Table 1.

Example of model definition file (extracted from Supplementary Table 1 or Example_1_toymodel_model.txt).

//Reactions
Id	For Stoichiometry Matrix	For Atom mapping	Atom mapping	Link to external ID
v1	AcCoA + OAC-- > Cit	AcCoA + OAC-- > Cit	AB + CDEF-- > FEDBAC	(kegg:R00351)
v2	Cit-- > AKG + CO2ex	Cit-- > AKG + CO2ex	ABCDEF-- > ABCDE + F	(kegg:R00709)
v3	AKG-- > Glu	AKG-- > Glu	ABCDE-- > ABCDE	(kegg:R00243)
v4	AKG-- > Suc + CO2ex	AKG-- > Suc + CO2ex	ABCDE-- > BCDE + A	(kegg:R01197)
v5	Suc-- > Fum	Suc-- > Fum	ABCD-- > ABCD	(kegg:R02164)
v6	Fum-- > OAC	Fum-- > OAC	ABCD-- > ABCD	(kegg:R01082)
v7	OAC-- > Fum	OAC-- > Fum	ABCD-- > ABCD	(kegg:R01082)
v8	Asp-- > OAC	Asp-- > OAC	ABCD-- > ABCD	(kegg:R00355)
v9	Glu-- > Gluex	nd	nd	(kegg:R00243)
//Metabolites
Name	Number of carbons	Symmetry	Carbon source	Excreted metabolite
CO2ex	1	no	no	excreted
AcCoA	2	no	carbonsource	no
OAC	4	no	no	no
Cit	6	no	no	no
AKG	5	no	no	no
Suc	4	symmetry	no	no
Fum	4	symmetry	no	no
Glu	5	no	no	no
Gluex	5	no	no	excreted
Asp	4	no	carbonsource	no