Table 3. Options used for the benchmarked ODE methods displayed in the main text figure.

Model:	Multistate	Multisite2	Egfr_net	BCR	Fceri_gamma2
Julia solver 1	Vern6	BS5	VCABM	QNDF1,2,3,4	QNDF1,2,3,4
Julia solver 2	Vern7	Vern8	BS5	FBDF1,2,3,4	FBDF1,2,3,4
Julia solver 3	Tsit5	Tsit5	Vern6	KenCarp41,2,3,4	TRBDF21,2,3,4
Catalyst lsoda	lsoda	lsoda	lsoda	lsoda	lsoda
Catalyst CVODE	CVODE	CVODE1	CVODE1	CVODE1,2,4	CVODE1,2,4
BioNetGen	CVODE1	CVODE1	CVODE1	CVODE	CVODE1
COPASI	CVODE	CVODE	CVODE	CVODE	CVODE
GillesPy2	lsoda	lsoda	lsoda	lsoda	lsoda
Matlab	CVODE	CVODE	CVODE	CVODE	CVODE

For each model the options used for the 3 most performant native Julia solvers, the Julia lsoda and CVODE implementations, and each other tool (the results using these benchmarks are found in Fig 3). Each field contains the method used for that model. Further options (including whenever a specific linear solver was selected) are described through superscript tags.

¹GMRES linear solver was used.

²Sparse Jacobian representation was used (a Catalyst option only).

³Automatic differentiation (as a mean of Jacobian calculation) was turned off (a Catalyst option only).

⁴An incomplete LU preconditioner was supplied to the GMRES linear solver (a Catalyst option only).