Growth medium definition
Growth medium file format
A user gapfill medium can be defined in a 3-column comma-(csv) or tab-(tsv)-separated table.
1st column “compounds”: Should list the compounds’ identifier
2nd column “name”: List of compound names
3rd column “maxFlux”: Defines the maximum uptake rate of the compound in
mmol/gDW/hr
Example: M9-like medium (aerobic) with limited Glucose+Oxygen uptake and virtually unlimited salts/ions.
compounds,name,maxFlux
cpd00001,H2O,100
cpd00007,O2,10
cpd00009,Phosphate,100
cpd00027,D-Glucose,5
cpd00030,Mn2+,100
cpd00034,Zn2+,100
cpd00048,Sulfate,100
cpd00058,Cu2+,100
cpd00063,Ca2+,100
cpd00067,H+,100
cpd00099,Cl-,100
cpd00149,Co2+,100
cpd00205,K+,100
cpd00254,Mg,100
cpd00531,Hg2+,100
cpd00971,Na+,100
cpd01012,Cd2+,100
cpd01048,Arsenate,100
cpd10515,Fe2+,100
cpd10516,fe3,100
cpd11595,chromate,100
cpd00013,NH3,100
List of potential nutrients
A table with all nutrients (IDs and names), that can be part of a growth medium definition is stored in your gapseq installation (dat/nutrients.tsv
) or accessed also directly on github.
A list of database-specific compounds, which might diverge from metabolite entries in other databases, is given in the database section.
Predicting a growth medium
Comming up with a suited growth medium for gapfilling and flux-balance-analysis can be difficult, especially for organisms that are not-yet well characterized in their growth requirements.
gapseq provides a module that can predict a growth medium based on the results generated by gapseq find
and gapseq draft
. The predicted growth medium can directly be used also as gapfilling medium in gapseq fill
.
The medium prediction module requires two inputs: The pathway prediction table (generated by gapseq find
) and the draft model (generated by gapseq draft
). An example:
gapseq medium -m ecoli-draft.RDS -p ecoli-all-Pathways.tbl
Using the optional flag -c
specific metabolites can be added/removed from the medium prediction. The syntax for the flag option is
-c "[CompoundID_1]:[maxFlux_1];[CompoundID_2]:[maxFlux_2]"
.
For example, to remove oxygen from the final medium you can use:
gapseq medium -m ecoli-draft.RDS -p ecoli-all-Pathways.tbl -c "cpd00007:0"
This option is for instance helpful to ensure an anaerobic environment.
To remove oxygen and add L-Lactate with 10 mmol/gDW/hr to the final medium you can use:
gapseq medium -m ecoli-draft.RDS -p ecoli-all-Pathways.tbl -c "cpd00007:0;cpd00159:10"