Using PEtab

This notebook illustrates how to use PEtab with AMICI.

[1]:
from amici.petab_import import import_petab_problem
from amici.petab_objective import simulate_petab
import petab

import os

We use an example model from the benchmark collection:

[2]:
!git clone --depth 1 https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git tmp/benchmark-models || (cd tmp/benchmark-models && git pull)
Cloning into 'tmp/benchmark-models'...
remote: Enumerating objects: 142, done.
remote: Counting objects: 100% (142/142), done.
remote: Compressing objects: 100% (122/122), done.
remote: Total 142 (delta 41), reused 104 (delta 18), pack-reused 0
Receiving objects: 100% (142/142), 648.29 KiB | 1.23 MiB/s, done.
Resolving deltas: 100% (41/41), done.
[3]:
folder_base = "tmp/benchmark-models/Benchmark-Models/"
!ls -l $folder_base
total 68
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Alkan_SciSignal2018
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Beer_MolBioSystems2014
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Boehm_JProteomeRes2014
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Borghans_BiophysChem1997
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Brannmark_JBC2010
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Bruno_JExpBio2016
-rwxr-xr-x 1 yannik yannik  654 Mär 17 15:27 checkBenchmarkModels.py
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Chen_MSB2009
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Crauste_CellSystems2017
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Elowitz_Nature2000
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Fiedler_BMC2016
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Fujita_SciSignal2010
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Perelson_Science1996
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Rahman_MBS2016
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Sneyd_PNAS2002
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Weber_BMC2015
drwxr-xr-x 2 yannik yannik 4096 Mär 17 15:27 Zheng_PNAS2012

We import a model to PEtab from a provided yaml file:

[4]:
model_name = "Boehm_JProteomeRes2014"
yaml_file = os.path.join(folder_base, model_name, model_name + ".yaml")
petab_problem = petab.Problem.from_yaml(yaml_file)

Next, we import the model to amici, compile it and obtain a function handle:

[5]:
amici_model = import_petab_problem(petab_problem)
2020-03-17 15:27:27.586 - amici.petab_import - INFO - Importing model ...
2020-03-17 15:27:27.593 - amici.petab_import - INFO - Model name is 'Boehm_JProteomeRes2014'. Writing model code to '/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014'.
2020-03-17 15:27:27.598 - amici.petab_import - INFO - Species: 8
2020-03-17 15:27:27.599 - amici.petab_import - INFO - Global parameters: 9
2020-03-17 15:27:27.599 - amici.petab_import - INFO - Reactions: 9
2020-03-17 15:27:27.715 - amici.petab_import - INFO - Observables: 3
2020-03-17 15:27:27.715 - amici.petab_import - INFO - Sigmas: 3
2020-03-17 15:27:27.722 - amici.petab_import - DEBUG - Adding output parameters to model: OrderedDict([('noiseParameter1_pSTAT5A_rel', None), ('noiseParameter1_pSTAT5B_rel', None), ('noiseParameter1_rSTAT5A_rel', None)])
2020-03-17 15:27:27.725 - amici.petab_import - DEBUG - Condition table: (1, 1)
2020-03-17 15:27:27.726 - amici.petab_import - DEBUG - Fixed parameters are []
2020-03-17 15:27:27.728 - amici.petab_import - INFO - Overall fixed parameters: 0
2020-03-17 15:27:27.729 - amici.petab_import - INFO - Variable parameters: 12
2020-03-17 15:27:27.735 - amici.sbml_import - INFO - Finished processing SBML parameters            (1.25E-03s)
2020-03-17 15:27:27.749 - amici.sbml_import - INFO - Finished processing SBML species               (1.26E-02s)
2020-03-17 15:27:27.829 - amici.sbml_import - INFO - Finished processing SBML reactions             (7.41E-02s)
2020-03-17 15:27:27.833 - amici.sbml_import - INFO - Finished processing SBML compartments          (4.23E-04s)
2020-03-17 15:27:27.898 - amici.sbml_import - INFO - Finished processing SBML rules                 (6.47E-02s)
2020-03-17 15:27:28.012 - amici.sbml_import - INFO - Finished processing SBML observables           (6.77E-02s)
2020-03-17 15:27:28.139 - amici.ode_export - INFO - Finished writing J.cpp                          (1.14E-01s)
2020-03-17 15:27:28.160 - amici.ode_export - INFO - Finished writing JB.cpp                         (2.04E-02s)
2020-03-17 15:27:28.167 - amici.ode_export - INFO - Finished writing JDiag.cpp                      (6.41E-03s)
2020-03-17 15:27:28.187 - amici.ode_export - INFO - Finished writing JSparse.cpp                    (1.91E-02s)
2020-03-17 15:27:28.217 - amici.ode_export - INFO - Finished writing JSparseB.cpp                   (2.73E-02s)
2020-03-17 15:27:28.236 - amici.ode_export - INFO - Finished writing Jy.cpp                         (1.65E-02s)
2020-03-17 15:27:28.344 - amici.ode_export - INFO - Finished writing dJydsigmay.cpp                 (1.07E-01s)
2020-03-17 15:27:28.389 - amici.ode_export - INFO - Finished writing dJydy.cpp                      (3.99E-02s)
2020-03-17 15:27:28.466 - amici.ode_export - INFO - Finished writing dwdp.cpp                       (7.61E-02s)
2020-03-17 15:27:28.473 - amici.ode_export - INFO - Finished writing dwdx.cpp                       (5.87E-03s)
2020-03-17 15:27:28.497 - amici.ode_export - INFO - Finished writing dxdotdw.cpp                    (2.32E-02s)
2020-03-17 15:27:28.533 - amici.ode_export - INFO - Finished writing dxdotdp_explicit.cpp           (3.38E-02s)
2020-03-17 15:27:28.756 - amici.ode_export - INFO - Finished writing dydx.cpp                       (1.98E-01s)
2020-03-17 15:27:28.910 - amici.ode_export - INFO - Finished writing dydp.cpp                       (1.53E-01s)
2020-03-17 15:27:28.926 - amici.ode_export - INFO - Finished writing dsigmaydp.cpp                  (1.40E-02s)
2020-03-17 15:27:28.931 - amici.ode_export - INFO - Finished writing sigmay.cpp                     (2.46E-03s)
2020-03-17 15:27:28.950 - amici.ode_export - INFO - Finished writing w.cpp                          (1.55E-02s)
2020-03-17 15:27:28.967 - amici.ode_export - INFO - Finished writing x0.cpp                         (1.57E-02s)
2020-03-17 15:27:28.975 - amici.ode_export - INFO - Finished writing x0_fixedParameters.cpp         (4.78E-03s)
2020-03-17 15:27:29.027 - amici.ode_export - INFO - Finished writing sx0.cpp                        (5.01E-02s)
2020-03-17 15:27:29.069 - amici.ode_export - INFO - Finished writing sx0_fixedParameters.cpp        (3.14E-02s)
2020-03-17 15:27:29.104 - amici.ode_export - INFO - Finished writing xdot.cpp                       (3.43E-02s)
2020-03-17 15:27:29.129 - amici.ode_export - INFO - Finished writing y.cpp                          (2.16E-02s)
2020-03-17 15:27:29.136 - amici.ode_export - INFO - Finished writing x_rdata.cpp                    (4.95E-03s)
2020-03-17 15:27:29.138 - amici.ode_export - INFO - Finished writing total_cl.cpp                   (6.59E-04s)
2020-03-17 15:27:29.147 - amici.ode_export - INFO - Finished writing x_solver.cpp                   (7.72E-03s)
2020-03-17 15:27:29.166 - amici.ode_export - INFO - Finished generating cpp code                    (1.14E+00s)
2020-03-17 15:27:46.200 - amici.ode_export - INFO - Finished compiling cpp code                     (1.70E+01s)
2020-03-17 15:27:46.204 - amici.petab_import - INFO - Finished Importing PEtab model                (1.86E+01s)
2020-03-17 15:27:46.209 - amici.petab_import - INFO - Successfully loaded model Boehm_JProteomeRes2014 from /home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014.
running build_ext
building 'Boehm_JProteomeRes2014._Boehm_JProteomeRes2014' extension
swigging swig/Boehm_JProteomeRes2014.i to swig/Boehm_JProteomeRes2014_wrap.cpp
swig -python -c++ -modern -outdir Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/swig -I/home/yannik/amici/python/sdist/amici/include -o swig/Boehm_JProteomeRes2014_wrap.cpp swig/Boehm_JProteomeRes2014.i
creating build
creating build/temp.linux-x86_64-3.7
creating build/temp.linux-x86_64-3.7/swig
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c swig/Boehm_JProteomeRes2014_wrap.cpp -o build/temp.linux-x86_64-3.7/swig/Boehm_JProteomeRes2014_wrap.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dxdotdw.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdw.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_total_cl.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_total_cl.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_x_rdata.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_x_rdata.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dxdotdp_implicit_colptrs.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdp_implicit_colptrs.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dsigmaydp.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dsigmaydp.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_y.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_y.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dydp.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dydp.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_w.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_w.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_JSparseB_rowvals.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JSparseB_rowvals.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dxdotdw_rowvals.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdw_rowvals.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dwdx_rowvals.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dwdx_rowvals.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_x0.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_x0.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dwdx.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dwdx.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dJydy_colptrs.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dJydy_colptrs.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_JSparseB.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JSparseB.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_JSparseB_colptrs.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JSparseB_colptrs.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dxdotdp_explicit_colptrs.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdp_explicit_colptrs.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_sx0_fixedParameters.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_sx0_fixedParameters.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_JSparse_rowvals.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JSparse_rowvals.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dxdotdp_explicit.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdp_explicit.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dJydy.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dJydy.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dwdp_colptrs.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dwdp_colptrs.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_x0_fixedParameters.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_x0_fixedParameters.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dxdotdw_colptrs.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdw_colptrs.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dJydsigmay.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dJydsigmay.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dxdotdp_implicit_rowvals.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdp_implicit_rowvals.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dwdp.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dwdp.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_sx0.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_sx0.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_JB.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JB.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dwdx_colptrs.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dwdx_colptrs.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c wrapfunctions.cpp -o build/temp.linux-x86_64-3.7/wrapfunctions.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_x_solver.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_x_solver.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_JSparse.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JSparse.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_xdot.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_xdot.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dJydy_rowvals.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dJydy_rowvals.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dwdp_rowvals.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dwdp_rowvals.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_JSparse_colptrs.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JSparse_colptrs.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_J.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_J.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dydx.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dydx.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_JDiag.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JDiag.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_Jy.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_Jy.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_sigmay.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_sigmay.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/yannik/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014 -I/home/yannik/amici/python/sdist/amici/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/gsl -I/home/yannik/amici/python/sdist/amici/ThirdParty/sundials/include -I/home/yannik/amici/python/sdist/amici/ThirdParty/SuiteSparse/include -I/usr/include/hdf5/serial -I/home/yannik/anaconda3/include/python3.7m -c Boehm_JProteomeRes2014_dxdotdp_explicit_rowvals.cpp -o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdp_explicit_rowvals.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
g++ -pthread -shared -B /home/yannik/anaconda3/compiler_compat -L/home/yannik/anaconda3/lib -Wl,-rpath=/home/yannik/anaconda3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/swig/Boehm_JProteomeRes2014_wrap.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdw.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_total_cl.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_x_rdata.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdp_implicit_colptrs.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dsigmaydp.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_y.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dydp.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_w.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JSparseB_rowvals.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdw_rowvals.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dwdx_rowvals.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_x0.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dwdx.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dJydy_colptrs.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JSparseB.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JSparseB_colptrs.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdp_explicit_colptrs.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_sx0_fixedParameters.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JSparse_rowvals.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdp_explicit.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dJydy.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dwdp_colptrs.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_x0_fixedParameters.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdw_colptrs.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dJydsigmay.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdp_implicit_rowvals.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dwdp.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_sx0.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JB.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dwdx_colptrs.o build/temp.linux-x86_64-3.7/wrapfunctions.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_x_solver.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JSparse.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_xdot.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dJydy_rowvals.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dwdp_rowvals.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JSparse_colptrs.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_J.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dydx.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_JDiag.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_Jy.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_sigmay.o build/temp.linux-x86_64-3.7/Boehm_JProteomeRes2014_dxdotdp_explicit_rowvals.o -L/usr/lib/x86_64-linux-gnu/hdf5/serial -L/home/yannik/amici/python/sdist/amici/libs -lamici -lsundials -lsuitesparse -lcblas -lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5 -o /home/yannik/amici/python/examples/amici_models/Boehm_JProteomeRes2014/Boehm_JProteomeRes2014/_Boehm_JProteomeRes2014.cpython-37m-x86_64-linux-gnu.so

That’s it. Now, we can use the model to perform simulations. For more involved purposes, consider using the objective function provided by pyPESTO. For simple simulations, a function simulate_petab is available:

[6]:
simulate_petab(petab_problem, amici_model)
[6]:
{'llh': -138.22199570334107,
 'sllh': None,
 'rdatas': [<amici.numpy.ReturnDataView at 0x7f030e1a0fd0>]}

This performs a simulation at the nominal parameters. Parameters can also be directly specified, both scaled and unscaled:

[7]:
parameters = {
    x_id: x_val for x_id, x_val in
    zip(petab_problem.x_ids, petab_problem.x_nominal_scaled)
}
simulate_petab(petab_problem, amici_model, problem_parameters=parameters, scaled_parameters=True)
[7]:
{'llh': -138.22199570334107,
 'sllh': None,
 'rdatas': [<amici.numpy.ReturnDataView at 0x7f030e198590>]}

For further information, see the documentation.