sbml: Add biomass reaction definitions for undetected models

This adds the `biomass` key in model.yaml for those SBML models where the biomass could not be automatically identified.
zhanglab · May 19, 2015 · b4249ed · b4249ed
1 parent 34d35b8
commit b4249ed
Show file tree

Hide file tree

Showing 23 changed files with 23 additions and 0 deletions.
diff --git a/sbml/AORYZAE_COBRA/model.yaml b/sbml/AORYZAE_COBRA/model.yaml
@@ -1,4 +1,5 @@
 name: A. oryzae genome-scale model
+biomass: R_r2359
 default_flux_limit: 1000.0
 compounds:
 - include: compounds.yaml

diff --git a/sbml/AbyMBEL891/model.yaml b/sbml/AbyMBEL891/model.yaml
@@ -1,4 +1,5 @@
 name: Acinetobacter_baumannii_AYE
+biomass: R761
 compounds:
 - include: compounds.yaml
 reactions:

diff --git a/sbml/PpaMBEL1254/model.yaml b/sbml/PpaMBEL1254/model.yaml
@@ -1,4 +1,5 @@
 name: Pichia_pastoris
+biomass: R01288
 compounds:
 - include: compounds.yaml
 reactions:

diff --git a/sbml/PpuMBEL1071/model.yaml b/sbml/PpuMBEL1071/model.yaml
@@ -1,4 +1,5 @@
 name: Pseudomonas_putida_KT2440
+biomass: R_Biomass
 compounds:
 - include: compounds.yaml
 reactions:

diff --git a/sbml/S_coelicolor/model.yaml b/sbml/S_coelicolor/model.yaml
@@ -1,4 +1,5 @@
 name: GBic
+biomass: R_biomass
 compounds:
 - include: compounds.yaml
 reactions:

diff --git a/sbml/SpoMBEL1693/model.yaml b/sbml/SpoMBEL1693/model.yaml
@@ -1,4 +1,5 @@
 name: Schizosaccharomyces_pombe
+biomass: RXNBiomass
 compounds:
 - include: compounds.yaml
 reactions:

diff --git a/sbml/VvuMBEL943/model.yaml b/sbml/VvuMBEL943/model.yaml
@@ -1,4 +1,5 @@
 name: HyunUkKim2010_VvuMBEL943_MetabolicModeling
+biomass: R806
 compounds:
 - include: compounds.yaml
 reactions:

diff --git a/sbml/iAC560/model.yaml b/sbml/iAC560/model.yaml
@@ -1,4 +1,5 @@
 name: iAC560_def_med
+biomass: R_BIOMASS_LM3
 compounds:
 - include: compounds.yaml
 reactions:

diff --git a/sbml/iAI549/model.yaml b/sbml/iAI549/model.yaml
@@ -1,4 +1,5 @@
 name: iAI549
+biomass: R_BIO_CBDB1_DM_855
 compounds:
 - include: compounds.yaml
 reactions:

diff --git a/sbml/iCce806/model.yaml b/sbml/iCce806/model.yaml
@@ -1,4 +1,5 @@
 name: iCce806
+biomass: r_CYANOBM
 default_flux_limit: 1000.0
 compounds:
 - include: compounds.yaml

diff --git a/sbml/iLC915/model.yaml b/sbml/iLC915/model.yaml
@@ -1,4 +1,5 @@
 name: Pichia pastoris
+biomass: R_r1187
 default_flux_limit: 1000.0
 compounds:
 - include: compounds.yaml

diff --git a/sbml/iMA871/model.yaml b/sbml/iMA871/model.yaml
@@ -1,4 +1,5 @@
 name: A. niger genome-scale model
+biomass: R_1024
 default_flux_limit: 1000.0
 compounds:
 - include: compounds.yaml

diff --git a/sbml/iMA945/model.yaml b/sbml/iMA945/model.yaml
@@ -1,4 +1,5 @@
 name: iMA945
+biomass: R_ST_biomass_core
 compounds:
 - include: compounds.yaml
 reactions:

diff --git a/sbml/iMM1415/model.yaml b/sbml/iMM1415/model.yaml
@@ -1,4 +1,5 @@
 name: mouse1415
+biomass: R_biomass_mm_1_no_glygln
 compounds:
 - include: compounds.yaml
 reactions:

diff --git a/sbml/iMO1056/model.yaml b/sbml/iMO1056/model.yaml
@@ -1,4 +1,5 @@
 name: model
+biomass: R_PA_Biomass6_DM
 compounds:
 - include: compounds.yaml
 reactions:

diff --git a/sbml/iMR1_799/model.yaml b/sbml/iMR1_799/model.yaml
@@ -1,4 +1,5 @@
 name: iMR1_799_xml
+biomass: R_SO_BIOMASSMACRO_DM_NOATP2
 default_flux_limit: 1000.0
 compounds:
 - include: compounds.yaml

diff --git a/sbml/iPS189/model.yaml b/sbml/iPS189/model.yaml
@@ -1,4 +1,5 @@
 name: iPS189
+biomass: R_Biomass
 compounds:
 - include: compounds.yaml
 reactions:

diff --git a/sbml/iRC1080/model.yaml b/sbml/iRC1080/model.yaml
@@ -1,4 +1,5 @@
 name: iRC1080
+biomass: R_Biomass_Chlamy_hetero
 default_flux_limit: 1000.0
 compounds:
 - include: compounds.yaml

diff --git a/sbml/iRsp1095/model.yaml b/sbml/iRsp1095/model.yaml
@@ -1,4 +1,5 @@
 name: Rhodobacter_sphaeroides_metabolic_model_iRsp1095
+biomass: RXN1391
 default_flux_limit: 1000.0
 compounds:
 - include: compounds.yaml

diff --git a/sbml/iSR432/model.yaml b/sbml/iSR432/model.yaml
@@ -1,4 +1,5 @@
 name: Model2008_08_15_12_13_14
+biomass: R_biomass_target
 compounds:
 - include: compounds.yaml
 reactions:

diff --git a/sbml/iSS884/model.yaml b/sbml/iSS884/model.yaml
@@ -1,4 +1,5 @@
 name: Pichia stipitis
+biomass: R_biomass
 default_flux_limit: 1000.0
 compounds:
 - include: compounds.yaml

diff --git a/sbml/iSyn731/model.yaml b/sbml/iSyn731/model.yaml
@@ -1,4 +1,5 @@
 name: Synechocystis sp. PCC 6803 iSyn731
+biomass: Biomass_Hetero
 compounds:
 - include: compounds.yaml
 reactions:

diff --git a/sbml/mus_musculus/model.yaml b/sbml/mus_musculus/model.yaml
@@ -1,4 +1,5 @@
 name: Mus musculus GSM
+biomass: BIO028
 compounds:
 - include: compounds.yaml
 reactions: