Problem constructing reaction system from SBML Biomodel

jchitpin · July 2, 2024, 8:52pm

I am encountering difficulties loading an SBML file from BioModels (see here). Following the SBMLToolKit instructions, I loaded the SBML file but am having issues constructing the reaction system with warnings that certain bidirectional reactions cannot be split. Is there any way around this?

using SBMLToolkit, ModelingToolkit, OrdinaryDiffEq

mdl = readSBML("E_coli_Millard2016.xml", doc -> begin
    set_level_and_version(2, 4)(doc) # level 2 and version 4 according to Biomodels
    convert_promotelocals_expandfuns(doc)
end)

rs = ReactionSystem(mdl) # fails with warnings on splitting reactions

The error I get is:

julia> rs = ReactionSystem(mdl) 
┌ Warning: Cannot separate bidirectional kineticLaw `(XCH_ACE1_Vmax*(ACEx(t) / (XCH_ACE1_Km*ce
ll) + (-ACEp(t)) / (XCH_ACE1_Km*cell_periplasm))) / (1.0 + ACEx(t) / (XCH_ACE1_Km*cell) + ACEp
(t) / (XCH_ACE1_Km*cell_periplasm))` to forward and reverse part. Setting forward to `(XCH_ACE
1_Vmax*(ACEx(t) / (XCH_ACE1_Km*cell) + (-ACEp(t)) / (XCH_ACE1_Km*cell_periplasm))) / (1.0 + AC
Ex(t) / (XCH_ACE1_Km*cell) + ACEp(t) / (XCH_ACE1_Km*cell_periplasm))` and reverse to `0`. Stoc
hastic simulations will be inexact.
└ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:35
┌ Warning: Cannot separate bidirectional kineticLaw `(GLT_Vmax*cell*((-COA*CIT(t)) / (GLT_Keq*
(cell^2)) + (OAA(t)*ACCOA(t)) / (cell^2))) / (GLT_KdACCOA0*GLT_KmOAA0*((CIT(t)*OAA(t)*ACCOA(t)
) / (GLT_KdACCOA0*GLT_KdcsCIT*GLT_KmOAA0*(cell^3)) + (GLT_KmcsCOA*CIT(t)*ACCOA(t)) / (GLT_KdAC
COA0*GLT_KdcsCOA*GLT_KmcsCIT*(cell^2)) + (ACCOA(t)*(1.0 + AKG(t) / (GLT_Ki1AKG*cell) + NADH(t)
 / (GLT_Ki1NADH*cell))) / (GLT_KdACCOA0*cell) + (GLT_KmcsCOA*CIT(t)) / (GLT_KdcsCOA*GLT_KmcsCI
T*cell) + ((1.0 + NADH(t) / (GLT_Ki2NADH*cell) + AKG(t) / (GLT_Ki2AKG*cell))*OAA(t)*ACCOA(t)) 
/ (GLT_KdACCOA0*GLT_KmOAA0*(cell^2)) + (CIT(t)*OAA(t)) / (GLT_KmOAA0*GLT_KmcsCIT*(cell^2)) + C
OA / (GLT_KdcsCOA*cell) + (COA*CIT(t)*OAA(t)) / (GLT_KdcsCOA*GLT_KdcsOAA*GLT_KmcsCIT*(cell^3))
 + (COA*GLT_KmACCOA0*OAA(t)) / (GLT_KdACCOA0*GLT_KdcsCOA*GLT_KmOAA0*(cell^2)) + (1.0 + (GLT_Km
ACCOA0*OAA(t)) / (GLT_KdACCOA0*GLT_KmOAA0*cell))*(1.0 + ATP(t) / (GLT_KiATP*cell))))` to forwa
rd and reverse part. Setting forward to `(GLT_Vmax*cell*((-COA*CIT(t)) / (GLT_Keq*(cell^2)) + 
(OAA(t)*ACCOA(t)) / (cell^2))) / (GLT_KdACCOA0*GLT_KmOAA0*((CIT(t)*OAA(t)*ACCOA(t)) / (GLT_KdA
CCOA0*GLT_KdcsCIT*GLT_KmOAA0*(cell^3)) + (GLT_KmcsCOA*CIT(t)*ACCOA(t)) / (GLT_KdACCOA0*GLT_Kdc
sCOA*GLT_KmcsCIT*(cell^2)) + (ACCOA(t)*(1.0 + AKG(t) / (GLT_Ki1AKG*cell) + NADH(t) / (GLT_Ki1N
ADH*cell))) / (GLT_KdACCOA0*cell) + (GLT_KmcsCOA*CIT(t)) / (GLT_KdcsCOA*GLT_KmcsCIT*cell) + ((
1.0 + NADH(t) / (GLT_Ki2NADH*cell) + AKG(t) / (GLT_Ki2AKG*cell))*OAA(t)*ACCOA(t)) / (GLT_KdACC
OA0*GLT_KmOAA0*(cell^2)) + (CIT(t)*OAA(t)) / (GLT_KmOAA0*GLT_KmcsCIT*(cell^2)) + COA / (GLT_Kd
csCOA*cell) + (COA*CIT(t)*OAA(t)) / (GLT_KdcsCOA*GLT_KdcsOAA*GLT_KmcsCIT*(cell^3)) + (COA*GLT_
KmACCOA0*OAA(t)) / (GLT_KdACCOA0*GLT_KdcsCOA*GLT_KmOAA0*(cell^2)) + (1.0 + (GLT_KmACCOA0*OAA(t
)) / (GLT_KdACCOA0*GLT_KmOAA0*cell))*(1.0 + ATP(t) / (GLT_KiATP*cell))))` and reverse to `0`. 
Stochastic simulations will be inexact.
└ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:35
┌ Warning: Cannot separate bidirectional kineticLaw `PIT_Vmax*((-PIT_Kr*P(t)) / ((PIT_KmP + P(
t) / cell)*cell*(1.0 + 0.18861169701161387(log((cell*Hout(t)) / (Hin*cell_periplasm))^2.0))) +
 (0.18861169701161387Pp(t)*(log((cell*Hout(t)) / (Hin*cell_periplasm))^2.0)) / ((PIT_KmPp + Pp
(t) / cell_periplasm)*cell_periplasm*(1.0 + 0.18861169701161387(log((cell*Hout(t)) / (Hin*cell
_periplasm))^2.0))))` to forward and reverse part. Setting forward to `PIT_Vmax*((-PIT_Kr*P(t)
) / ((PIT_KmP + P(t) / cell)*cell*(1.0 + 0.18861169701161387(log((cell*Hout(t)) / (Hin*cell_pe
riplasm))^2.0))) + (0.18861169701161387Pp(t)*(log((cell*Hout(t)) / (Hin*cell_periplasm))^2.0))
 / ((PIT_KmPp + Pp(t) / cell_periplasm)*cell_periplasm*(1.0 + 0.18861169701161387(log((cell*Ho
ut(t)) / (Hin*cell_periplasm))^2.0))))` and reverse to `0`. Stochastic simulations will be ine
xact.
└ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:35
┌ Warning: Cannot separate bidirectional kineticLaw `(ACEA_Vmax*cell*(ICIT(t) / cell + (-GLX(t
)*SUC(t)) / (ACEA_Keq*(cell^2)))) / (ACEA_KmICIT*(1.0 + ((1.0 + ICIT(t) / (ACEA_KdICITsuc*cell
))*SUC(t)) / (ACEA_KdSUC*cell) + (ICIT(t)*(1.0 + PEP(t) / (ACEA_KdPEPicit*cell))) / (ACEA_KmIC
IT*cell) + (GLX(t)*SUC(t)) / (ACEA_KdSUC*ACEA_KmGLX*(cell^2)) + (ACEA_KmSUC*GLX(t)*(1.0 + PEP(
t) / (ACEA_KdPEPglx*cell))) / (ACEA_KdSUC*ACEA_KmGLX*cell) + PEP(t) / (ACEA_KdPEP*cell) + PGA3
(t) / (ACEA_KdPGA3*cell)))` to forward and reverse part. Setting forward to `(ACEA_Vmax*cell*(
ICIT(t) / cell + (-GLX(t)*SUC(t)) / (ACEA_Keq*(cell^2)))) / (ACEA_KmICIT*(1.0 + ((1.0 + ICIT(t
) / (ACEA_KdICITsuc*cell))*SUC(t)) / (ACEA_KdSUC*cell) + (ICIT(t)*(1.0 + PEP(t) / (ACEA_KdPEPi
cit*cell))) / (ACEA_KmICIT*cell) + (GLX(t)*SUC(t)) / (ACEA_KdSUC*ACEA_KmGLX*(cell^2)) + (ACEA_
KmSUC*GLX(t)*(1.0 + PEP(t) / (ACEA_KdPEPglx*cell))) / (ACEA_KdSUC*ACEA_KmGLX*cell) + PEP(t) / 
(ACEA_KdPEP*cell) + PGA3(t) / (ACEA_KdPGA3*cell)))` and reverse to `0`. Stochastic simulations
 will be inexact.
└ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:35
┌ Warning: Cannot separate bidirectional kineticLaw `(PDH_Vmax*cell*((COA*PYR(t)*NAD(t)) / (ce
ll^3) + (-HCO3*ACCOA(t)*NADH(t)) / (PDH_Keq*(cell^3)))) / (PDH_KmCOA*PDH_KmNAD*PDH_KmPYR*((ACC
OA(t)*NADH(t)) / (PDH_KmACCOA*PDH_KmNADH*(cell^2)) + (COA*NADH(t)) / (PDH_KmCOA*PDH_KmNADH*(ce
ll^2)) + ((1.0 + PYR(t) / (PDH_KmPYR*cell) + COA / (PDH_KmCOA*cell))*NAD(t)) / (PDH_KmNAD*cell
) + (COA*ACCOA(t)*NADH(t)) / (PDH_KmACCOA*PDH_KmCOA*PDH_KmNADH*(cell^3)) + (COA*ACCOA(t)*PYR(t
)) / (PDH_KmACCOA*PDH_KmCOA*PDH_KmPYR*(cell^3)) + (COA*NAD(t)*NADH(t)) / (PDH_KmCOA*PDH_KmNAD*
PDH_KmNADH*(cell^3)) + (NAD(t)*NADH(t)) / (PDH_KmNAD*PDH_KmNADH*(cell^2)) + NADH(t) / (PDH_KmN
ADH*cell) + (COA*(1.0 + NAD(t) / (PDH_KmNAD*cell))*PYR(t)) / (PDH_KmCOA*PDH_KmPYR*(cell^2)) + 
(ACCOA(t)*PYR(t)) / (PDH_KmACCOA*PDH_KmPYR*(cell^2)) + ACCOA(t) / (PDH_KmACCOA*cell))*(1.0 + H
CO3 / (PDH_KmHCO3*cell)))` to forward and reverse part. Setting forward to `(PDH_Vmax*cell*((C
OA*PYR(t)*NAD(t)) / (cell^3) + (-HCO3*ACCOA(t)*NADH(t)) / (PDH_Keq*(cell^3)))) / (PDH_KmCOA*PD
H_KmNAD*PDH_KmPYR*((ACCOA(t)*NADH(t)) / (PDH_KmACCOA*PDH_KmNADH*(cell^2)) + (COA*NADH(t)) / (P
DH_KmCOA*PDH_KmNADH*(cell^2)) + ((1.0 + PYR(t) / (PDH_KmPYR*cell) + COA / (PDH_KmCOA*cell))*NA
D(t)) / (PDH_KmNAD*cell) + (COA*ACCOA(t)*NADH(t)) / (PDH_KmACCOA*PDH_KmCOA*PDH_KmNADH*(cell^3)
) + (COA*ACCOA(t)*PYR(t)) / (PDH_KmACCOA*PDH_KmCOA*PDH_KmPYR*(cell^3)) + (COA*NAD(t)*NADH(t)) 
/ (PDH_KmCOA*PDH_KmNAD*PDH_KmNADH*(cell^3)) + (NAD(t)*NADH(t)) / (PDH_KmNAD*PDH_KmNADH*(cell^2
)) + NADH(t) / (PDH_KmNADH*cell) + (COA*(1.0 + NAD(t) / (PDH_KmNAD*cell))*PYR(t)) / (PDH_KmCOA
*PDH_KmPYR*(cell^2)) + (ACCOA(t)*PYR(t)) / (PDH_KmACCOA*PDH_KmPYR*(cell^2)) + ACCOA(t) / (PDH_
KmACCOA*cell))*(1.0 + HCO3 / (PDH_KmHCO3*cell)))` and reverse to `0`. Stochastic simulations w
ill be inexact.
└ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:35
┌ Warning: Cannot separate bidirectional kineticLaw `(XCH_ACE2_Vmax*(ACEp(t) / (XCH_ACE2_Km*ce
ll_periplasm) + (-ACEx_0(t)) / (XCH_ACE2_Km*extracellular))) / (1.0 + ACEp(t) / (XCH_ACE2_Km*c
ell_periplasm) + ACEx_0(t) / (XCH_ACE2_Km*extracellular))` to forward and reverse part. Settin
g forward to `(XCH_ACE2_Vmax*(ACEp(t) / (XCH_ACE2_Km*cell_periplasm) + (-ACEx_0(t)) / (XCH_ACE
2_Km*extracellular))) / (1.0 + ACEp(t) / (XCH_ACE2_Km*cell_periplasm) + ACEx_0(t) / (XCH_ACE2_
Km*extracellular))` and reverse to `0`. Stochastic simulations will be inexact.
└ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:35
┌ Warning: Cannot separate bidirectional kineticLaw `(ICD_kcat*((NADP(t)*ICIT(t)) / (cell^2) +
 (-NADPH(t)*AKG(t)) / (ICD_Keq*(cell^2)))*icd(t)) / (ICD_KmICIT*ICD_KmNADP*(-1.0 + (1.0 + ICIT
(t) / (ICD_KmICIT*cell))*(1.0 + NADP(t) / (ICD_KmNADP*cell)) + (1.0 + NADPH(t) / (ICD_KmNADPH*
cell))*(1.0 + AKG(t) / (ICD_KmAKG*cell))))` to forward and reverse part. Setting forward to `(
ICD_kcat*((NADP(t)*ICIT(t)) / (cell^2) + (-NADPH(t)*AKG(t)) / (ICD_Keq*(cell^2)))*icd(t)) / (I
CD_KmICIT*ICD_KmNADP*(-1.0 + (1.0 + ICIT(t) / (ICD_KmICIT*cell))*(1.0 + NADP(t) / (ICD_KmNADP*
cell)) + (1.0 + NADPH(t) / (ICD_KmNADPH*cell))*(1.0 + AKG(t) / (ICD_KmAKG*cell))))` and revers
e to `0`. Stochastic simulations will be inexact.
└ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:35
┌ Warning: Cannot separate bidirectional kineticLaw `ADK_k*cell*((AMP(t)*ATP(t)) / (cell^2) + 
(-((ADP(t) / cell)^2.0)) / ADK_Keq)` to forward and reverse part. Setting forward to `ADK_k*ce
ll*((AMP(t)*ATP(t)) / (cell^2) + (-((ADP(t) / cell)^2.0)) / ADK_Keq)` and reverse to `0`. Stoc
hastic simulations will be inexact.
└ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:35
┌ Warning: Cannot separate bidirectional kineticLaw `(SDH_Vmax*cell*((-FUM(t)*FADH2(t)) / (SDH
_Keq*(cell^2)) + (SUC(t)*FAD(t)) / (cell^2))) / (SDH_KefSUC*SDH_KmQ*(1.0 + FUM(t) / (SDH_KefFU
M*cell) + (FUM(t)*FADH2(t)) / (SDH_KefFUM*SDH_KmQH2*(cell^2)) + (SDH_KmSUC*FAD(t)) / (SDH_KefS
UC*SDH_KmQ*cell) + (SDH_KmFUM*FADH2(t)) / (SDH_KefFUM*SDH_KmQH2*cell) + (SUC(t)*FAD(t)) / (SDH
_KefSUC*SDH_KmQ*(cell^2)) + SUC(t) / (SDH_KefSUC*cell)))` to forward and reverse part. Setting
 forward to `(SDH_Vmax*cell*((-FUM(t)*FADH2(t)) / (SDH_Keq*(cell^2)) + (SUC(t)*FAD(t)) / (cell
^2))) / (SDH_KefSUC*SDH_KmQ*(1.0 + FUM(t) / (SDH_KefFUM*cell) + (FUM(t)*FADH2(t)) / (SDH_KefFU
M*SDH_KmQH2*(cell^2)) + (SDH_KmSUC*FAD(t)) / (SDH_KefSUC*SDH_KmQ*cell) + (SDH_KmFUM*FADH2(t)) 
/ (SDH_KefFUM*SDH_KmQH2*cell) + (SUC(t)*FAD(t)) / (SDH_KefSUC*SDH_KmQ*(cell^2)) + SUC(t) / (SD
H_KefSUC*cell)))` and reverse to `0`. Stochastic simulations will be inexact.
└ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:35
┌ Warning: Cannot separate bidirectional kineticLaw `cell*((-PTS_1_k2*ei(t)*hprP(t)) / (cell^2
) + (PTS_1_k1*hpr(t)*eiP(t)) / (cell^2))` to forward and reverse part. Setting forward to `cel
l*((-PTS_1_k2*ei(t)*hprP(t)) / (cell^2) + (PTS_1_k1*hpr(t)*eiP(t)) / (cell^2))` and reverse to
 `0`. Stochastic simulations will be inexact.
└ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:35
┌ Warning: Cannot separate bidirectional kineticLaw `ACEK_1_k*cell*((icd(t)*ATP(t)) / (cell^2)
 + (-icdP(t)*ADP(t)) / (ACEK_1_Keq*(cell^2)))` to forward and reverse part. Setting forward to
 `ACEK_1_k*cell*((icd(t)*ATP(t)) / (cell^2) + (-icdP(t)*ADP(t)) / (ACEK_1_Keq*(cell^2)))` and 
reverse to `0`. Stochastic simulations will be inexact.
└ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:35
┌ Warning: Cannot separate bidirectional kineticLaw `(FBA_Vmax*cell*((-GAP(t)*DAP(t)) / (FBA_K
eq*(cell^2)) + FDP(t) / cell)) / (FBA_KmFDP*(1.0 + PEP(t) / (FBA_KmPEP*cell) + FDP(t) / (FBA_K
mFDP*cell) + DAP(t) / (FBA_KmDAP*cell) + (GAP(t)*DAP(t)) / (FBA_KmDAP*FBA_KmGAP*(cell^2))))` t
o forward and reverse part. Setting forward to `(FBA_Vmax*cell*((-GAP(t)*DAP(t)) / (FBA_Keq*(c
ell^2)) + FDP(t) / cell)) / (FBA_KmFDP*(1.0 + PEP(t) / (FBA_KmPEP*cell) + FDP(t) / (FBA_KmFDP*
cell) + DAP(t) / (FBA_KmDAP*cell) + (GAP(t)*DAP(t)) / (FBA_KmDAP*FBA_KmGAP*(cell^2))))` and re
verse to `0`. Stochastic simulations will be inexact.
└ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:35
ERROR: StackOverflowError:
Stacktrace:
     [1] unsorted_arguments(x::SymbolicUtils.BasicSymbolic{Real})
       @ SymbolicUtils ~/.julia/packages/SymbolicUtils/c0xQb/src/types.jl:138
     [2] (::SymbolicUtils.Rewriters.Walk{…})(x::SymbolicUtils.BasicSymbolic{…})
       @ SymbolicUtils.Rewriters ~/.julia/packages/SymbolicUtils/c0xQb/src/rewriters.jl:198
     [3] (::SymbolicUtils.Rewriters.PassThrough{SymbolicUtils.Rewriters.Walk{…}})(x::SymbolicU
tils.BasicSymbolic{Real})
       @ SymbolicUtils.Rewriters ~/.julia/packages/SymbolicUtils/c0xQb/src/rewriters.jl:188
     [4] iterate(g::Base.Generator, s::Vararg{Any})
       @ Base ./generator.jl:47 [inlined]
     [5] _collect(c::Vector{…}, itr::Base.Generator{…}, ::Base.EltypeUnknown, isz::Base.HasSha
pe{…})
       @ Base ./array.jl:854
     [6] collect_similar
       @ ./array.jl:763 [inlined]
     [7] map(f::Any, A::Any)
       @ Base ./abstractarray.jl:3282 [inlined]
--- the last 6 lines are repeated 13073 more times ---
 [78446] (::SymbolicUtils.Rewriters.Walk{…})(x::SymbolicUtils.BasicSymbolic{…})
       @ SymbolicUtils.Rewriters ~/.julia/packages/SymbolicUtils/c0xQb/src/rewriters.jl:198
 [78447] simplify_fractions(x::SymbolicUtils.BasicSymbolic{Real}; polyform::Bool)
       @ SymbolicUtils ~/.julia/packages/SymbolicUtils/c0xQb/src/polyform.jl:325
 [78448] simplify_fractions(x::SymbolicUtils.BasicSymbolic{Real})
       @ SymbolicUtils ~/.julia/packages/SymbolicUtils/c0xQb/src/polyform.jl:323
 [78449] simplify_div(d::SymbolicUtils.BasicSymbolic{Real})
       @ SymbolicUtils ~/.julia/packages/SymbolicUtils/c0xQb/src/polyform.jl:280
 [78450] (::SymbolicUtils.var"#sdiv#135")(a::SymbolicUtils.BasicSymbolic{Real})
       @ SymbolicUtils ~/.julia/packages/SymbolicUtils/c0xQb/src/polyform.jl:329
 [78451] call_composed
       @ ./operators.jl:1044 [inlined]
 [78452] (::ComposedFunction{…})(x::SymbolicUtils.BasicSymbolic{…}; kw::@Kwargs{})
       @ Base ./operators.jl:1041
 [78453] (::SymbolicUtils.Rewriters.Walk{…})(x::SymbolicUtils.BasicSymbolic{…})
       @ SymbolicUtils.Rewriters ~/.julia/packages/SymbolicUtils/c0xQb/src/rewriters.jl:200
 [78454] simplify_fractions(x::SymbolicUtils.BasicSymbolic{Real}; polyform::Bool)
       @ SymbolicUtils ~/.julia/packages/SymbolicUtils/c0xQb/src/polyform.jl:331
 [78455] simplify_fractions(x::SymbolicUtils.BasicSymbolic{Real})
       @ SymbolicUtils ~/.julia/packages/SymbolicUtils/c0xQb/src/polyform.jl:323
 [78456] simplify_fractions(n::Num; kw::@Kwargs{})
       @ Symbolics ~/.julia/packages/Symbolics/Eas9m/src/Symbolics.jl:165
 [78457] simplify_fractions
       @ ~/.julia/packages/Symbolics/Eas9m/src/Symbolics.jl:165 [inlined]
 [78458] get_massaction(kl::Num, reactants::Vector{Num}, stoich::Vector{Int64})
       @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:187
 [78459] use_rate(kl::Num, react::Vector{Num}, stoich::Vector{Int64})
       @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:150
 [78460] add_reaction!(rxs::Vector{…}, kl::Num, reactant_references::Vector{…}, product_refere
nces::Vector{…}, model::SBML.Model; enforce_rate::Bool)
       @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:66
 [78461] add_reaction!
       @ ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:55 [inlined]
 [78462] get_reactions(model::SBML.Model)
       @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/reactions.jl:22
 [78463] ReactionSystem(model::SBML.Model; kwargs::@Kwargs{})
       @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/systems.jl:55
 [78464] ReactionSystem(model::SBML.Model)
       @ SBMLToolkit ~/.julia/packages/SBMLToolkit/JL9bj/src/systems.jl:53
Some type information was truncated. Use `show(err)` to see complete types.

julia>

ChrisRackauckas · July 3, 2024, 6:32am

Can you open an issue? It seems that SBML file is hitting a construct that’s not supported. It would be good to get that documented. The SBML spec is huge so there’s a few bits which still aren’t fully covered.

jchitpin · July 3, 2024, 1:16pm

Thanks and will do @ChrisRackauckas. I opened an issue.