:
   path: "essentiality/"
   experiments:
     knockouts:
-      medium:  model_min_media
+      medium:      no_carbon
       filename: "syn_elo_knockdown.csv"
       label: "knock-out library"
-minimal_growth_rate: 0.05
+
+#minimal_growth_rate: 0.05

syn_elong/data/media/min_media_all_wavelength.csv

@@ -0,0 +1,29 @@
+exchange,uptake
+EX_h2o_e,100
+EX_h_e,100
+EX_no3_e,100
+EX_pi_e,100
+EX_so4_e,100
+EX_nh4_e,100
+EX_mg2_e,100
+EX_fe3_e,100
+EX_cobalt2_e,100
+EX_k_e,100
+EX_na1_e,100
+EX_hco3_e,100
+EX_co2_e,100
+EX_photon430_e,1000.0
+EX_photon450_e,1000.0
+EX_photon470_e,1000.0
+EX_photon410_e,1000.0
+EX_photon490_e,1000.0
+EX_photon510_e,1000.0
+EX_photon530_e,1000.0
+EX_photon550_e,1000.0
+EX_photon570_e,1000.0
+EX_photon590_e,1000.0
+EX_photon610_e,1000.0
+EX_photon630_e,1000.0
+EX_photon650_e,1000.0
+EX_photon670_e,1000.0
+EX_photon690_e,1000.0