Bidkhori2012 Work-Precision Diagrams

The following benchmark is of 109 ODEs and 188 parameters that describe a stiff SBML model, modelling the EGFR signalling between normal and NSCLC cells Bidkhori et al.. It is referenced from Biomodels Database, and the model was parsed to Julia are finally to ODEs using ModelingToolkit.

using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters,
      Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq,
      LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, JLD2

gr()

par = load(joinpath(@__DIR__, "params_Bidkhori2012.jld2"))

Dict{String, Any} with 188 entries:
  "reaction_mw3994e898_7232_4b70_9c58_b3476e8655f5_mw3676a900_b098_4… => 10
.0
  "reaction_mw26fdabae_323b_4a78_b134_4c2eb70ea6a7_mw8b269d52_eda9_4… => 0.
2
  "reaction_mw584a64d0_560a_4297_9882_80cb4eff73f3_mwdf20ff60_f0b7_4… => 0.
05
  "reaction_mw5c806b00_59a1_491e_99a1_2c932b2d5d7a_mw5a798f7a_b4eb_4… => 20
.0
  "reaction_mw45d92b79_0656_4795_87d0_7a465949ca43_mwba545ecf_c7d4_4… => 1.
0
  "reaction_mwaa65a34e_fabf_4d6d_ae0b_f1d08b068f33_mw2eed2db0_ba78_4… => 0.
01833
  "reaction_mwc5aae1f8_52e4_4bcd_b044_3768f90b7b19_mwba77a9ba_078d_4… => 0.
2
  "reaction_mwd3a36af9_3ccc_4bb1_9867_3b9823ba4ac8_mw901b5284_bdae_4… => 0.
09
  "reaction_mw0a51fbf0_409b_4b45_b4ac_0220af4c4e3c_mw0b6eb5f7_b133_4… => 0.
01
  "reaction_mwb49058ff_2997_4187_abe7_4dce4ccf6ff4_mw432640ec_11b9_4… => 2.
9
  "reaction_mw0dd5a91d_d76c_494e_9dd6_57f2836aaa19_mw8ed5885f_774e_4… => 0.
001
  "reaction_mw9544e67b_b6d0_4941_b7e0_ecd4f400a335_mwb0744746_88a2_4… => 0.
2661
  "reaction_mwcf9f1b1d_e19a_4fa8_85ba_8f17e2cec730_mw1ddaf9f4_dcab_4… => 0.
0426
  "reaction_mwbb77e3d6_6065_4344_9361_e30c03514f4e_mw7e09242b_bd80_4… => 20
2.9
  "reaction_mw5c806b00_59a1_491e_99a1_2c932b2d5d7a_mw54178365_18c1_4… => 0.
1
  "reaction_mw602726ea_89ee_41b8_bda6_e2811bb42c1d_mw2e0b4751_7227_4… => 5.
0
  "reaction_mw85e457d1_73f8_4236_bb61_a128d300003f_mw97b9ab43_02ae_4… => 0.
005
  "reaction_mw7bb43f0a_c87e_41ff_8a43_cdf45c8f05e6_mwd12a67b3_6d98_4… => 2.
661
  "reaction_mwa67e40c1_693d_4214_adc8_b2f2b71cef12_mw575f7f49_3663_4… => 10
0.0
  ⋮                                                                   => ⋮

Defining the reaction system

function sbml_model!(du, u, p, t)
    # assignmentRule: variable = mwa6994523_5d45_4000_af0c_3e94073bf183
    u88 = u[80] + u[79]

    reaction_mwa67e40c1_693d_4214_adc8_b2f2b71cef12 = p["reaction_mwa67e40c1_693d_4214_adc8_b2f2b71cef12_mw575f7f49_3663_47f1_b492_5b92c1c4345d"] * u[1] * u[2] - p["reaction_mwa67e40c1_693d_4214_adc8_b2f2b71cef12_mw53c64fd3_9a1c_4947_a734_74a73554964c"] * u[3]

    reaction_mw877cd1e3_b48b_42e8_ab23_682dd893fd9d = p["reaction_mw877cd1e3_b48b_42e8_ab23_682dd893fd9d_mw8cfaf07f_dabe_45de_93cc_ef2c7fd31104"] * u[3] * u[3] - p["reaction_mw877cd1e3_b48b_42e8_ab23_682dd893fd9d_mwab52aceb_4b19_4317_b2da_97ccbb973dab"] * u[4]

    reaction_mw413c6d45_ab23_4d3e_87b3_a8ed4629b923 = p["reaction_mw413c6d45_ab23_4d3e_87b3_a8ed4629b923_mw6b97a1ec_2cba_4bce_96f7_ec1d0fa2d16c"] * u[4]

    reaction_mwf61e086d_0345_4d4c_b91d_0b105e543d04 = p["reaction_mwf61e086d_0345_4d4c_b91d_0b105e543d04_mwf1697f55_a3f4_4fb6_ae1d_f96f09ad1daa"] * u[5] * u[7] - p["reaction_mwf61e086d_0345_4d4c_b91d_0b105e543d04_mw880a5942_7549_4466_bd19_0e1768a3a533"] * u[8]

    reaction_mw91f49311_efdc_47c6_b8b8_a619e042d644 = p["reaction_mw91f49311_efdc_47c6_b8b8_a619e042d644_mw7e889122_d26c_4d09_bae4_d313b992dc8e"] * u[5] * u[9] - p["reaction_mw91f49311_efdc_47c6_b8b8_a619e042d644_mwff6f49f7_268a_4f08_8d36_3ad8449d7472"] * u[10]

    reaction_mw974c39f5_b82e_44b3_abec_7a724f46c526 = p["reaction_mw974c39f5_b82e_44b3_abec_7a724f46c526_mwe645e76e_bb00_4c22_b25e_a2e77a6aada2"] * u[8]

    reaction_mw9544e67b_b6d0_4941_b7e0_ecd4f400a335 = p["reaction_mw9544e67b_b6d0_4941_b7e0_ecd4f400a335_mwb0744746_88a2_488e_a483_266747a044c6"] * u[10]

    reaction_mw486c5261_3d03_4589_a1e9_978b62ad2dfe = p["reaction_mw486c5261_3d03_4589_a1e9_978b62ad2dfe_mw9e24066c_51a5_4c7a_af7c_4656155a4eb0"] * u[11] - p["reaction_mw486c5261_3d03_4589_a1e9_978b62ad2dfe_mwab1ef4d4_2acc_4fa2_b07c_fac51fb7bfaf"] * u[5] * u[12]

    reaction_mw2cf8a809_63d8_4717_91fc_070516e6f3db = p["reaction_mw2cf8a809_63d8_4717_91fc_070516e6f3db_mwc4824ff0_2b51_4d66_ad48_1145f670a6e1"] * u[12] * u[9] - p["reaction_mw2cf8a809_63d8_4717_91fc_070516e6f3db_mw0f1d282f_1c6b_455c_8254_3760632c6ecc"] * u[13]

    reaction_mweda6a945_fb5d_4d99_9958_11b2b2840308 = p["reaction_mweda6a945_fb5d_4d99_9958_11b2b2840308_mw0aa92e25_f9aa_461e_92b8_23b1b5b3ab92"] * u[13]

    reaction_mwd4bf58ea_70c9_43ea_a831_1fcde130ba28 = p["reaction_mwd4bf58ea_70c9_43ea_a831_1fcde130ba28_mw2a4ed8a2_fce4_44a4_adb9_edc24a06b4e1"] * u[12]

    reaction_mw4817365e_a33b_451f_bee1_de748377ede2 = p["reaction_mw4817365e_a33b_451f_bee1_de748377ede2_mwe879a9ac_4b8d_4c9a_a157_a3751761cf63"] * u[11] * u[14] - p["reaction_mw4817365e_a33b_451f_bee1_de748377ede2_mwa18578d7_236f_4939_baca_52259e38fe15"] * u[15]

    reaction_mw03998474_934b_4e4a_8c0c_ca359e402ac2 = p["reaction_mw03998474_934b_4e4a_8c0c_ca359e402ac2_mw289fed85_e6ee_43e6_a69f_77b5f487a452"] * u[15] * u[9] - p["reaction_mw03998474_934b_4e4a_8c0c_ca359e402ac2_mw8768b5c7_b227_4825_aa55_a525b0d915c2"] * u[16]

    reaction_mw7bb43f0a_c87e_41ff_8a43_cdf45c8f05e6 = p["reaction_mw7bb43f0a_c87e_41ff_8a43_cdf45c8f05e6_mwd12a67b3_6d98_40e9_a54b_282a577498eb"] * u[16]

    reaction_mwd9262331_e35a_4614_943a_89bcf8a492e3 = p["reaction_mwd9262331_e35a_4614_943a_89bcf8a492e3_mw6ac313e2_e8a9_42a9_b13a_27e55c1012a2"] * u[15] * u[17] - p["reaction_mwd9262331_e35a_4614_943a_89bcf8a492e3_mw93f832d7_eefb_43dd_853c_a0d7a76023cf"] * u[18]

    reaction_mwc5f121dc_d27d_4c3d_90f2_67d0adaf144a = p["reaction_mwc5f121dc_d27d_4c3d_90f2_67d0adaf144a_mwbb727dc5_30e8_45f4_9d15_3b34be5c1e93"] * u[14] * u[17] - p["reaction_mwc5f121dc_d27d_4c3d_90f2_67d0adaf144a_mw7ae1ee96_563e_4684_bc9a_8f4ef373620e"] * u[20]

    reaction_mw23a29b42_9813_4e46_b8ae_966e3215e6dc = p["reaction_mw23a29b42_9813_4e46_b8ae_966e3215e6dc_mwbc5340b6_06b7_4081_bd0c_e7a397f06a92"] * u[11] * u[20] - p["reaction_mw23a29b42_9813_4e46_b8ae_966e3215e6dc_mw0df80c0e_c32b_4f90_99bd_e8f90e4c8109"] * u[18]

    reaction_mw0e459167_515b_4c4d_8b67_bf0a5b3e9d61 = p["reaction_mw0e459167_515b_4c4d_8b67_bf0a5b3e9d61_mwc585e0e4_b7e7_4290_8a6d_10fcd9759a2d"] * u[5] * u[14] - p["reaction_mw0e459167_515b_4c4d_8b67_bf0a5b3e9d61_mwf44d37d0_fe7f_4e47_bf10_1e734fbc3391"] * u[21]

    reaction_mwc52e0f9b_1e0c_46ca_8d18_f05ef4a080cb = p["reaction_mwc52e0f9b_1e0c_46ca_8d18_f05ef4a080cb_mw3d564c3c_aa54_4c16_90be_662cfcbf8bc8"] * u[21] * u[9] - p["reaction_mwc52e0f9b_1e0c_46ca_8d18_f05ef4a080cb_mw371642bb_3836_4ded_93a5_68fa9b464896"] * u[22]

    reaction_mw4f89bf6c_8691_41a6_a1ac_13e6aa8c4b93 = p["reaction_mw4f89bf6c_8691_41a6_a1ac_13e6aa8c4b93_mw736e4a7b_4a25_4d32_b96b_b088e3bd41e7"] * u[22]

    reaction_mw35f71989_f89b_4440_b1a4_ebc7b4cc18b2 = p["reaction_mw35f71989_f89b_4440_b1a4_ebc7b4cc18b2_mw084cd67b_f328_48a7_8e16_1d6256c8c137"] * u[21] * u[17] - p["reaction_mw35f71989_f89b_4440_b1a4_ebc7b4cc18b2_mw43f177dc_f522_4dd1_b8e5_21b2b8fdfdba"] * u[23]

    reaction_mwd0d92dd4_81b7_4385_bfd7_5de82e193ecd = p["reaction_mwd0d92dd4_81b7_4385_bfd7_5de82e193ecd_mwfa6a58ab_0ca5_4c05_92b0_870593ac135d"] * u[5] * u[20] - p["reaction_mwd0d92dd4_81b7_4385_bfd7_5de82e193ecd_mwb9547c37_09b7_4258_95ab_8039d4088298"] * u[23]

    reaction_mwbb77e3d6_6065_4344_9361_e30c03514f4e = p["reaction_mwbb77e3d6_6065_4344_9361_e30c03514f4e_mw7e09242b_bd80_4af0_90c8_e0cddace89fe"] * u[18] * u[25] - p["reaction_mwbb77e3d6_6065_4344_9361_e30c03514f4e_mw2dfc8a19_1792_4e12_af38_8bfbda31a577"] * u[26]

    reaction_mw921ee820_1dbb_4b5f_866c_87da620d8f89 = p["reaction_mw921ee820_1dbb_4b5f_866c_87da620d8f89_mw553c0b3c_af7f_4309_8c61_0f1e2c32347c"] * u[27]

    reaction_mw0bcfad86_59b9_42ff_bcb7_fbb44845049d = p["reaction_mw0bcfad86_59b9_42ff_bcb7_fbb44845049d_mwfc146e94_8070_4727_8416_fb55829068cb"] * u[26]

    reaction_mwe9b50ac7_dac3_4eba_b1db_b3fd392d8fb7 = p["reaction_mwe9b50ac7_dac3_4eba_b1db_b3fd392d8fb7_mw26688d02_8ab9_4123_89c4_022b981cb72c"] * u[28]

    reaction_mw934c3638_603e_4ff0_a763_68f9405fa01f = p["reaction_mw934c3638_603e_4ff0_a763_68f9405fa01f_mw5639395a_a5cd_46dd_81b8_30fe72400a2e"] * u[23] * u[25] - p["reaction_mw934c3638_603e_4ff0_a763_68f9405fa01f_mw9cc637fe_d9ca_47d2_a4dc_66009d458094"] * u[28]

    reaction_mw3c617363_649b_4460_a694_36f7a3127a62 = p["reaction_mw3c617363_649b_4460_a694_36f7a3127a62_mw19173345_925d_427b_8658_add0978e5931"] * u[27] * u[29] - p["reaction_mw3c617363_649b_4460_a694_36f7a3127a62_mw9f6790d7_19ce_41d9_b4de_a1658c047501"] * u[30]

    reaction_mwf31259aa_32b7_4104_be70_045297b9a512 = p["reaction_mwf31259aa_32b7_4104_be70_045297b9a512_mw23e16d40_acbb_4658_a336_be5d0b0dd86a"] * u[30]

    reaction_mw0a51fbf0_409b_4b45_b4ac_0220af4c4e3c = p["reaction_mw0a51fbf0_409b_4b45_b4ac_0220af4c4e3c_mw10c97b8e_72aa_4f56_b3b9_c94baad7e213"] * u[5] * u[29] - p["reaction_mw0a51fbf0_409b_4b45_b4ac_0220af4c4e3c_mw0b6eb5f7_b133_4b3d_bf15_9fd6c2e9332d"] * u[31]

    reaction_mw33baddbd_a23f_45bb_b126_0ba60bbf6c53 = p["reaction_mw33baddbd_a23f_45bb_b126_0ba60bbf6c53_mwe483687f_b591_4c42_9abc_7ea9f47470bf"] * u[31] * u[27] - p["reaction_mw33baddbd_a23f_45bb_b126_0ba60bbf6c53_mwcf964aba_9db6_46c5_b687_beafc5d89169"] * u[32]

    reaction_mw652570eb_c9d3_499b_b877_61d360b10980 = p["reaction_mw652570eb_c9d3_499b_b877_61d360b10980_mwb881f20a_cf8a_493a_aa84_59ee90f26dd9"] * u[32]

    reaction_mwc5aae1f8_52e4_4bcd_b044_3768f90b7b19 = p["reaction_mwc5aae1f8_52e4_4bcd_b044_3768f90b7b19_mwb4c6ed27_c7ec_438f_bafd_4a09a9f356f1"] * u[31] * u[9] - p["reaction_mwc5aae1f8_52e4_4bcd_b044_3768f90b7b19_mwba77a9ba_078d_4ec6_a8b8_d7042a2cefe7"] * u[33]

    reaction_mw642ac312_2ee7_4e66_8f3e_e2da2bb6412a = p["reaction_mw642ac312_2ee7_4e66_8f3e_e2da2bb6412a_mwe1743f7b_ca2c_47d4_91d7_aed2748d98c5"] * u[33]

    reaction_mw584a64d0_560a_4297_9882_80cb4eff73f3 = p["reaction_mw584a64d0_560a_4297_9882_80cb4eff73f3_mw9f1dbbe6_8aa3_4180_bcea_04343649d7ba"] * u[34] * u[27] - p["reaction_mw584a64d0_560a_4297_9882_80cb4eff73f3_mwdf20ff60_f0b7_4c2a_b393_586ec1337e67"] * u[35]

    reaction_mw42c97708_4f85_45a8_9141_d0ae529409ca = p["reaction_mw42c97708_4f85_45a8_9141_d0ae529409ca_mw91f2ca92_9556_4fb8_ae12_0b72f3e3f261"] * u[35]

    reaction_mwaa65a34e_fabf_4d6d_ae0b_f1d08b068f33 = p["reaction_mwaa65a34e_fabf_4d6d_ae0b_f1d08b068f33_mw77c60377_28ae_4aad_b911_5768fc8b824f"] * u[36] * u[37] - p["reaction_mwaa65a34e_fabf_4d6d_ae0b_f1d08b068f33_mw2eed2db0_ba78_435b_b2c8_ee91efdba1b4"] * u[38]

    reaction_mw1bd186cf_4762_480a_b70d_d7a775462398 = p["reaction_mw1bd186cf_4762_480a_b70d_d7a775462398_mw7e974605_8d9c_4250_8f69_072aab1f24f7"] * u[38]

    reaction_mwf5573ddf_ad7f_478a_a784_557a9cddaaf2 = p["reaction_mwf5573ddf_ad7f_478a_a784_557a9cddaaf2_mw11cdaca9_941c_4a59_ba2a_3bfeafb65aeb"] * u[36] * u[39] - p["reaction_mwf5573ddf_ad7f_478a_a784_557a9cddaaf2_mw58c37b3e_91e7_445e_846e_77cd0b2320af"] * u[40]

    reaction_mwb49058ff_2997_4187_abe7_4dce4ccf6ff4 = p["reaction_mwb49058ff_2997_4187_abe7_4dce4ccf6ff4_mw432640ec_11b9_484d_ba26_415538ab9a10"] * u[40]

    reaction_mw8301b154_9463_4516_b4c5_c8f8b68691fe = p["reaction_mw8301b154_9463_4516_b4c5_c8f8b68691fe_mw11bb74b8_d908_46f0_ac4d_06e8dd1aa5ae"] * u[41] * u[42] - p["reaction_mw8301b154_9463_4516_b4c5_c8f8b68691fe_mwb44117f5_20b2_495e_adf3_3467cd119fd6"] * u[43]

    reaction_mwf95f743d_6108_49fe_8ffd_bdcc1a9f9a8d = p["reaction_mwf95f743d_6108_49fe_8ffd_bdcc1a9f9a8d_mwa4c71b8d_fb74_465b_b76e_cec4e4c95484"] * u[43]

    reaction_mw51d9d6b8_f0c0_4763_9d11_9be61b5cf5c9 = p["reaction_mw51d9d6b8_f0c0_4763_9d11_9be61b5cf5c9_mwc40b3165_cc16_4f78_86b5_e34f2731dcbb"] * u[41] * u[44] - p["reaction_mw51d9d6b8_f0c0_4763_9d11_9be61b5cf5c9_mw8bff2fe0_b582_4020_8f05_83f14451b1c0"] * u[45]

    reaction_mw6fd24d16_f57d_46c6_82f5_3f00759fa16b = p["reaction_mw6fd24d16_f57d_46c6_82f5_3f00759fa16b_mw3d07dc22_f821_49a5_9712_820ba9592353"] * u[45]

    reaction_mw9c208e18_c70d_4231_af0b_ad17cd0bba2d = p["reaction_mw9c208e18_c70d_4231_af0b_ad17cd0bba2d_mwa8f70790_9f44_4548_988e_49d13016d2f1"] * u[36] * u[47] - p["reaction_mw9c208e18_c70d_4231_af0b_ad17cd0bba2d_mwaad540b6_783e_4576_8862_ad522fd897db"] * u[48]

    reaction_mw87711dc1_43d7_40fc_b9e9_a24e2f92419d = p["reaction_mw87711dc1_43d7_40fc_b9e9_a24e2f92419d_mwfbc395b5_05b8_4e27_9696_c3ba52edaf74"] * u[48]

    reaction_mw4b445876_bdce_42d0_867b_fd3c74128a6b = p["reaction_mw4b445876_bdce_42d0_867b_fd3c74128a6b_mwc489f472_68ce_44e7_aad1_f8d2f6dda4ff"] * u[41] * u[49] - p["reaction_mw4b445876_bdce_42d0_867b_fd3c74128a6b_mw56f1bdc0_66fd_47c0_806a_beeaf123e2f2"] * u[50]

    reaction_mw40950d59_1012_4361_8418_73e25758e367 = p["reaction_mw40950d59_1012_4361_8418_73e25758e367_mwa17c895f_29d8_4977_a99f_cf9bf6216785"] * u[50]

    reaction_mwbfa79c95_487d_4c6f_b437_9e579451a419 = p["reaction_mwbfa79c95_487d_4c6f_b437_9e579451a419_mwafd23622_952d_44b3_a437_4aa12422add7"] * u[39] * u[49] - p["reaction_mwbfa79c95_487d_4c6f_b437_9e579451a419_mw9d9a7d08_b19a_44f1_a806_151597049345"] * u[51]

    reaction_mwa4b69c77_6226_46da_b78c_3e6027d0be41 = p["reaction_mwa4b69c77_6226_46da_b78c_3e6027d0be41_mwac85fd83_4e73_43f1_9c42_01773349d50f"] * u[51]

    reaction_mwf8bb22e2_5aa3_4c25_a022_a266b1856a48 = p["reaction_mwf8bb22e2_5aa3_4c25_a022_a266b1856a48_mwd23d026b_c5b7_4742_aab9_b9beb18ec9bc"] * u[46] * u[52] - p["reaction_mwf8bb22e2_5aa3_4c25_a022_a266b1856a48_mwf4c4d7a7_1498_4f6c_9d72_cd5cb012146c"] * u[54]

    reaction_mw61305f93_7b2d_4a2d_8d16_f7be026d8671 = p["reaction_mw61305f93_7b2d_4a2d_8d16_f7be026d8671_mwe3e5abe4_9f92_43eb_92e4_cea771f5bf14"] * u[54]

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    reaction_mwb71945c2_03a8_4fad_a995_e1caeee98525 = p["reaction_mwb71945c2_03a8_4fad_a995_e1caeee98525_mw7aba6db3_c7ec_4192_bb5e_0ac4b466c1a5"] * u[105]

    reaction_mwd189238c_e8f9_40be_b4ea_18a42bba1b4f = p["reaction_mwd189238c_e8f9_40be_b4ea_18a42bba1b4f_mw31eb851a_c381_419d_b694_f158b7f5cfb6"] * u[104]

    reaction_mwcb637bf1_7618_4d8a_ab5c_399145ecf1df = p["reaction_mwcb637bf1_7618_4d8a_ab5c_399145ecf1df_mwe09b67b9_0d2a_4b82_91ef_5284216beb94"] * u[91] * u[6] - p["reaction_mwcb637bf1_7618_4d8a_ab5c_399145ecf1df_mw77a6c207_ff8c_463c_9b4e_8a7d96652b79"] * u[106]

    reaction_mw401dde7e_c0a1_4780_b6cc_8f98681c862e = p["reaction_mw401dde7e_c0a1_4780_b6cc_8f98681c862e_mw1df53838_48e5_4331_9084_3790409ad5ff"] * u[106] * u[60] - p["reaction_mw401dde7e_c0a1_4780_b6cc_8f98681c862e_mwe4573b2c_5f99_40d0_9f9e_c238caa5ccbe"] * u[107]

    reaction_mw0dd5a91d_d76c_494e_9dd6_57f2836aaa19 = p["reaction_mw0dd5a91d_d76c_494e_9dd6_57f2836aaa19_mw8ed5885f_774e_48a0_9338_fe8cdd512023"] * u[107]

    reaction_mwb205f533_4013_406b_8a4b_691ec3949555 = p["reaction_mwb205f533_4013_406b_8a4b_691ec3949555_mwa6ef5f75_f152_414d_811c_dd037d4b3ca1"] * u[65] * u[6] - p["reaction_mwb205f533_4013_406b_8a4b_691ec3949555_mwee51df1b_3f69_43f8_a1d5_5a8c5d0215f2"] * u[108]

    reaction_mw602726ea_89ee_41b8_bda6_e2811bb42c1d = p["reaction_mw602726ea_89ee_41b8_bda6_e2811bb42c1d_mw2e0b4751_7227_4815_bf6f_fa5e2370b1d3"] * u[108] * u[60] - p["reaction_mw602726ea_89ee_41b8_bda6_e2811bb42c1d_mwa8eec8e9_74b9_4afc_b6db_1116fe48e858"] * u[109]

    reaction_mwfab3a9ec_b094_44f0_bd59_12ac56ca1c99 = p["reaction_mwfab3a9ec_b094_44f0_bd59_12ac56ca1c99_mwc3426c7e_3452_4507_9189_4b83ab147bdd"] * u[109]

    reaction_mw4fceada8_6eb0_4230_a083_b2ab094d2961 = p["reaction_mw4fceada8_6eb0_4230_a083_b2ab094d2961_mw9cafad09_6002_46e1_8336_bb91c3716d70"] * u[73]

    # Species:   id = mwe2fff28d_182c_4a1c_9882_f17774c0958a; name = EGF; affected by kineticLaw
    du[1] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwa67e40c1_693d_4214_adc8_b2f2b71cef12))

    # Species:   id = mw93907b2d_53db_4080_9e3f_3eb304441ab9; name = EGFR; affected by kineticLaw
    du[2] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwa67e40c1_693d_4214_adc8_b2f2b71cef12) + (1.0 * reaction_mw47dee769_daa0_4af4_978a_5ab17e504c2f))

    # Species:   id = mw7eacabf9_d68c_491a_aba2_ec0809a8ecc8; name = EGF-EGFR; affected by kineticLaw
    du[3] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwa67e40c1_693d_4214_adc8_b2f2b71cef12) + (-1.0 * reaction_mw877cd1e3_b48b_42e8_ab23_682dd893fd9d) + (-1.0 * reaction_mw877cd1e3_b48b_42e8_ab23_682dd893fd9d))

    # Species:   id = mwa8f2e7b2_0927_4ab4_a817_dddc43bb4fa3; name = EGF-EGFR2; affected by kineticLaw
    du[4] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw877cd1e3_b48b_42e8_ab23_682dd893fd9d) + (-1.0 * reaction_mw413c6d45_ab23_4d3e_87b3_a8ed4629b923) + (1.0 * reaction_mw9544e67b_b6d0_4941_b7e0_ecd4f400a335) + (1.0 * reaction_mw7bb43f0a_c87e_41ff_8a43_cdf45c8f05e6) + (1.0 * reaction_mw4f89bf6c_8691_41a6_a1ac_13e6aa8c4b93) + (1.0 * reaction_mw642ac312_2ee7_4e66_8f3e_e2da2bb6412a))

    # Species:   id = mwbfcf6773_1915_432c_b1d2_1f246094cc74; name = pEGF-EGFR2; affected by kineticLaw
    du[5] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw413c6d45_ab23_4d3e_87b3_a8ed4629b923) + (-1.0 * reaction_mwf61e086d_0345_4d4c_b91d_0b105e543d04) + (-1.0 * reaction_mw91f49311_efdc_47c6_b8b8_a619e042d644) + (1.0 * reaction_mw486c5261_3d03_4589_a1e9_978b62ad2dfe) + (-1.0 * reaction_mw0e459167_515b_4c4d_8b67_bf0a5b3e9d61) + (-1.0 * reaction_mwd0d92dd4_81b7_4385_bfd7_5de82e193ecd) + (-1.0 * reaction_mw0a51fbf0_409b_4b45_b4ac_0220af4c4e3c) + (1.0 * reaction_mwcf9f1b1d_e19a_4fa8_85ba_8f17e2cec730) + (1.0 * reaction_mw4685274a_2b55_429f_927f_3fd863592af6) + (-1.0 * reaction_mw85e457d1_73f8_4236_bb61_a128d300003f) + (-1.0 * reaction_mw77484632_4e33_468a_9937_24e9bfd0e17d) + (1.0 * reaction_mwd3a36af9_3ccc_4bb1_9867_3b9823ba4ac8) + (-1.0 * reaction_mwe8647e48_f4a9_40f4_9b32_f89ded572e01) + (1.0 * reaction_mw65b9e026_bc6c_4c94_8b37_8b9acdf50c8a) + (-1.0 * reaction_mw1c9d29fa_bff4_4d2f_9d5f_f1791e4882a3))

    # Species:   id = mw19122f7d_f92e_4dc0_922f_6b681db65b0b; name = cbl; affected by kineticLaw
    du[6] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwbd8a133e_1b70_44e8_bef8_78b14141166b) + (1.0 * reaction_mw363a5271_1f51_4d5e_87a7_42ea25cb5657) + (-1.0 * reaction_mw6bee0112_92dc_4169_9109_2633772b3aa4) + (1.0 * reaction_mweb93165f_cf03_48f1_b035_59d79e324314) + (-1.0 * reaction_mw85e457d1_73f8_4236_bb61_a128d300003f) + (1.0 * reaction_mwc9b3b248_3290_452a_9b7c_8fdada3e6687) + (-1.0 * reaction_mwcb637bf1_7618_4d8a_ab5c_399145ecf1df) + (1.0 * reaction_mw0dd5a91d_d76c_494e_9dd6_57f2836aaa19) + (-1.0 * reaction_mwb205f533_4013_406b_8a4b_691ec3949555))

    # Species:   id = mw3c2e1b43_29ca_491a_93e9_c723a993d6fb; name = Shc; affected by kineticLaw
    du[7] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwf61e086d_0345_4d4c_b91d_0b105e543d04) + (1.0 * reaction_mweda6a945_fb5d_4d99_9958_11b2b2840308) + (1.0 * reaction_mwd4bf58ea_70c9_43ea_a831_1fcde130ba28))

    # Species:   id = mw5198d3c2_879c_4f0d_b4f8_cd40efe0b1cf; name = pEGF-EGFR2-Shc; affected by kineticLaw
    du[8] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwf61e086d_0345_4d4c_b91d_0b105e543d04) + (-1.0 * reaction_mw974c39f5_b82e_44b3_abec_7a724f46c526))

    # Species:   id = mwe57c3282_5935_405c_8c0b_7fadb7a5de17; name = SHP; affected by kineticLaw
    du[9] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw91f49311_efdc_47c6_b8b8_a619e042d644) + (1.0 * reaction_mw9544e67b_b6d0_4941_b7e0_ecd4f400a335) + (-1.0 * reaction_mw2cf8a809_63d8_4717_91fc_070516e6f3db) + (1.0 * reaction_mweda6a945_fb5d_4d99_9958_11b2b2840308) + (-1.0 * reaction_mw03998474_934b_4e4a_8c0c_ca359e402ac2) + (1.0 * reaction_mw7bb43f0a_c87e_41ff_8a43_cdf45c8f05e6) + (-1.0 * reaction_mwc52e0f9b_1e0c_46ca_8d18_f05ef4a080cb) + (1.0 * reaction_mw4f89bf6c_8691_41a6_a1ac_13e6aa8c4b93) + (-1.0 * reaction_mwc5aae1f8_52e4_4bcd_b044_3768f90b7b19) + (1.0 * reaction_mw642ac312_2ee7_4e66_8f3e_e2da2bb6412a))

    # Species:   id = mw954e8fcb_ac0a_459d_8878_f19080208a17; name = pEGF-EGFR2-SHP2; affected by kineticLaw
    du[10] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw91f49311_efdc_47c6_b8b8_a619e042d644) + (-1.0 * reaction_mw9544e67b_b6d0_4941_b7e0_ecd4f400a335))

    # Species:   id = mwa98802cb_c977_4fe0_9e67_5000904c2c36; name = pEGF-EGFR2-pShc; affected by kineticLaw
    du[11] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw974c39f5_b82e_44b3_abec_7a724f46c526) + (-1.0 * reaction_mw486c5261_3d03_4589_a1e9_978b62ad2dfe) + (-1.0 * reaction_mw4817365e_a33b_451f_bee1_de748377ede2) + (-1.0 * reaction_mw23a29b42_9813_4e46_b8ae_966e3215e6dc))

    # Species:   id = mwa0349407_8187_48fc_9e94_5698ccc4e06d; name = pShc; affected by kineticLaw
    du[12] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw486c5261_3d03_4589_a1e9_978b62ad2dfe) + (-1.0 * reaction_mw2cf8a809_63d8_4717_91fc_070516e6f3db) + (-1.0 * reaction_mwd4bf58ea_70c9_43ea_a831_1fcde130ba28) + (1.0 * reaction_mw7bb43f0a_c87e_41ff_8a43_cdf45c8f05e6) + (1.0 * reaction_mwcf9f1b1d_e19a_4fa8_85ba_8f17e2cec730) + (1.0 * reaction_mw363a5271_1f51_4d5e_87a7_42ea25cb5657))

    # Species:   id = mwf9999977_6f0e_4e35_9b73_75587f3448e9; name = pShc-SHP2; affected by kineticLaw
    du[13] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw2cf8a809_63d8_4717_91fc_070516e6f3db) + (-1.0 * reaction_mweda6a945_fb5d_4d99_9958_11b2b2840308))

    # Species:   id = mwf430a579_ecbf_48ba_80c2_06e455808f2a; name = Grb2; affected by kineticLaw
    du[14] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw4817365e_a33b_451f_bee1_de748377ede2) + (1.0 * reaction_mw7bb43f0a_c87e_41ff_8a43_cdf45c8f05e6) + (-1.0 * reaction_mwc5f121dc_d27d_4c3d_90f2_67d0adaf144a) + (-1.0 * reaction_mw0e459167_515b_4c4d_8b67_bf0a5b3e9d61) + (1.0 * reaction_mw4f89bf6c_8691_41a6_a1ac_13e6aa8c4b93) + (1.0 * reaction_mwcf9f1b1d_e19a_4fa8_85ba_8f17e2cec730) + (1.0 * reaction_mw4685274a_2b55_429f_927f_3fd863592af6))

    # Species:   id = mw504578d8_96c3_471f_8a7e_8c14e7535d3d; name = pEGF-EGFR2-pShc-Grb2; affected by kineticLaw
    du[15] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw4817365e_a33b_451f_bee1_de748377ede2) + (-1.0 * reaction_mw03998474_934b_4e4a_8c0c_ca359e402ac2) + (-1.0 * reaction_mwd9262331_e35a_4614_943a_89bcf8a492e3))

    # Species:   id = mw45ab688a_6467_4a3e_a779_2118fa84d69e; name = pEGF-EGFR2-pShc-Grb2-SHP2; affected by kineticLaw
    du[16] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw03998474_934b_4e4a_8c0c_ca359e402ac2) + (-1.0 * reaction_mw7bb43f0a_c87e_41ff_8a43_cdf45c8f05e6))

    # Species:   id = mw9dcaa655_a755_426e_a3fa_1ad7c3c45575; name = SOS; affected by kineticLaw
    du[17] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwd9262331_e35a_4614_943a_89bcf8a492e3) + (-1.0 * reaction_mwc5f121dc_d27d_4c3d_90f2_67d0adaf144a) + (-1.0 * reaction_mw35f71989_f89b_4440_b1a4_ebc7b4cc18b2) + (1.0 * reaction_mw8e331e43_16b4_478d_880b_d5a3244540e4))

    # Species:   id = mwfbda4e09_0cbb_49bc_ae69_f88b7a79ed21; name = pEGF-EGFR2-pShc-Grb2-SOS; affected by kineticLaw
    du[18] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwd9262331_e35a_4614_943a_89bcf8a492e3) + (1.0 * reaction_mw23a29b42_9813_4e46_b8ae_966e3215e6dc) + (-1.0 * reaction_mwbb77e3d6_6065_4344_9361_e30c03514f4e) + (1.0 * reaction_mw0bcfad86_59b9_42ff_bcb7_fbb44845049d) + (-1.0 * reaction_mw8dec1159_1925_45d9_af25_3cb709a5017c) + (-1.0 * reaction_mwbd8a133e_1b70_44e8_bef8_78b14141166b))

    # Species:   id = mwb1bc2058_e6d8_4680_9e6c_d27bb366cde0; name = pEGF-EGFR2-pShc-Grb2-SOS-cbl; affected by kineticLaw
    du[19] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwbd8a133e_1b70_44e8_bef8_78b14141166b) + (-1.0 * reaction_mw3a87ca5a_845d_4ac4_8806_e343cbbfc630))

    # Species:   id = mw1093b3af_1864_4ba3_a541_6009a9921282; name = Grb2-SOS; affected by kineticLaw
    du[20] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwc5f121dc_d27d_4c3d_90f2_67d0adaf144a) + (-1.0 * reaction_mw23a29b42_9813_4e46_b8ae_966e3215e6dc) + (-1.0 * reaction_mwd0d92dd4_81b7_4385_bfd7_5de82e193ecd) + (1.0 * reaction_mw363a5271_1f51_4d5e_87a7_42ea25cb5657) + (1.0 * reaction_mweb93165f_cf03_48f1_b035_59d79e324314))

    # Species:   id = mwd9462e5b_a272_4b66_ab66_fde9266b1a43; name = pEGF-EGFR2-Grb2; affected by kineticLaw
    du[21] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw0e459167_515b_4c4d_8b67_bf0a5b3e9d61) + (-1.0 * reaction_mwc52e0f9b_1e0c_46ca_8d18_f05ef4a080cb) + (-1.0 * reaction_mw35f71989_f89b_4440_b1a4_ebc7b4cc18b2))

    # Species:   id = mw925b938a_fe73_4664_ba6f_e72e57780891; name = pEGF-EGFR2-Grb2-SHP2; affected by kineticLaw
    du[22] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwc52e0f9b_1e0c_46ca_8d18_f05ef4a080cb) + (-1.0 * reaction_mw4f89bf6c_8691_41a6_a1ac_13e6aa8c4b93))

    # Species:   id = mwf8cc7834_bf4f_4ccd_8235_d0890badf0f6; name = pEGF-EGFR2-Grb2-SOS; affected by kineticLaw
    du[23] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw35f71989_f89b_4440_b1a4_ebc7b4cc18b2) + (1.0 * reaction_mwd0d92dd4_81b7_4385_bfd7_5de82e193ecd) + (1.0 * reaction_mwe9b50ac7_dac3_4eba_b1db_b3fd392d8fb7) + (-1.0 * reaction_mw934c3638_603e_4ff0_a763_68f9405fa01f) + (-1.0 * reaction_mwa5c135b4_77e2_4411_98e1_2000c39d4b30) + (-1.0 * reaction_mw6bee0112_92dc_4169_9109_2633772b3aa4))

    # Species:   id = mw481cd12b_61ba_44e5_93bf_8b88c6c4a4e7; name = pEGF-EGFR2-Grb2-SOS-cbl; affected by kineticLaw
    du[24] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw6bee0112_92dc_4169_9109_2633772b3aa4) + (-1.0 * reaction_mwbac9e6ff_2df1_45eb_b3f4_4cae74c64014))

    # Species:   id = mw8f5a7b5c_ca4c_4a4c_85b1_e5d640c426bf; name = Ras-GDP; affected by kineticLaw
    du[25] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwbb77e3d6_6065_4344_9361_e30c03514f4e) + (1.0 * reaction_mw921ee820_1dbb_4b5f_866c_87da620d8f89) + (-1.0 * reaction_mw934c3638_603e_4ff0_a763_68f9405fa01f) + (1.0 * reaction_mwf31259aa_32b7_4104_be70_045297b9a512) + (1.0 * reaction_mw652570eb_c9d3_499b_b877_61d360b10980))

    # Species:   id = mwf40d6176_abfc_4a30_886f_83a19fcffc48; name = pEGF-EGFR2-pShc-Grb2-SOS-Ras-GDP; affected by kineticLaw
    du[26] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwbb77e3d6_6065_4344_9361_e30c03514f4e) + (-1.0 * reaction_mw0bcfad86_59b9_42ff_bcb7_fbb44845049d))

    # Species:   id = mwa54a9c38_c98b_45e5_8432_4119fb777e44; name = Ras-GTP; affected by kineticLaw
    du[27] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw921ee820_1dbb_4b5f_866c_87da620d8f89) + (1.0 * reaction_mw0bcfad86_59b9_42ff_bcb7_fbb44845049d) + (1.0 * reaction_mwe9b50ac7_dac3_4eba_b1db_b3fd392d8fb7) + (-1.0 * reaction_mw3c617363_649b_4460_a694_36f7a3127a62) + (-1.0 * reaction_mw33baddbd_a23f_45bb_b126_0ba60bbf6c53) + (-1.0 * reaction_mw584a64d0_560a_4297_9882_80cb4eff73f3) + (1.0 * reaction_mw42c97708_4f85_45a8_9141_d0ae529409ca))

    # Species:   id = mw28464aad_8013_4a23_ae09_a406954859a6; name = pEGF-EGFR2-Grb2-SOS-Ras-GDP; affected by kineticLaw
    du[28] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwe9b50ac7_dac3_4eba_b1db_b3fd392d8fb7) + (1.0 * reaction_mw934c3638_603e_4ff0_a763_68f9405fa01f))

    # Species:   id = mw7cff9a0e_094d_498e_bf7f_7b162c61d63a; name = Ras-GAP; affected by kineticLaw
    du[29] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw3c617363_649b_4460_a694_36f7a3127a62) + (1.0 * reaction_mwf31259aa_32b7_4104_be70_045297b9a512) + (-1.0 * reaction_mw0a51fbf0_409b_4b45_b4ac_0220af4c4e3c) + (1.0 * reaction_mw642ac312_2ee7_4e66_8f3e_e2da2bb6412a))

    # Species:   id = mwdf82303e_323f_4c51_a858_56a59233cd98; name = Ras-GTP-Ras-GAP; affected by kineticLaw
    du[30] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw3c617363_649b_4460_a694_36f7a3127a62) + (-1.0 * reaction_mwf31259aa_32b7_4104_be70_045297b9a512))

    # Species:   id = mwd39388fd_4f85_4d1c_b2a3_37857c595a2d; name = pEGF-EGFR2-Ras-GAP; affected by kineticLaw
    du[31] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw0a51fbf0_409b_4b45_b4ac_0220af4c4e3c) + (-1.0 * reaction_mw33baddbd_a23f_45bb_b126_0ba60bbf6c53) + (1.0 * reaction_mw652570eb_c9d3_499b_b877_61d360b10980) + (-1.0 * reaction_mwc5aae1f8_52e4_4bcd_b044_3768f90b7b19))

    # Species:   id = mwd7bf31ba_b05c_4c45_bb2f_6a2468a2a507; name = pEGF-EGFR2-Ras-GAP-Ras-GTP; affected by kineticLaw
    du[32] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw33baddbd_a23f_45bb_b126_0ba60bbf6c53) + (-1.0 * reaction_mw652570eb_c9d3_499b_b877_61d360b10980))

    # Species:   id = mwbf5cb039_b830_4282_aa22_a3dda6272ec1; name = pEGF-EGFR2-Ras-GAP-SHP2; affected by kineticLaw
    du[33] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwc5aae1f8_52e4_4bcd_b044_3768f90b7b19) + (-1.0 * reaction_mw642ac312_2ee7_4e66_8f3e_e2da2bb6412a))

    # Species:   id = mw66ac98c4_7e7b_4071_954d_43eb17584220; name = Raf1; affected by kineticLaw
    du[34] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw584a64d0_560a_4297_9882_80cb4eff73f3) + (1.0 * reaction_mw87711dc1_43d7_40fc_b9e9_a24e2f92419d))

    # Species:   id = mw83de7813_4941_45a6_a320_a551165bf22a; name = Raf1-Ras-GTP; affected by kineticLaw
    du[35] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw584a64d0_560a_4297_9882_80cb4eff73f3) + (-1.0 * reaction_mw42c97708_4f85_45a8_9141_d0ae529409ca))

    # Species:   id = mwaff92910_ed3d_40b9_a29c_e4866167e828; name = Raf1active; affected by kineticLaw
    du[36] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw42c97708_4f85_45a8_9141_d0ae529409ca) + (-1.0 * reaction_mwaa65a34e_fabf_4d6d_ae0b_f1d08b068f33) + (1.0 * reaction_mw1bd186cf_4762_480a_b70d_d7a775462398) + (-1.0 * reaction_mwf5573ddf_ad7f_478a_a784_557a9cddaaf2) + (1.0 * reaction_mwb49058ff_2997_4187_abe7_4dce4ccf6ff4) + (-1.0 * reaction_mw9c208e18_c70d_4231_af0b_ad17cd0bba2d) + (-1.0 * reaction_mw950485f2_4463_4309_a4e4_cc81d16ffb7f) + (1.0 * reaction_mw62f71309_e066_47d2_9b99_01f78a51c218))

    # Species:   id = mw0834731b_0477_4217_a53b_30cef851191b; name = MEK; affected by kineticLaw
    du[37] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwaa65a34e_fabf_4d6d_ae0b_f1d08b068f33) + (1.0 * reaction_mwa4b69c77_6226_46da_b78c_3e6027d0be41))

    # Species:   id = mw4628f984_eb87_4922_9760_4975095ce6eb; name = Raf1active-MEK; affected by kineticLaw
    du[38] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwaa65a34e_fabf_4d6d_ae0b_f1d08b068f33) + (-1.0 * reaction_mw1bd186cf_4762_480a_b70d_d7a775462398))

    # Species:   id = mw9b25f809_18a1_4c14_8f4b_cf18e6d93c28; name = pMEK; affected by kineticLaw
    du[39] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw1bd186cf_4762_480a_b70d_d7a775462398) + (-1.0 * reaction_mwf5573ddf_ad7f_478a_a784_557a9cddaaf2) + (1.0 * reaction_mw40950d59_1012_4361_8418_73e25758e367) + (-1.0 * reaction_mwbfa79c95_487d_4c6f_b437_9e579451a419))

    # Species:   id = mw12ba4000_d452_420c_be63_96d2848aca32; name = Raf1active-pMEK; affected by kineticLaw
    du[40] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwf5573ddf_ad7f_478a_a784_557a9cddaaf2) + (-1.0 * reaction_mwb49058ff_2997_4187_abe7_4dce4ccf6ff4))

    # Species:   id = mwf816df4c_4593_4d23_990f_0d7c15ddde5d; name = ppMEK; affected by kineticLaw
    du[41] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwb49058ff_2997_4187_abe7_4dce4ccf6ff4) + (-1.0 * reaction_mw8301b154_9463_4516_b4c5_c8f8b68691fe) + (1.0 * reaction_mwf95f743d_6108_49fe_8ffd_bdcc1a9f9a8d) + (-1.0 * reaction_mw51d9d6b8_f0c0_4763_9d11_9be61b5cf5c9) + (1.0 * reaction_mw6fd24d16_f57d_46c6_82f5_3f00759fa16b) + (-1.0 * reaction_mw4b445876_bdce_42d0_867b_fd3c74128a6b))

    # Species:   id = mw7e23b961_186b_47a0_a8b5_5e9957766792; name = ERK; affected by kineticLaw
    du[42] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw8301b154_9463_4516_b4c5_c8f8b68691fe) + (1.0 * reaction_mwcc31b497_6c50_446c_bbc2_6c5739507252))

    # Species:   id = mwcedf8ecd_67bd_4b91_aa04_d58782dec2a4; name = ppMEK-ERK; affected by kineticLaw
    du[43] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw8301b154_9463_4516_b4c5_c8f8b68691fe) + (-1.0 * reaction_mwf95f743d_6108_49fe_8ffd_bdcc1a9f9a8d))

    # Species:   id = mwcc894c94_0ddf_42cc_913e_cdcc4d471d94; name = pERK; affected by kineticLaw
    du[44] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwf95f743d_6108_49fe_8ffd_bdcc1a9f9a8d) + (-1.0 * reaction_mw51d9d6b8_f0c0_4763_9d11_9be61b5cf5c9) + (1.0 * reaction_mw61305f93_7b2d_4a2d_8d16_f7be026d8671) + (-1.0 * reaction_mw1d8c2435_bb85_4352_a25f_82033250579e))

    # Species:   id = mw6cb74b27_ffef_49bb_8ffb_622d552caa9e; name = ppMEK-pERK; affected by kineticLaw
    du[45] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw51d9d6b8_f0c0_4763_9d11_9be61b5cf5c9) + (-1.0 * reaction_mw6fd24d16_f57d_46c6_82f5_3f00759fa16b))

    # Species:   id = mwd784228d_0cb5_468a_ac70_02d8f04b3d9c; name = ppERK; affected by kineticLaw
    du[46] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw6fd24d16_f57d_46c6_82f5_3f00759fa16b) + (-1.0 * reaction_mwf8bb22e2_5aa3_4c25_a022_a266b1856a48) + (-1.0 * reaction_mw8dec1159_1925_45d9_af25_3cb709a5017c) + (1.0 * reaction_mwcf9f1b1d_e19a_4fa8_85ba_8f17e2cec730) + (-1.0 * reaction_mwa5c135b4_77e2_4411_98e1_2000c39d4b30) + (1.0 * reaction_mw4685274a_2b55_429f_927f_3fd863592af6))

    # Species:   id = mwbaaeb210_4806_4076_9d60_219f4ed945b6; name = Pase; affected by kineticLaw
    du[47] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw9c208e18_c70d_4231_af0b_ad17cd0bba2d) + (1.0 * reaction_mw87711dc1_43d7_40fc_b9e9_a24e2f92419d))

    # Species:   id = mw19a33ad5_5ba4_46c7_84eb_c1287f02bcd5; name = Raf1active-Pase; affected by kineticLaw
    du[48] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw9c208e18_c70d_4231_af0b_ad17cd0bba2d) + (-1.0 * reaction_mw87711dc1_43d7_40fc_b9e9_a24e2f92419d))

    # Species:   id = mwf9e2a044_7774_400b_a74e_a111b4a21f30; name = Pase2; affected by kineticLaw
    du[49] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw4b445876_bdce_42d0_867b_fd3c74128a6b) + (1.0 * reaction_mw40950d59_1012_4361_8418_73e25758e367) + (-1.0 * reaction_mwbfa79c95_487d_4c6f_b437_9e579451a419) + (1.0 * reaction_mwa4b69c77_6226_46da_b78c_3e6027d0be41))

    # Species:   id = mwcb572fe2_c3ac_40e7_8141_da7d55fce18a; name = ppMEK-Pase2; affected by kineticLaw
    du[50] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw4b445876_bdce_42d0_867b_fd3c74128a6b) + (-1.0 * reaction_mw40950d59_1012_4361_8418_73e25758e367))

    # Species:   id = mwa0acc0ac_5fac_4a42_a3be_e36db44994b0; name = pMEK-Pase2; affected by kineticLaw
    du[51] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwbfa79c95_487d_4c6f_b437_9e579451a419) + (-1.0 * reaction_mwa4b69c77_6226_46da_b78c_3e6027d0be41))

    # Species:   id = mwd087f76b_65dc_47f1_ba21_c43774457686; name = Pase3; affected by kineticLaw
    du[52] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwf8bb22e2_5aa3_4c25_a022_a266b1856a48) + (1.0 * reaction_mw61305f93_7b2d_4a2d_8d16_f7be026d8671) + (1.0 * reaction_mwcc31b497_6c50_446c_bbc2_6c5739507252) + (-1.0 * reaction_mw1d8c2435_bb85_4352_a25f_82033250579e))

    # Species:   id = mw35f5adaa_d1c0_433c_817d_76e317f4cb15; name = pERK-Pase3; affected by kineticLaw
    du[53] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwcc31b497_6c50_446c_bbc2_6c5739507252) + (1.0 * reaction_mw1d8c2435_bb85_4352_a25f_82033250579e))

    # Species:   id = mwa7e3103a_6394_472c_b0f4_8ed527f68604; name = ppERK-Pase3; affected by kineticLaw
    du[54] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwf8bb22e2_5aa3_4c25_a022_a266b1856a48) + (-1.0 * reaction_mw61305f93_7b2d_4a2d_8d16_f7be026d8671))

    # Species:   id = mw5babe3d5_a9af_4dfd_ac01_35474ef64af2; name = ppERK-pEGF-EGFR2-pShc-Grb2-SOS; affected by kineticLaw
    du[55] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw8dec1159_1925_45d9_af25_3cb709a5017c) + (-1.0 * reaction_mwcf9f1b1d_e19a_4fa8_85ba_8f17e2cec730))

    # Species:   id = mw31ac308f_da36_4f73_830f_67f3e5b945d9; name = pSOS; affected by kineticLaw
    du[56] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwcf9f1b1d_e19a_4fa8_85ba_8f17e2cec730) + (1.0 * reaction_mw4685274a_2b55_429f_927f_3fd863592af6) + (-1.0 * reaction_mw8e331e43_16b4_478d_880b_d5a3244540e4))

    # Species:   id = mw31261227_9cd6_4059_a0bb_04dbf4888080; name = ppERK-pEGF-EGFR2-Grb2-SOS; affected by kineticLaw
    du[57] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwa5c135b4_77e2_4411_98e1_2000c39d4b30) + (-1.0 * reaction_mw4685274a_2b55_429f_927f_3fd863592af6))

    # Species:   id = mw0a0ca6ba_cb28_44c7_a0c0_1593cb720966; name = ProEGFR; affected by kineticLaw
    du[58] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw47dee769_daa0_4af4_978a_5ab17e504c2f))

    # Species:   id = mw06b8aada_c92a_48eb_8ee7_af3778cfe62f; name = pEGF-EGFR2-pShc-Grb2-SOS-cbl-EPn; affected by kineticLaw
    du[59] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw3a87ca5a_845d_4ac4_8806_e343cbbfc630) + (-1.0 * reaction_mw363a5271_1f51_4d5e_87a7_42ea25cb5657))

    # Species:   id = mwb2366216_0b3c_4f28_8303_fec92c68dd57; name = EPn; affected by kineticLaw
    du[60] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw3a87ca5a_845d_4ac4_8806_e343cbbfc630) + (1.0 * reaction_mw363a5271_1f51_4d5e_87a7_42ea25cb5657) + (-1.0 * reaction_mwbac9e6ff_2df1_45eb_b3f4_4cae74c64014) + (1.0 * reaction_mweb93165f_cf03_48f1_b035_59d79e324314) + (-1.0 * reaction_mw6b159c8f_eee0_4337_b711_2e230c9e2cf6) + (1.0 * reaction_mwc9b3b248_3290_452a_9b7c_8fdada3e6687) + (-1.0 * reaction_mw401dde7e_c0a1_4780_b6cc_8f98681c862e) + (1.0 * reaction_mw0dd5a91d_d76c_494e_9dd6_57f2836aaa19) + (-1.0 * reaction_mw602726ea_89ee_41b8_bda6_e2811bb42c1d) + (1.0 * reaction_mwfab3a9ec_b094_44f0_bd59_12ac56ca1c99))

    # Species:   id = mw1d5948e7_5504_4224_9d71_227911b4f1ee; name = pEGF-EGFR2-Grb2-SOS-cbl-EPn; affected by kineticLaw
    du[61] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwbac9e6ff_2df1_45eb_b3f4_4cae74c64014) + (-1.0 * reaction_mweb93165f_cf03_48f1_b035_59d79e324314))

    # Species:   id = mwec1b368b_8f73_47eb_9636_9956389836eb; name = pEGF-EGFR2-cbl; affected by kineticLaw
    du[62] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw85e457d1_73f8_4236_bb61_a128d300003f) + (-1.0 * reaction_mw6b159c8f_eee0_4337_b711_2e230c9e2cf6))

    # Species:   id = mwa455ec7e_1a12_4659_95a2_a5695d09ca60; name = pEGF-EGFR2-cbl-EPn; affected by kineticLaw
    du[63] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw6b159c8f_eee0_4337_b711_2e230c9e2cf6) + (-1.0 * reaction_mwc9b3b248_3290_452a_9b7c_8fdada3e6687))

    # Species:   id = mw2ba1db9a_4483_44fa_a3a2_b4a5ea66898c; name = PI3K; affected by kineticLaw
    du[64] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw77484632_4e33_468a_9937_24e9bfd0e17d) + (1.0 * reaction_mwd15926b3_069a_4b16_a6fc_c0c15083d621) + (1.0 * reaction_mwfab3a9ec_b094_44f0_bd59_12ac56ca1c99))

    # Species:   id = mw0dc4e5eb_4366_4799_bebc_cfcffe5c06f5; name = pEGF-EGFR2-PI3K; affected by kineticLaw
    du[65] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw77484632_4e33_468a_9937_24e9bfd0e17d) + (-1.0 * reaction_mw2c5858f3_0988_49b0_a94a_057853b84e91) + (-1.0 * reaction_mwd3a36af9_3ccc_4bb1_9867_3b9823ba4ac8) + (-1.0 * reaction_mwb205f533_4013_406b_8a4b_691ec3949555))

    # Species:   id = mw1e591998_65c0_484e_8a3b_537a38d94de1; name = pEGF-EGFR2-pPI3K; affected by kineticLaw
    du[66] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw2c5858f3_0988_49b0_a94a_057853b84e91))

    # Species:   id = mw78e207c4_4faf_4b48_8e22_1ee666e9cc4c; name = pPI3K; affected by kineticLaw
    du[67] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwd3a36af9_3ccc_4bb1_9867_3b9823ba4ac8) + (-1.0 * reaction_mw9f000f29_2512_4d4a_9dd9_e59aaf296d31) + (-1.0 * reaction_mw3a5e0932_d50f_4fe6_b8cb_0ad649f305b0) + (1.0 * reaction_mw5dcc8719_3180_4bd0_8797_08e256131961))

    # Species:   id = mwfc4a9c3d_3ebb_4033_8b7d_f4d7613d2078; name = TP4; affected by kineticLaw
    du[68] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw9f000f29_2512_4d4a_9dd9_e59aaf296d31) + (1.0 * reaction_mwd15926b3_069a_4b16_a6fc_c0c15083d621))

    # Species:   id = mwbd6bb050_89bd_41df_8cea_d2e1fb77bafe; name = TP4-pPI3K; affected by kineticLaw
    du[69] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw9f000f29_2512_4d4a_9dd9_e59aaf296d31) + (-1.0 * reaction_mw837b5ad7_4a8c_4c55_94ff_0fdd63048044))

    # Species:   id = mw7033dfd6_53c5_433b_a132_f8cb34dea20f; name = TP4-PI3K; affected by kineticLaw
    du[70] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw837b5ad7_4a8c_4c55_94ff_0fdd63048044) + (-1.0 * reaction_mwd15926b3_069a_4b16_a6fc_c0c15083d621))

    # Species:   id = mwb561d9f3_a9ed_4bdb_8d40_87be5cc3237a; name = PIP2; affected by kineticLaw
    du[71] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw3a5e0932_d50f_4fe6_b8cb_0ad649f305b0) + (1.0 * reaction_mw4fceada8_6eb0_4230_a083_b2ab094d2961))

    # Species:   id = mw014cc419_b720_4b90_9192_2ec6e706c87d; name = pPI3K-PIP2; affected by kineticLaw
    du[72] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw3a5e0932_d50f_4fe6_b8cb_0ad649f305b0) + (-1.0 * reaction_mw5dcc8719_3180_4bd0_8797_08e256131961))

    # Species:   id = mwd7f41594_8377_4e2e_9528_45d5a82ffdb4; name = PIP3; affected by kineticLaw
    du[73] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw5dcc8719_3180_4bd0_8797_08e256131961) + (-1.0 * reaction_mw376b0685_ef73_4fcc_94af_2ada24cf8a8b) + (1.0 * reaction_mw12311a84_3f8d_40c6_8b14_961a8a58d1b6) + (-1.0 * reaction_mw4fceada8_6eb0_4230_a083_b2ab094d2961))

    # Species:   id = mwcef73e0e_d195_4077_ae71_723664ee1602; name = Akt; affected by kineticLaw
    du[74] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw376b0685_ef73_4fcc_94af_2ada24cf8a8b) + (1.0 * reaction_mw2698f402_d00b_451e_8b22_93a322fe9a92))

    # Species:   id = mw62bf5275_ce02_4e86_b3b6_3f87a335e1de; name = Aktm; affected by kineticLaw
    du[75] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw376b0685_ef73_4fcc_94af_2ada24cf8a8b) + (-1.0 * reaction_mwcc7cfa9c_4945_403a_938e_b237c371a5ef) + (1.0 * reaction_mw362ca1b3_224a_42fb_a14b_6ff467748a5e))

    # Species:   id = mw6e01967b_3e2a_433d_bec6_9f9cf3ba243c; name = PDK1; affected by kineticLaw
    du[76] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwcc7cfa9c_4945_403a_938e_b237c371a5ef) + (1.0 * reaction_mw31369230_1f14_45bd_be02_a44a275c6e31))

    # Species:   id = mw6353aa36_d4a4_4254_8a1f_1f7f571d4233; name = Aktm-PDK1; affected by kineticLaw
    du[77] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwcc7cfa9c_4945_403a_938e_b237c371a5ef) + (-1.0 * reaction_mw98da32e0_b061_40c5_9d32_40744134f3fa) + (1.0 * reaction_mw4a334f7d_9bce_4690_b623_a427ed66a174))

    # Species:   id = mwc1935afc_56b1_4a87_923c_ae6d82455d80; name = pAktm-PDK1; affected by kineticLaw
    du[78] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw98da32e0_b061_40c5_9d32_40744134f3fa) + (-1.0 * reaction_mw31369230_1f14_45bd_be02_a44a275c6e31) + (-1.0 * reaction_mw3994e898_7232_4b70_9c58_b3476e8655f5))

    # Species:   id = mw3d81860d_d786_4fcc_b8bb_64f1a2d7739d; name = pAktm; affected by kineticLaw
    du[79] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw31369230_1f14_45bd_be02_a44a275c6e31) + (-1.0 * reaction_mw12311a84_3f8d_40c6_8b14_961a8a58d1b6) + (-1.0 * reaction_mwc5e0c166_6a3a_4913_9ed1_dafe97bdb371))

    # Species:   id = mw16796ffe_4764_4a9f_942e_149f42c1cd28; name = pAkt; affected by kineticLaw
    du[80] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw12311a84_3f8d_40c6_8b14_961a8a58d1b6) + (-1.0 * reaction_mw028e8b3e_b531_4466_9c3a_e3fcf7fc9be9))

    # Species:   id = mwa6e82fc9_a0ce_461c_93c8_17f3c807c1a1; name = pAkt-Takt; affected by kineticLaw
    du[81] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwf3d393e9_ae09_4eab_a39a_ed0eef0f54bc) + (1.0 * reaction_mw028e8b3e_b531_4466_9c3a_e3fcf7fc9be9))

    # Species:   id = mw236a3250_4c96_4f6e_b94c_ab3d12852801; name = Akt-Takt; affected by kineticLaw
    du[82] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwf3d393e9_ae09_4eab_a39a_ed0eef0f54bc) + (-1.0 * reaction_mw2698f402_d00b_451e_8b22_93a322fe9a92))

    # Species:   id = mw11a8b702_b8ac_4513_b4aa_063e51089812; name = Takt; affected by kineticLaw
    du[83] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw2698f402_d00b_451e_8b22_93a322fe9a92) + (-1.0 * reaction_mw028e8b3e_b531_4466_9c3a_e3fcf7fc9be9) + (-1.0 * reaction_mwc5e0c166_6a3a_4913_9ed1_dafe97bdb371) + (1.0 * reaction_mw362ca1b3_224a_42fb_a14b_6ff467748a5e) + (-1.0 * reaction_mw3994e898_7232_4b70_9c58_b3476e8655f5) + (1.0 * reaction_mw4a334f7d_9bce_4690_b623_a427ed66a174))

    # Species:   id = mw1a0cb97a_b657_430b_963c_92217f643081; name = pAktm-Takt; affected by kineticLaw
    du[84] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwc5e0c166_6a3a_4913_9ed1_dafe97bdb371) + (-1.0 * reaction_mw94b3bae0_4da9_4358_a5ac_a46a5cbf621b))

    # Species:   id = mw9b937ca3_0d82_46d5_8f5a_0f9701002797; name = Aktm-Takt; affected by kineticLaw
    du[85] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw94b3bae0_4da9_4358_a5ac_a46a5cbf621b) + (-1.0 * reaction_mw362ca1b3_224a_42fb_a14b_6ff467748a5e))

    # Species:   id = mw57a44eb0_ace7_4294_905a_219e87d3c281; name = pAktm-PDK1-Takt; affected by kineticLaw
    du[86] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw3994e898_7232_4b70_9c58_b3476e8655f5) + (-1.0 * reaction_mw75acd2d1_3fdf_4c3f_8d99_6d62f825d5e2))

    # Species:   id = mwd746a5d5_5e65_4a4c_9f84_0e4a3cb7d2fc; name = Aktm-PDK1-Takt; affected by kineticLaw
    du[87] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw75acd2d1_3fdf_4c3f_8d99_6d62f825d5e2) + (-1.0 * reaction_mw4a334f7d_9bce_4690_b623_a427ed66a174))

    # Species:   id = mwa6994523_5d45_4000_af0c_3e94073bf183, name = pAkt_total, defined in a rule 	du[88] = u[88]

    # Species:   id = mwdf92bdc0_f426_45b0_9ad0_876521f41312; name = pRaf1active; affected by kineticLaw
    du[89] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw950485f2_4463_4309_a4e4_cc81d16ffb7f) + (-1.0 * reaction_mw62f71309_e066_47d2_9b99_01f78a51c218))

    # Species:   id = mw13abe2a6_9905_40e5_8c23_3fc8834b572a; name = STAT3c; affected by kineticLaw
    du[90] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwe8647e48_f4a9_40f4_9b32_f89ded572e01) + (1.0 * reaction_mwe9988e4a_083c_4f8e_b154_3e599c9307b0) + (-1.0 * reaction_mw177fa7b0_f0be_4c3e_8b47_2ac4e13159a2) + (1.0 * reaction_mwd189238c_e8f9_40be_b4ea_18a42bba1b4f) + (1.0 * reaction_mw0dd5a91d_d76c_494e_9dd6_57f2836aaa19))

    # Species:   id = mw2fd710a6_7fe2_4484_bca6_59c187bade8b; name = pEGF-EGFR2-STAT3c; affected by kineticLaw
    du[91] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwe8647e48_f4a9_40f4_9b32_f89ded572e01) + (-1.0 * reaction_mw65b9e026_bc6c_4c94_8b37_8b9acdf50c8a) + (-1.0 * reaction_mwcb637bf1_7618_4d8a_ab5c_399145ecf1df))

    # Species:   id = mwb6a9aa2c_62e7_410f_9c33_dbe36dfcc4af; name = pSTAT3c; affected by kineticLaw
    du[92] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw65b9e026_bc6c_4c94_8b37_8b9acdf50c8a) + (-1.0 * reaction_mw1c9d29fa_bff4_4d2f_9d5f_f1791e4882a3) + (-1.0 * reaction_mwad97bd5a_3dae_49d9_990b_2e6574740618) + (-1.0 * reaction_mwf8bacf1a_6c1a_49b6_b344_2d3bd404a735) + (-1.0 * reaction_mwf8bacf1a_6c1a_49b6_b344_2d3bd404a735) + (-1.0 * reaction_mw177fa7b0_f0be_4c3e_8b47_2ac4e13159a2))

    # Species:   id = mw341082a0_8017_4cc7_9d00_b1211a196072; name = pEGF-EGFR2-pSTAT3c; affected by kineticLaw
    du[93] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw1c9d29fa_bff4_4d2f_9d5f_f1791e4882a3))

    # Species:   id = mwcea1f1c1_2f85_4af1_98ea_ef14cf580c09; name = PP1; affected by kineticLaw
    du[94] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwad97bd5a_3dae_49d9_990b_2e6574740618) + (1.0 * reaction_mwe9988e4a_083c_4f8e_b154_3e599c9307b0) + (-1.0 * reaction_mwc9b945cf_3a14_4bd9_b253_7064498c75e2) + (1.0 * reaction_mw75c6078f_fb76_4ca9_9fdd_e221e3ba57ad))

    # Species:   id = mwdc34472c_a6f9_4002_951d_e0e8da64eb42; name = pSTAT3c-PP1; affected by kineticLaw
    du[95] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwad97bd5a_3dae_49d9_990b_2e6574740618) + (-1.0 * reaction_mwe9988e4a_083c_4f8e_b154_3e599c9307b0))

    # Species:   id = mw472d5cb9_120e_4f60_bbae_1ae2552837dd; name = pSTAT3c-pSTAT3c-PP1; affected by kineticLaw
    du[96] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwc9b945cf_3a14_4bd9_b253_7064498c75e2) + (-1.0 * reaction_mw75c6078f_fb76_4ca9_9fdd_e221e3ba57ad))

    # Species:   id = mw4f575c55_7dff_45d7_94ad_cda9621d5b63; name = pSTAT3c-pSTAT3c; affected by kineticLaw
    du[97] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwf8bacf1a_6c1a_49b6_b344_2d3bd404a735) + (-1.0 * reaction_mwc9b945cf_3a14_4bd9_b253_7064498c75e2) + (-1.0 * reaction_mwec4127b5_6bcf_4128_aff4_a6b3c470f690))

    # Species:   id = mwd2c465fb_eea7_499a_8ea4_f318a64cb9ee; name = STAT3c-pSTAT3c; affected by kineticLaw
    du[98] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw75c6078f_fb76_4ca9_9fdd_e221e3ba57ad) + (1.0 * reaction_mw177fa7b0_f0be_4c3e_8b47_2ac4e13159a2))

    # Species:   id = mw4110f531_7513_4786_8896_7c9d969ff558; name = pSTAT3n-pSTAT3n; affected by kineticLaw
    du[99] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwec4127b5_6bcf_4128_aff4_a6b3c470f690) + (1.0 * reaction_mw5c806b00_59a1_491e_99a1_2c932b2d5d7a) + (-1.0 * reaction_mw26fdabae_323b_4a78_b134_4c2eb70ea6a7))

    # Species:   id = mwe3fd7f65_b0d1_44d9_b6f3_d2f7d332f664; name = pSTAT3n; affected by kineticLaw
    du[100] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw5c806b00_59a1_491e_99a1_2c932b2d5d7a) + (-1.0 * reaction_mw5c806b00_59a1_491e_99a1_2c932b2d5d7a) + (-1.0 * reaction_mwc38a99c8_74cf_49f2_a16b_f6610ca1a0a7) + (-1.0 * reaction_mw45d92b79_0656_4795_87d0_7a465949ca43))

    # Species:   id = mw0e1be972_fded_4bff_a93d_091ec942485f; name = PP2; affected by kineticLaw
    du[101] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mw26fdabae_323b_4a78_b134_4c2eb70ea6a7) + (1.0 * reaction_mw3b0c171c_6d60_41ca_8193_83cd5e6c188c) + (-1.0 * reaction_mw45d92b79_0656_4795_87d0_7a465949ca43) + (1.0 * reaction_mwb71945c2_03a8_4fad_a995_e1caeee98525))

    # Species:   id = mw0facb8f2_95cf_4ddf_a959_b24ba64f320b; name = pSTAT3n-pSTAT3n-PP2; affected by kineticLaw
    du[102] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw26fdabae_323b_4a78_b134_4c2eb70ea6a7) + (-1.0 * reaction_mw3b0c171c_6d60_41ca_8193_83cd5e6c188c))

    # Species:   id = mw9686f53e_d343_45fd_b441_9c992219546a; name = STAT3n-pSTAT3n; affected by kineticLaw
    du[103] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw3b0c171c_6d60_41ca_8193_83cd5e6c188c) + (1.0 * reaction_mwc38a99c8_74cf_49f2_a16b_f6610ca1a0a7))

    # Species:   id = mw960bddeb_e567_46dd_b2f3_ed5e6a5c7972; name = STAT3n; affected by kineticLaw
    du[104] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((-1.0 * reaction_mwc38a99c8_74cf_49f2_a16b_f6610ca1a0a7) + (1.0 * reaction_mwb71945c2_03a8_4fad_a995_e1caeee98525) + (-1.0 * reaction_mwd189238c_e8f9_40be_b4ea_18a42bba1b4f))

    # Species:   id = mw8c85ff7f_6368_4b11_a2ed_ce83481b55e6; name = pSTAT3n-PP2; affected by kineticLaw
    du[105] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw45d92b79_0656_4795_87d0_7a465949ca43) + (-1.0 * reaction_mwb71945c2_03a8_4fad_a995_e1caeee98525))

    # Species:   id = mw548c81c2_c626_4df8_9177_a1a6fc3d4ce8; name = pEGF-EGFR2-STAT3c-cbl; affected by kineticLaw
    du[106] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwcb637bf1_7618_4d8a_ab5c_399145ecf1df) + (-1.0 * reaction_mw401dde7e_c0a1_4780_b6cc_8f98681c862e))

    # Species:   id = mw142e6dc4_ec15_459d_a184_6b20be04f08d; name = pEGF-EGFR2-STAT3c-cbl-EPn; affected by kineticLaw
    du[107] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw401dde7e_c0a1_4780_b6cc_8f98681c862e) + (-1.0 * reaction_mw0dd5a91d_d76c_494e_9dd6_57f2836aaa19))

    # Species:   id = mw2c47ae3f_06d9_40ec_a252_535db0ae5caa; name = pEGF-EGFR2-PI3K-cbl; affected by kineticLaw
    du[108] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mwb205f533_4013_406b_8a4b_691ec3949555) + (-1.0 * reaction_mw602726ea_89ee_41b8_bda6_e2811bb42c1d))

    # Species:   id = mwd32d108b_49c2_4df2_9b67_d6c6b84f54b9; name = pEGF-EGFR2-PI3K-cbl-EPn; affected by kineticLaw
    du[109] = (1 / (p["compartment_mw1637dd35_5f09_4a8d_bb7f_58717cdf1612"])) * ((1.0 * reaction_mw602726ea_89ee_41b8_bda6_e2811bb42c1d) + (-1.0 * reaction_mwfab3a9ec_b094_44f0_bd59_12ac56ca1c99))

end

u0=zeros(109)
u0[1] = 0.0081967
u0[2] = 0.3
u0[3] = 0.0
u0[4] = 0.0
u0[5] = 0.0
u0[6] = 0.8
u0[7] = 1.0
u0[8] = 0.0
u0[9] = 0.1
u0[10] = 0.0
u0[11] = 0.0
u0[12] = 0.0
u0[13] = 0.0
u0[14] = 1.0
u0[15] = 0.0
u0[16] = 0.0
u0[17] = 0.3
u0[18] = 0.0
u0[19] = 0.0
u0[20] = 0.0
u0[21] = 0.0
u0[22] = 0.0
u0[23] = 0.0
u0[24] = 0.0
u0[25] = 0.15
u0[26] = 0.0
u0[27] = 0.0
u0[28] = 0.0
u0[29] = 0.1
u0[30] = 0.0
u0[31] = 0.0
u0[32] = 0.0
u0[33] = 0.0
u0[34] = 0.5
u0[35] = 0.0
u0[36] = 0.0
u0[37] = 0.68
u0[38] = 0.0
u0[39] = 0.0
u0[40] = 0.0
u0[41] = 0.0
u0[42] = 0.4
u0[43] = 0.0
u0[44] = 0.0
u0[45] = 0.0
u0[46] = 0.0
u0[47] = 0.5
u0[48] = 0.0
u0[49] = 0.02
u0[50] = 0.0
u0[51] = 0.0
u0[52] = 0.002
u0[53] = 0.0
u0[54] = 0.0
u0[55] = 0.0
u0[56] = 0.0
u0[57] = 0.0
u0[58] = 1.0
u0[59] = 0.0
u0[60] = 0.5
u0[61] = 0.0
u0[62] = 0.0
u0[63] = 0.0
u0[64] = 0.2
u0[65] = 0.0
u0[66] = 0.0
u0[67] = 0.0
u0[68] = 0.2
u0[69] = 0.0
u0[70] = 0.0
u0[71] = 0.5
u0[72] = 0.0
u0[73] = 0.0
u0[74] = 0.1
u0[75] = 0.0
u0[76] = 0.1
u0[77] = 0.0
u0[78] = 0.0
u0[79] = 0.0
u0[80] = 0.0
u0[81] = 0.0
u0[82] = 0.0
u0[83] = 0.1
u0[84] = 0.0
u0[85] = 0.0
u0[86] = 0.0
u0[87] = 0.0
u0[88] = 0.0
u0[89] = 0.0
u0[90] = 1.0
u0[91] = 0.0
u0[92] = 0.0
u0[93] = 0.0
u0[94] = 0.5
u0[95] = 0.0
u0[96] = 0.0
u0[97] = 0.0
u0[98] = 0.0
u0[99] = 0.0
u0[100] = 0.0
u0[101] = 0.6
u0[102] = 0.0
u0[103] = 0.0
u0[104] = 0.0
u0[105] = 0.0
u0[106] = 0.0
u0[107] = 0.0
u0[108] = 0.0
u0[109] = 0.0

tspan = (0.0,100.0)

prob = ODEProblem{true,SciMLBase.FullSpecialize}(sbml_model!, u0, tspan, par)

sys = modelingtoolkitize(prob)

sys = structural_simplify(sys)


const to = TimerOutput()

@timeit to "ODEProb No Jac" oprob = ODEProblem{true,SciMLBase.FullSpecialize}(sys, Float64[], tspan, Float64[])
@timeit to "ODEProb DenseJac" densejacprob = ODEProblem{true,SciMLBase.FullSpecialize}(sys, Float64[], tspan, Float64[], jac=true)

ODEProblem with uType Vector{Float64} and tType Float64. In-place: true
timespan: (0.0, 100.0)
u0: 109-element Vector{Float64}:
 0.0081967
 0.3
 0.0
 0.0
 0.0
 0.8
 1.0
 0.0
 0.1
 0.0
 ⋮
 0.6
 0.0
 0.0
 0.0
 0.0
 0.0
 0.0
 0.0
 0.0

@timeit to "ODEProb SparseJac" sparsejacprob = ODEProblem{true,SciMLBase.FullSpecialize}(sys, Float64[], tspan, Float64[], jac=true, sparse=true)
show(to)

───────────────────────────────────────────────────────────────────────────
───
                                     Time                    Allocations   
   
                            ───────────────────────   ─────────────────────
───
     Tot / % measured:           12.1s /  94.6%           1.52GiB /  97.5% 
   

Section             ncalls     time    %tot     avg     alloc    %tot      
avg
───────────────────────────────────────────────────────────────────────────
───
ODEProb No Jac           1    4.44s   38.7%   4.44s    567MiB   37.3%   567
MiB
ODEProb DenseJac         1    4.30s   37.4%   4.30s    643MiB   42.3%   643
MiB
ODEProb SparseJac        1    2.75s   23.9%   2.75s    311MiB   20.5%   311
MiB
───────────────────────────────────────────────────────────────────────────
───

Picture of the solution

sol = solve(oprob, CVODE_BDF())
plot(sol, legend=false, fmt=:png)

For these benchmarks we will be using the time-series error with these saving points since the final time point is not well-indicative of the solution behavior (capturing the oscillation is the key!).

Generate Test Solution

@time sol = solve(oprob, CVODE_BDF(), abstol=1/10^14, reltol=1/10^14)
test_sol  = TestSolution(sol)

0.185379 seconds (126.64 k allocations: 11.849 MiB, 16.83% gc time, 89.39
% compilation time)
retcode: Success
Interpolation: 3rd order Hermite
t: nothing
u: nothing

Setups

abstols = 1.0 ./ 10.0 .^ (9:13)
reltols = 1.0 ./ 10.0 .^ (6:10)

setups = [
            Dict(:alg=>CVODE_BDF()),
            Dict(:alg=>KenCarp4()),
            Dict(:alg=>Rodas4()),
            Dict(:alg=>QNDF()),
            Dict(:alg=>lsoda()),
            Dict(:alg=>radau()),
            Dict(:alg=>seulex()),
            Dict(:alg=>ImplicitEulerExtrapolation(min_order = 8, init_order = 9,threading = OrdinaryDiffEq.PolyesterThreads())),
            Dict(:alg=>ImplicitEulerExtrapolation(min_order = 8, init_order = 9,threading = false)),
            Dict(:alg=>ImplicitEulerBarycentricExtrapolation(min_order = 7, init_order = 8,threading = OrdinaryDiffEq.PolyesterThreads())),
            Dict(:alg=>ImplicitEulerBarycentricExtrapolation(min_order = 7, init_order = 8,threading = false)),
            Dict(:alg=>ImplicitHairerWannerExtrapolation(init_order = 5,threading = OrdinaryDiffEq.PolyesterThreads())),
            Dict(:alg=>ImplicitHairerWannerExtrapolation(init_order = 5, threading = false)),
            ]

solnames = ["CVODE_BDF","KenCarp4","Rodas4","QNDF","lsoda","radau","seulex","ImplEulerExtpl (threaded)", "ImplEulerExtpl (non-threaded)",
            "ImplEulerBaryExtpl (threaded)","ImplEulerBaryExtpl (non-threaded)","ImplHWExtpl (threaded)","ImplHWExtpl (non-threaded)"]

13-element Vector{String}:
 "CVODE_BDF"
 "KenCarp4"
 "Rodas4"
 "QNDF"
 "lsoda"
 "radau"
 "seulex"
 "ImplEulerExtpl (threaded)"
 "ImplEulerExtpl (non-threaded)"
 "ImplEulerBaryExtpl (threaded)"
 "ImplEulerBaryExtpl (non-threaded)"
 "ImplHWExtpl (threaded)"
 "ImplHWExtpl (non-threaded)"

Automatic Jacobian Solves

First we test using auto-generated Jacobians (finite difference)

wp = WorkPrecisionSet(oprob,abstols,reltols,setups;
                      names = solnames,appxsol=test_sol,save_everystep=false,maxiters=Int(1e5),numruns=10)

plot(wp, title = "Implicit Methods: SBML Model",legend=:outertopleft,size = (1000,500),
     xticks = 10.0 .^ (-15:1:1),
     yticks = 10.0 .^ (-6:0.3:5),
     bottom_margin= 5Plots.mm)

Analytical Jacobian

Now we test using the generated analytic Jacobian function.

setups = [
            Dict(:alg=>CVODE_BDF()),
            Dict(:alg=>KenCarp4()),
            Dict(:alg=>Rodas4()),
            Dict(:alg=>QNDF()),
            #Dict(:alg=>lsoda()),
            #Dict(:alg=>radau()),
            #Dict(:alg=>seulex()),
            Dict(:alg=>ImplicitEulerExtrapolation(min_order = 8, init_order = 9,threading = OrdinaryDiffEq.PolyesterThreads())),
            Dict(:alg=>ImplicitEulerExtrapolation(min_order = 8, init_order = 9,threading = false)),
            Dict(:alg=>ImplicitEulerBarycentricExtrapolation(min_order = 7, init_order = 8,threading = OrdinaryDiffEq.PolyesterThreads())),
            Dict(:alg=>ImplicitEulerBarycentricExtrapolation(min_order = 7, init_order = 8,threading = false)),
            Dict(:alg=>ImplicitHairerWannerExtrapolation(init_order = 5,threading = OrdinaryDiffEq.PolyesterThreads())),
            Dict(:alg=>ImplicitHairerWannerExtrapolation(init_order = 5, threading = false)),
            ]

solnames = ["CVODE_BDF","KenCarp4","Rodas4","QNDF","ImplEulerExtpl (threaded)", "ImplEulerExtpl (non-threaded)",
            "ImplEulerBaryExtpl (threaded)","ImplEulerBaryExtpl (non-threaded)","ImplHWExtpl (threaded)","ImplHWExtpl (non-threaded)"]

wp = WorkPrecisionSet(densejacprob,abstols,reltols,setups;
                      names = solnames,appxsol=test_sol,save_everystep=false,maxiters=Int(1e5),numruns=10)

plot(wp, title = "Implicit Methods: SBML Model",legend=:outertopleft,size = (1000,500),
     xticks = 10.0 .^ (-15:1:1),
     yticks = 10.0 .^ (-6:0.3:5),
     bottom_margin= 5Plots.mm)

Sparse Jacobian

Finally we test using the generated sparse analytic Jacobian function.

Note that the extrapolation methods currently do not support sparse Jacobians.

setups = [
            #Dict(:alg=>CVODE_BDF()), #Fails!
            Dict(:alg=>KenCarp4(autodiff = false)),
            Dict(:alg=>Rodas4(autodiff = false)),
            Dict(:alg=>QNDF(autodiff = false)),
            #Dict(:alg=>lsoda()),
            #Dict(:alg=>radau()),
            #Dict(:alg=>seulex()),
            #Dict(:alg=>ImplicitEulerExtrapolation(autodiff = false,min_order = 8, init_order = 9,threading = OrdinaryDiffEq.PolyesterThreads())),
            #Dict(:alg=>ImplicitEulerExtrapolation(autodiff = false,min_order = 8, init_order = 9,threading = false)),
            #Dict(:alg=>ImplicitEulerBarycentricExtrapolation(autodiff = false,min_order = 7, init_order = 8,threading = OrdinaryDiffEq.PolyesterThreads())),
            #Dict(:alg=>ImplicitEulerBarycentricExtrapolation(autodiff = false,min_order = 7, init_order = 8,threading = false)),
            #Dict(:alg=>ImplicitHairerWannerExtrapolation(autodiff = false,init_order = 5,threading = OrdinaryDiffEq.PolyesterThreads())),
            #Dict(:alg=>ImplicitHairerWannerExtrapolation(autodiff = false,init_order = 5, threading = false)),
            ]

solnames = ["KenCarp4","Rodas4","QNDF",#"ImplEulerExtpl (threaded)", "ImplEulerExtpl (non-threaded)",
            #"ImplEulerBaryExtpl (threaded)","ImplEulerBaryExtpl (non-threaded)","ImplHWExtpl (threaded)","ImplHWExtpl (non-threaded)"
            ]

wp = WorkPrecisionSet(sparsejacprob ,abstols,reltols,setups;
                      names = solnames,appxsol=test_sol,save_everystep=false,maxiters=Int(1e5),numruns=10)

plot(wp, title = "Implicit Methods: SBML Model",legend=:outertopleft,size = (1000,500),
     xticks = 10.0 .^ (-15:1:1),
     yticks = 10.0 .^ (-6:0.3:5),
     bottom_margin= 5Plots.mm)

Appendix

These benchmarks are a part of the SciMLBenchmarks.jl repository, found at: https://github.com/SciML/SciMLBenchmarks.jl. For more information on high-performance scientific machine learning, check out the SciML Open Source Software Organization https://sciml.ai.

To locally run this benchmark, do the following commands:

using SciMLBenchmarks
SciMLBenchmarks.weave_file("benchmarks/Bio","Bidkhori2012.jmd")

Computer Information:

Julia Version 1.10.6
Commit 67dffc4a8ae (2024-10-28 12:23 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 128 × AMD EPYC 7502 32-Core Processor
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver2)
Threads: 128 default, 0 interactive, 64 GC (on 128 virtual cores)
Environment:
  JULIA_CPU_THREADS = 128
  JULIA_DEPOT_PATH = /cache/julia-buildkite-plugin/depots/5b300254-1738-4989-ae0a-f4d2d937f953

Package Information:

Status `/cache/build/exclusive-amdci1-0/julialang/scimlbenchmarks-dot-jl/benchmarks/Bio/Project.toml`
  [6e4b80f9] BenchmarkTools v1.5.0
  [479239e8] Catalyst v14.4.1
  [2b5f629d] DiffEqBase v6.160.0
  [f3b72e0c] DiffEqDevTools v2.45.1
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⌃ [033835bb] JLD2 v0.5.8
  [7f56f5a3] LSODA v0.7.5
  [7ed4a6bd] LinearSolve v2.37.0
⌃ [961ee093] ModelingToolkit v9.50.0
  [54ca160b] ODEInterface v0.5.0
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  [c3572dad] Sundials v4.26.1
  [a759f4b9] TimerOutputs v0.5.25
Info Packages marked with ⌃ have new versions available and may be upgradable.

And the full manifest:

Status `/cache/build/exclusive-amdci1-0/julialang/scimlbenchmarks-dot-jl/benchmarks/Bio/Manifest.toml`
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⌃ [4fba245c] ArrayInterface v7.17.0
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  [01d81517] RecipesPipeline v0.6.12
  [731186ca] RecursiveArrayTools v3.27.3
  [f2c3362d] RecursiveFactorization v0.2.23
  [189a3867] Reexport v1.2.2
  [05181044] RelocatableFolders v1.0.1
  [ae029012] Requires v1.3.0
  [ae5879a3] ResettableStacks v1.1.1
  [79098fc4] Rmath v0.8.0
  [47965b36] RootedTrees v2.23.1
  [7e49a35a] RuntimeGeneratedFunctions v0.5.13
  [94e857df] SIMDTypes v0.1.0
  [476501e8] SLEEFPirates v0.6.43
⌃ [0bca4576] SciMLBase v2.61.0
  [31c91b34] SciMLBenchmarks v0.1.3
  [19f34311] SciMLJacobianOperators v0.1.1
  [c0aeaf25] SciMLOperators v0.3.12
⌃ [53ae85a6] SciMLStructures v1.5.0
  [6c6a2e73] Scratch v1.2.1
  [efcf1570] Setfield v1.1.1
  [992d4aef] Showoff v1.0.3
  [777ac1f9] SimpleBufferStream v1.2.0
  [727e6d20] SimpleNonlinearSolve v2.0.0
  [699a6c99] SimpleTraits v0.9.4
  [ce78b400] SimpleUnPack v1.1.0
  [b85f4697] SoftGlobalScope v1.1.0
  [a2af1166] SortingAlgorithms v1.2.1
  [47a9eef4] SparseDiffTools v2.23.0
  [0a514795] SparseMatrixColorings v0.4.10
  [e56a9233] Sparspak v0.3.9
  [276daf66] SpecialFunctions v2.4.0
  [860ef19b] StableRNGs v1.0.2
  [aedffcd0] Static v1.1.1
  [0d7ed370] StaticArrayInterface v1.8.0
  [90137ffa] StaticArrays v1.9.8
  [1e83bf80] StaticArraysCore v1.4.3
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.3
  [4c63d2b9] StatsFuns v1.3.2
  [7792a7ef] StrideArraysCore v0.5.7
  [69024149] StringEncodings v0.3.7
⌅ [09ab397b] StructArrays v0.6.18
  [c3572dad] Sundials v4.26.1
  [2efcf032] SymbolicIndexingInterface v0.3.35
  [19f23fe9] SymbolicLimits v0.2.2
  [d1185830] SymbolicUtils v3.7.2
  [0c5d862f] Symbolics v6.21.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [62fd8b95] TensorCore v0.1.1
  [8ea1fca8] TermInterface v2.0.0
  [1c621080] TestItems v1.0.0
  [8290d209] ThreadingUtilities v0.5.2
  [a759f4b9] TimerOutputs v0.5.25
  [0796e94c] Tokenize v0.5.29
  [3bb67fe8] TranscodingStreams v0.11.3
  [d5829a12] TriangularSolve v0.2.1
  [410a4b4d] Tricks v0.1.9
  [781d530d] TruncatedStacktraces v1.4.0
  [5c2747f8] URIs v1.5.1
  [3a884ed6] UnPack v1.0.2
  [1cfade01] UnicodeFun v0.4.1
  [1986cc42] Unitful v1.21.0
  [45397f5d] UnitfulLatexify v1.6.4
  [a7c27f48] Unityper v0.1.6
  [41fe7b60] Unzip v0.2.0
  [3d5dd08c] VectorizationBase v0.21.71
  [81def892] VersionParsing v1.3.0
  [19fa3120] VertexSafeGraphs v0.2.0
  [44d3d7a6] Weave v0.10.12
  [ddb6d928] YAML v0.4.12
  [c2297ded] ZMQ v1.3.0
  [6e34b625] Bzip2_jll v1.0.8+2
  [83423d85] Cairo_jll v1.18.2+1
  [ee1fde0b] Dbus_jll v1.14.10+0
  [2702e6a9] EpollShim_jll v0.0.20230411+0
  [2e619515] Expat_jll v2.6.4+0
⌅ [b22a6f82] FFMPEG_jll v4.4.4+1
  [a3f928ae] Fontconfig_jll v2.13.96+0
  [d7e528f0] FreeType2_jll v2.13.2+0
  [559328eb] FriBidi_jll v1.0.14+0
  [0656b61e] GLFW_jll v3.4.0+1
  [d2c73de3] GR_jll v0.73.8+0
  [78b55507] Gettext_jll v0.21.0+0
  [f8c6e375] Git_jll v2.46.2+0
  [7746bdde] Glib_jll v2.80.5+0
  [3b182d85] Graphite2_jll v1.3.14+0
  [2e76f6c2] HarfBuzz_jll v8.3.1+0
  [1d5cc7b8] IntelOpenMP_jll v2024.2.1+0
  [aacddb02] JpegTurbo_jll v3.0.4+0
  [c1c5ebd0] LAME_jll v3.100.2+0
  [88015f11] LERC_jll v4.0.0+0
  [1d63c593] LLVMOpenMP_jll v18.1.7+0
  [aae0fff6] LSODA_jll v0.1.2+0
  [dd4b983a] LZO_jll v2.10.2+1
⌅ [e9f186c6] Libffi_jll v3.2.2+1
  [d4300ac3] Libgcrypt_jll v1.11.0+0
  [7e76a0d4] Libglvnd_jll v1.6.0+0
  [7add5ba3] Libgpg_error_jll v1.50.0+0
  [94ce4f54] Libiconv_jll v1.17.0+1
  [4b2f31a3] Libmount_jll v2.40.1+0
  [89763e89] Libtiff_jll v4.7.0+0
  [38a345b3] Libuuid_jll v2.40.1+0
  [856f044c] MKL_jll v2024.2.0+0
  [c771fb93] ODEInterface_jll v0.0.1+0
  [e7412a2a] Ogg_jll v1.3.5+1
  [458c3c95] OpenSSL_jll v3.0.15+1
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [91d4177d] Opus_jll v1.3.3+0
  [36c8627f] Pango_jll v1.54.1+0
  [30392449] Pixman_jll v0.43.4+0
  [c0090381] Qt6Base_jll v6.7.1+1
  [629bc702] Qt6Declarative_jll v6.7.1+2
  [ce943373] Qt6ShaderTools_jll v6.7.1+1
  [e99dba38] Qt6Wayland_jll v6.7.1+1
  [f50d1b31] Rmath_jll v0.5.1+0
⌅ [fb77eaff] Sundials_jll v5.2.2+0
  [a44049a8] Vulkan_Loader_jll v1.3.243+0
  [a2964d1f] Wayland_jll v1.21.0+1
  [2381bf8a] Wayland_protocols_jll v1.31.0+0
  [02c8fc9c] XML2_jll v2.13.5+0
  [aed1982a] XSLT_jll v1.1.41+0
  [ffd25f8a] XZ_jll v5.6.3+0
  [f67eecfb] Xorg_libICE_jll v1.1.1+0
  [c834827a] Xorg_libSM_jll v1.2.4+0
  [4f6342f7] Xorg_libX11_jll v1.8.6+0
  [0c0b7dd1] Xorg_libXau_jll v1.0.11+0
  [935fb764] Xorg_libXcursor_jll v1.2.0+4
  [a3789734] Xorg_libXdmcp_jll v1.1.4+0
  [1082639a] Xorg_libXext_jll v1.3.6+0
  [d091e8ba] Xorg_libXfixes_jll v5.0.3+4
  [a51aa0fd] Xorg_libXi_jll v1.7.10+4
  [d1454406] Xorg_libXinerama_jll v1.1.4+4
  [ec84b674] Xorg_libXrandr_jll v1.5.2+4
  [ea2f1a96] Xorg_libXrender_jll v0.9.11+0
  [14d82f49] Xorg_libpthread_stubs_jll v0.1.1+0
  [c7cfdc94] Xorg_libxcb_jll v1.17.0+0
  [cc61e674] Xorg_libxkbfile_jll v1.1.2+0
  [e920d4aa] Xorg_xcb_util_cursor_jll v0.1.4+0
  [12413925] Xorg_xcb_util_image_jll v0.4.0+1
  [2def613f] Xorg_xcb_util_jll v0.4.0+1
  [975044d2] Xorg_xcb_util_keysyms_jll v0.4.0+1
  [0d47668e] Xorg_xcb_util_renderutil_jll v0.3.9+1
  [c22f9ab0] Xorg_xcb_util_wm_jll v0.4.1+1
  [35661453] Xorg_xkbcomp_jll v1.4.6+0
  [33bec58e] Xorg_xkeyboard_config_jll v2.39.0+0
  [c5fb5394] Xorg_xtrans_jll v1.5.0+0
  [8f1865be] ZeroMQ_jll v4.3.5+1
  [3161d3a3] Zstd_jll v1.5.6+1
  [35ca27e7] eudev_jll v3.2.9+0
  [214eeab7] fzf_jll v0.53.0+0
  [1a1c6b14] gperf_jll v3.1.1+0
  [a4ae2306] libaom_jll v3.9.0+0
  [0ac62f75] libass_jll v0.15.2+0
  [1183f4f0] libdecor_jll v0.2.2+0
  [2db6ffa8] libevdev_jll v1.11.0+0
  [f638f0a6] libfdk_aac_jll v2.0.3+0
  [36db933b] libinput_jll v1.18.0+0
  [b53b4c65] libpng_jll v1.6.44+0
  [a9144af2] libsodium_jll v1.0.20+1
  [f27f6e37] libvorbis_jll v1.3.7+2
  [009596ad] mtdev_jll v1.1.6+0
  [1317d2d5] oneTBB_jll v2021.12.0+0
⌅ [1270edf5] x264_jll v2021.5.5+0
⌅ [dfaa095f] x265_jll v3.5.0+0
  [d8fb68d0] xkbcommon_jll v1.4.1+1
  [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
  [9abbd945] Profile
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays v1.10.0
  [10745b16] Statistics v1.10.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] LibCURL_jll v8.4.0+0
  [e37daf67] LibGit2_jll v1.6.4+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [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
  [efcefdf7] PCRE2_jll v10.42.0+1
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [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 be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`