Error constructing reaction system from SBML BioModel

[jchitpin]

Encountering an error when constructing a reaction system from a BioModels SBML file. The warnings indicate that specific bidirectional reactions cannot be split.

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

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.

• Output of using Pkg; Pkg.status()

julia> Pkg.status()
Status `~/Downloads/Transfer/reproduce-kinetic-paper
-2024/Project.toml`
⌅ [961ee093] ModelingToolkit v8.76.0
  [1dea7af3] OrdinaryDiffEq v6.85.0
  [86080e66] SBMLToolkit v0.1.25
Info Packages marked with ⌅ have new versions availa
ble but compatibility constraints restrict them from
 upgrading. To see why use `status --outdated`

• Output of using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)

julia> Pkg.status(; mode = PKGMODE_MANIFEST)
Status `~/Downloads/Transfer/reproduce-kinetic-paper-2024/Manifest.toml`
  [47edcb42] ADTypes v1.5.3
  [1520ce14] AbstractTrees v0.4.5
  [7d9f7c33] Accessors v0.1.36
  [79e6a3ab] Adapt v4.0.4
  [66dad0bd] AliasTables v1.1.3
  [ec485272] ArnoldiMethod v0.4.0
  [4fba245c] ArrayInterface v7.11.0
  [4c555306] ArrayLayouts v1.10.0
  [e2ed5e7c] Bijections v0.1.7
  [62783981] BitTwiddlingConvenienceFunctions v0.1.6
  [2a0fbf3d] CPUSummary v0.2.6
  [00ebfdb7] CSTParser v3.4.3
  [49dc2e85] Calculus v0.5.1
  [479239e8] Catalyst v13.5.1
  [d360d2e6] ChainRulesCore v1.24.0
  [fb6a15b2] CloseOpenIntervals v0.1.13
  [861a8166] Combinatorics v1.0.2
  [a80b9123] CommonMark v0.8.12
  [38540f10] CommonSolve v0.2.4
  [bbf7d656] CommonSubexpressions v0.3.0
  [f70d9fcc] CommonWorldInvalidations v1.0.0
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⌅ [459566f4] DiffEqCallbacks v2.37.0
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⌅ [5b8099bc] DomainSets v0.6.7
  [fa6b7ba4] DualNumbers v0.6.8
⌅ [7c1d4256] DynamicPolynomials v0.5.7
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  [8f5d6c58] EzXML v1.2.0
  [7034ab61] FastBroadcast v0.3.4
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  [29a986be] FastLapackInterface v2.0.4
  [1a297f60] FillArrays v1.11.0
  [6a86dc24] FiniteDiff v2.23.1
  [1fa38f19] Format v1.3.7
  [f6369f11] ForwardDiff v0.10.36
  [069b7b12] FunctionWrappers v1.1.3
  [77dc65aa] FunctionWrappersWrappers v0.1.3
  [d9f16b24] Functors v0.4.11
  [46192b85] GPUArraysCore v0.1.6
  [c145ed77] GenericSchur v0.5.4
  [c27321d9] Glob v1.3.1
  [86223c79] Graphs v1.11.2
  [3e5b6fbb] HostCPUFeatures v0.1.17
  [34004b35] HypergeometricFunctions v0.3.23
  [615f187c] IfElse v0.1.1
  [d25df0c9] Inflate v0.1.5
  [8197267c] IntervalSets v0.7.10
  [3587e190] InverseFunctions v0.1.14
  [92d709cd] IrrationalConstants v0.2.2
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.5.0
  [682c06a0] JSON v0.21.4
  [98e50ef6] JuliaFormatter v1.0.56
  [ccbc3e58] JumpProcesses v9.11.1
  [ef3ab10e] KLU v0.6.0
  [ba0b0d4f] Krylov v0.9.6
  [b964fa9f] LaTeXStrings v1.3.1
  [2ee39098] LabelledArrays v1.16.0
  [984bce1d] LambertW v0.4.6
  [23fbe1c1] Latexify v0.16.4
  [10f19ff3] LayoutPointers v0.1.17
  [5078a376] LazyArrays v2.1.2
  [d3d80556] LineSearches v7.2.0
  [7ed4a6bd] LinearSolve v2.30.2
  [2ab3a3ac] LogExpFunctions v0.3.28
  [bdcacae8] LoopVectorization v0.12.171
  [d8e11817] MLStyle v0.4.17
  [1914dd2f] MacroTools v0.5.13
  [d125e4d3] ManualMemory v0.1.8
  [abcecc63] MathML v0.1.15
  [bb5d69b7] MaybeInplace v0.1.3
  [e1d29d7a] Missings v1.2.0
⌅ [961ee093] ModelingToolkit v8.76.0
  [46d2c3a1] MuladdMacro v0.2.4
  [102ac46a] MultivariatePolynomials v0.5.6
  [d8a4904e] MutableArithmetics v1.4.5
  [d41bc354] NLSolversBase v7.8.3
  [2774e3e8] NLsolve v4.5.1
  [77ba4419] NaNMath v1.0.2
  [8913a72c] NonlinearSolve v3.13.1
  [6fe1bfb0] OffsetArrays v1.14.0
  [bac558e1] OrderedCollections v1.6.3
  [1dea7af3] OrdinaryDiffEq v6.85.0
  [90014a1f] PDMats v0.11.31
  [65ce6f38] PackageExtensionCompat v1.0.2
  [d96e819e] Parameters v0.12.3
  [69de0a69] Parsers v2.8.1
  [e409e4f3] PoissonRandom v0.4.4
  [f517fe37] Polyester v0.7.15
  [1d0040c9] PolyesterWeave v0.2.2
  [d236fae5] PreallocationTools v0.4.22
  [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [43287f4e] PtrArrays v1.2.0
  [1fd47b50] QuadGK v2.9.4
  [e6cf234a] RandomNumbers v1.5.3
  [3cdcf5f2] RecipesBase v1.3.4
  [731186ca] RecursiveArrayTools v3.23.1
  [f2c3362d] RecursiveFactorization v0.2.23
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.0
  [79098fc4] Rmath v0.7.1
  [7e49a35a] RuntimeGeneratedFunctions v0.5.13
  [e5567a89] SBML v1.5.1
  [86080e66] SBMLToolkit v0.1.25
  [94e857df] SIMDTypes v0.1.0
  [476501e8] SLEEFPirates v0.6.43
  [0bca4576] SciMLBase v2.42.0
  [c0aeaf25] SciMLOperators v0.3.8
  [53ae85a6] SciMLStructures v1.4.1
  [efcf1570] Setfield v1.1.1
  [727e6d20] SimpleNonlinearSolve v1.10.1
  [699a6c99] SimpleTraits v0.9.4
  [ce78b400] SimpleUnPack v1.1.0
  [a2af1166] SortingAlgorithms v1.2.1
  [47a9eef4] SparseDiffTools v2.19.0
  [0a514795] SparseMatrixColorings v0.3.3
  [e56a9233] Sparspak v0.3.9
  [276daf66] SpecialFunctions v2.4.0
  [aedffcd0] Static v1.1.0
  [0d7ed370] StaticArrayInterface v1.5.1
  [90137ffa] StaticArrays v1.9.7
  [1e83bf80] StaticArraysCore v1.4.3
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.3
  [4c63d2b9] StatsFuns v1.3.1
  [7792a7ef] StrideArraysCore v0.5.7
  [2efcf032] SymbolicIndexingInterface v0.3.22
  [19f23fe9] SymbolicLimits v0.2.1
⌅ [d1185830] SymbolicUtils v1.5.1
⌃ [0c5d862f] Symbolics v5.28.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.11.1
  [8290d209] ThreadingUtilities v0.5.2
  [a759f4b9] TimerOutputs v0.5.24
  [0796e94c] Tokenize v0.5.29
  [d5829a12] TriangularSolve v0.2.1
  [410a4b4d] Tricks v0.1.8
  [781d530d] TruncatedStacktraces v1.4.0
  [5c2747f8] URIs v1.5.1
  [3a884ed6] UnPack v1.0.2
  [1986cc42] Unitful v1.20.0
  [a7c27f48] Unityper v0.1.6
  [3d5dd08c] VectorizationBase v0.21.70
  [19fa3120] VertexSafeGraphs v0.2.0
  [1d5cc7b8] IntelOpenMP_jll v2024.1.0+0
  [94ce4f54] Libiconv_jll v1.17.0+0
  [856f044c] MKL_jll v2024.1.0+0
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [f50d1b31] Rmath_jll v0.4.2+0
  [bb12108a] SBML_jll v5.20.1+0
  [02c8fc9c] XML2_jll v2.13.1+0
  [1317d2d5] oneTBB_jll v2021.12.0+0
  [0dad84c5] ArgTools v1.1.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8ba89e20] Distributed
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching
  [9fa8497b] Future
  [b77e0a4c] InteractiveUtils
  [4af54fe1] LazyArtifacts
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.10.0
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
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  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
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  [10745b16] Statistics v1.10.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
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  [deac9b47] LibCURL_jll v8.4.0+0
  [e37daf67] LibGit2_jll v1.6.4+0
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  [c8ffd9c3] MbedTLS_jll v2.28.2+1
  [14a3606d] MozillaCACerts_jll v2023.1.10
  [4536629a] OpenBLAS_jll v0.3.23+4
  [05823500] OpenLibm_jll v0.8.1+2
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.8.0+1
  [8e850ede] nghttp2_jll v1.52.0+1
  [3f19e933] p7zip_jll v17.4.0+2
Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may
able, but those with ⌅ are restricted by compatibility constraints from upgradi
 why use `status --outdated -m`

• Output of versioninfo()

julia> versioninfo()
Julia Version 1.10.3
Commit 0b4590a550 (2024-04-30 10:59 UTC)
Build Info:

    Note: This is an unofficial build, please report bugs to the project
    responsible for this build and not to the Julia project unless you can
    reproduce the issue using official builds available at https://julialang.org/do
wnloads

Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: 8 × Intel(R) Core(TM) i5-8350U CPU @ 1.70GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, skylake)
Threads: 2 default, 0 interactive, 1 GC (on 8 virtual cores)
Environment:
  JULIA_NUM_THREADS = 8

[paulflang]

Hi @jchitpin , thanks a lot for reporting and apologies for not seeing this on discourse earlier. It's been a long wait for you, but #161 should fix your problem. Do you want to test on your end before I release or shall I just go ahead for now?

[jchitpin]

Hi @paulflang. No worries and feel free to go ahead with the release. I'll report back on any future issues.