.gitignore
AUTHORS.md
CLA.md
CODE_OF_CONDUCT.md
CONTRIBUTING.md
Dockerfile
LICENSE
README.md
commit.sh
poetry.lock
pyproject.toml
pytest.ini
setup.py
biosimulator_processes/__init__.py
biosimulator_processes/biosimulator_builder.py
biosimulator_processes/helpers.py
biosimulator_processes/io.py
biosimulator_processes.egg-info/PKG-INFO
biosimulator_processes.egg-info/SOURCES.txt
biosimulator_processes.egg-info/dependency_links.txt
biosimulator_processes.egg-info/requires.txt
biosimulator_processes.egg-info/top_level.txt
biosimulator_processes/api/README.md
biosimulator_processes/api/__init__.py
biosimulator_processes/api/build.py
biosimulator_processes/api/compare.py
biosimulator_processes/api/instance.py
biosimulator_processes/api/results.py
biosimulator_processes/api/run.py
biosimulator_processes/api/verify.py
biosimulator_processes/containers/__init__.py
biosimulator_processes/containers/exec.py
biosimulator_processes/containers/io.py
biosimulator_processes/data_model/__init__.py
biosimulator_processes/data_model/compare_data_model.py
biosimulator_processes/data_model/sed_data_model.py
biosimulator_processes/data_model/service_data_model.py
biosimulator_processes/data_model/verify_data_model.py
biosimulator_processes/experiments/__init__.py
biosimulator_processes/experiments/parameter_optimization.py
biosimulator_processes/experiments/parameter_scan.py
biosimulator_processes/experiments/predict.py
biosimulator_processes/processes/.DS_Store
biosimulator_processes/processes/__init__.py
biosimulator_processes/processes/amici_process.py
biosimulator_processes/processes/cobra_process.py
biosimulator_processes/processes/copasi_process.py
biosimulator_processes/processes/qiskit_process.py
biosimulator_processes/processes/sed_process.py
biosimulator_processes/processes/smoldyn_process.py
biosimulator_processes/processes/tellurium_process.py
biosimulator_processes/processes/utc_process.py
biosimulator_processes/processes/__pycache__/__init__.cpython-310.pyc
biosimulator_processes/processes/__pycache__/cobra_process.cpython-310.pyc
biosimulator_processes/processes/__pycache__/copasi_process.cpython-310.pyc
biosimulator_processes/processes/__pycache__/smoldyn_process.cpython-310.pyc
biosimulator_processes/processes/__pycache__/tellurium_process.cpython-310.pyc
biosimulator_processes/services/__init__.py
biosimulator_processes/services/rest_service.py
biosimulator_processes/steps/__init__.py
biosimulator_processes/steps/ode_simulation.py
biosimulator_processes/steps/parameter_scan.py
biosimulator_processes/steps/viz.py
demos/notebook_api.ipynb
demos/utc_process_comparison.ipynb
notebook_api/__init__.py
notebook_api/utc.py
scripts/build-container.sh
scripts/commit.sh
scripts/docker-pipeline.sh
scripts/enter-lab.sh
scripts/exec-docker.sh
scripts/fix-nb.sh
scripts/fix_notebooks.py
scripts/install-pbg-branches.sh
scripts/install-smoldyn-mac-silicon.sh
scripts/release-container.sh
scripts/release.sh
scripts/run-container.sh
scripts/trust-notebooks.sh
scripts/xvfb-startup.sh
test_outputs/test_ode_comparator_step_result.json
test_outputs/test_ode_comparator_step_result.txt
test_outputs/test_ode_comparison_object.json
test_outputs/repressilator-utc-comparison/LacI_mRNA_comparison.csv
test_outputs/repressilator-utc-comparison/LacI_protein_comparison.csv
test_outputs/repressilator-utc-comparison/TetR_mRNA_comparison.csv
test_outputs/repressilator-utc-comparison/TetR_protein_comparison.csv
test_outputs/repressilator-utc-comparison/cI_mRNA_comparison.csv
test_outputs/repressilator-utc-comparison/cI_protein_comparison.csv
test_suite/__init__.py
test_suite/misc.ipynb
test_suite/test_main.py
test_suite/examples/README.md
test_suite/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ.omex
test_suite/examples/bngl/test-bngl.omex
test_suite/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/Dolan2015.bngl
test_suite/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/Dolan2015.sedml
test_suite/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/Figure1.png
test_suite/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/expected-results.json
test_suite/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/manifest.xml
test_suite/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/metadata.rdf
test_suite/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/reports.h5
test_suite/examples/bngl/test-bngl/expected-results.json
test_suite/examples/bngl/test-bngl/manifest.xml
test_suite/examples/bngl/test-bngl/metadata.rdf
test_suite/examples/bngl/test-bngl/reports.h5
test_suite/examples/bngl/test-bngl/test.bngl
test_suite/examples/bngl/test-bngl/test.sedml
test_suite/examples/cellml/Elowitz-Nature-2000-Repressilator.omex
test_suite/examples/cellml/Lorenz-system.omex
test_suite/examples/cellml/Elowitz-Nature-2000-Repressilator/Figure_1a.png
test_suite/examples/cellml/Elowitz-Nature-2000-Repressilator/elowitz_leibler_2000.cellml
test_suite/examples/cellml/Elowitz-Nature-2000-Repressilator/expected-results.json
test_suite/examples/cellml/Elowitz-Nature-2000-Repressilator/manifest.xml
test_suite/examples/cellml/Elowitz-Nature-2000-Repressilator/metadata.rdf
test_suite/examples/cellml/Elowitz-Nature-2000-Repressilator/process-description-map.sbgn
test_suite/examples/cellml/Elowitz-Nature-2000-Repressilator/process-description-map.vg.json
test_suite/examples/cellml/Elowitz-Nature-2000-Repressilator/reports.h5
test_suite/examples/cellml/Elowitz-Nature-2000-Repressilator/simulation.sedml
test_suite/examples/cellml/Lorenz-system/expected-results.json
test_suite/examples/cellml/Lorenz-system/lorenz.cellml
test_suite/examples/cellml/Lorenz-system/manifest.xml
test_suite/examples/cellml/Lorenz-system/metadata.rdf
test_suite/examples/cellml/Lorenz-system/reports.h5
test_suite/examples/cellml/Lorenz-system/simulation.sedml
test_suite/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism.omex
test_suite/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism/GraphicalAbstract.jpg
test_suite/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism/WholeCellRBC_MA_Rates.xml
test_suite/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism/expected-results.json
test_suite/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism/manifest.xml
test_suite/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism/metadata.rdf
test_suite/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism/reports.h5
test_suite/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism/simulation.sedml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE.omex
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler.omex
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/KConductance.channel.nml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/LeakConductance.channel.nml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/NML2_SingleCompHHCell.nml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/NaConductance.channel.nml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/expected-results.json
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/manifest.xml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/metadata.rdf
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/model.xml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/reports.h5
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/simulation.sedml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/KConductance.channel.nml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/LeakConductance.channel.nml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/NML2_SingleCompHHCell.nml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/NaConductance.channel.nml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/expected-results.json
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/manifest.xml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/metadata.rdf
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/model.xml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/reports.h5
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/simulation.sedml
test_suite/examples/rba/Escherichia-coli-K12-WT.omex
test_suite/examples/rba/Escherichia-coli-K12-WT/FigureS13.jpg
test_suite/examples/rba/Escherichia-coli-K12-WT/data.zip
test_suite/examples/rba/Escherichia-coli-K12-WT/expected-results.json
test_suite/examples/rba/Escherichia-coli-K12-WT/flux-map.escher.json
test_suite/examples/rba/Escherichia-coli-K12-WT/flux-map.vg.json
test_suite/examples/rba/Escherichia-coli-K12-WT/manifest.xml
test_suite/examples/rba/Escherichia-coli-K12-WT/metadata.rdf
test_suite/examples/rba/Escherichia-coli-K12-WT/model.zip
test_suite/examples/rba/Escherichia-coli-K12-WT/reports.h5
test_suite/examples/rba/Escherichia-coli-K12-WT/simulation.sedml
test_suite/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex
test_suite/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex
test_suite/examples/sbml-core/Elowitz-Nature-2000-Repressilator.omex
test_suite/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex
test_suite/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex
test_suite/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex
test_suite/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock.omex
test_suite/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations/BIOMD0000000912_sim.sedml
test_suite/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations/Caravagna2010.xml
test_suite/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations/Figure1.jpg
test_suite/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations/expected-results.json
test_suite/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations/manifest.xml
test_suite/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations/metadata.rdf
test_suite/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations/reports.h5
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/BIOMD0000000297_url.xml
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/Figure1.jpg
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/Figure2.jpg
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/Figure3.vg.json
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/expected-results.json
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/manifest.xml
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/metadata.rdf
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/reports.h5
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/simulation_1.sedml
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/BIOMD0000000297_url.xml
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/Figure1.jpg
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/Figure2.jpg
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/Figure3.vg.json
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/expected-results.json
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/manifest.xml
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/metadata.rdf
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/reports.h5
test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/simulation_1.sedml
test_suite/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/BIOMD0000000002_sim.sedml
test_suite/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/BIOMD0000000002_url.xml
test_suite/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/Figure2.png
test_suite/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/Figure_4b.vg.json
test_suite/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/expected-results.json
test_suite/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/manifest.xml
test_suite/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/metadata.rdf
test_suite/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/reports.h5
test_suite/examples/sbml-core/Elowitz-Nature-2000-Repressilator/BIOMD0000000012_url.xml
test_suite/examples/sbml-core/Elowitz-Nature-2000-Repressilator/Figure_1a.png
test_suite/examples/sbml-core/Elowitz-Nature-2000-Repressilator/expected-results.json
test_suite/examples/sbml-core/Elowitz-Nature-2000-Repressilator/manifest.xml
test_suite/examples/sbml-core/Elowitz-Nature-2000-Repressilator/metadata.rdf
test_suite/examples/sbml-core/Elowitz-Nature-2000-Repressilator/process-description-map.sbgn
test_suite/examples/sbml-core/Elowitz-Nature-2000-Repressilator/process-description-map.vg.json
test_suite/examples/sbml-core/Elowitz-Nature-2000-Repressilator/reports.h5
test_suite/examples/sbml-core/Elowitz-Nature-2000-Repressilator/simulation.sedml
test_suite/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/BIOMD0000000734.xml
test_suite/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/Figure1.jpg
test_suite/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/Parmar2017_Deficient_Rich_tracer.sedml
test_suite/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/expected-results.json
test_suite/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/manifest.xml
test_suite/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/metadata.rdf
test_suite/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/reports.h5
test_suite/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/BIOMD0000000896_sim.sedml
test_suite/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/Figure1.jpg
test_suite/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/Szymanska2009.xml
test_suite/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/expected-results.json
test_suite/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/manifest.xml
test_suite/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/metadata.rdf
test_suite/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/reports.h5
test_suite/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/BIOMD0000000678_sim.sedml
test_suite/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/BIOMD0000000678_url.xml
test_suite/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/Figure3a.jpg
test_suite/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/Figure_3c.vg.json
test_suite/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/expected-results.json
test_suite/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/manifest.xml
test_suite/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/metadata.rdf
test_suite/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/reports.h5
test_suite/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/Figure1.jpg
test_suite/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/LSODA.sedml
test_suite/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/Varusai2018.xml
test_suite/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/expected-results.json
test_suite/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/manifest.xml
test_suite/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/metadata.rdf
test_suite/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/reports.h5
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/Figure1.jpg
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/expected-results.json
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/manifest.xml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/metadata.rdf
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/model.vcml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/model_ODE_deterministic.xml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/model_ODE_stochastic.xml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/reports.h5
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/simulation.sedml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/Figure1.jpg
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/expected-results.json
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/manifest.xml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/metadata.rdf
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/model.vcml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/model_ODE_deterministic.xml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/reports.h5
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/simulation.sedml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/Figure1.jpg
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/expected-results.json
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/manifest.xml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/metadata.rdf
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/model.vcml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/model_ODE_stochastic.xml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/reports.h5
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/simulation.sedml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/Figure1.jpg
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/expected-results.json
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/manifest.xml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/metadata.rdf
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/model.vcml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/model_ODE_stochastic.xml
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/reports.h5
test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/simulation.sedml
test_suite/examples/sbml-fbc/Escherichia-coli-core-metabolism.omex
test_suite/examples/sbml-fbc/Escherichia-coli-core-metabolism/expected-results.json
test_suite/examples/sbml-fbc/Escherichia-coli-core-metabolism/flux-map.escher.json
test_suite/examples/sbml-fbc/Escherichia-coli-core-metabolism/flux-map.vg.json
test_suite/examples/sbml-fbc/Escherichia-coli-core-metabolism/manifest.xml
test_suite/examples/sbml-fbc/Escherichia-coli-core-metabolism/metadata.rdf
test_suite/examples/sbml-fbc/Escherichia-coli-core-metabolism/model.xml
test_suite/examples/sbml-fbc/Escherichia-coli-core-metabolism/reports.h5
test_suite/examples/sbml-fbc/Escherichia-coli-core-metabolism/simulation.sedml
test_suite/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling.omex
test_suite/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle.omex
test_suite/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/BIOMD0000000562_url.xml
test_suite/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/Figure3.jpg
test_suite/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/expected-results.json
test_suite/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/manifest.xml
test_suite/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/metadata.rdf
test_suite/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/reports.h5
test_suite/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/simulation.sedml
test_suite/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle/Figure2.jpg
test_suite/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle/activity-flow-diagram.ginml
test_suite/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle/activity-flow-diagram.vg.json
test_suite/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle/expected-results.json
test_suite/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle/manifest.xml
test_suite/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle/metadata.rdf
test_suite/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle/model.xml
test_suite/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle/reports.h5
test_suite/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle/simulation.sedml
test_suite/examples/smoldyn/Lotka-Volterra.omex
test_suite/examples/smoldyn/Lotka-Volterra/expected-results.json
test_suite/examples/smoldyn/Lotka-Volterra/manifest.xml
test_suite/examples/smoldyn/Lotka-Volterra/metadata.rdf
test_suite/examples/smoldyn/Lotka-Volterra/model.txt
test_suite/examples/smoldyn/Lotka-Volterra/reports.h5
test_suite/examples/smoldyn/Lotka-Volterra/simulation.sedml
test_suite/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength.omex
test_suite/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/Figure6.webp
test_suite/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/biomodel_100596964.sedml
test_suite/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/biomodel_100596964.vcml
test_suite/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/expected-results.json
test_suite/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/manifest.xml
test_suite/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/metadata.rdf
test_suite/examples/vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength/reports.h5
test_suite/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells.omex
test_suite/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells/Figure4.gif
test_suite/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells/GH3_Katp.ode
test_suite/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells/expected-results.json
test_suite/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells/manifest.xml
test_suite/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells/metadata.rdf
test_suite/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells/reports.h5
test_suite/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells/simulation.sedml
test_suite/test_processes/__init__.py
test_suite/test_processes/test_cobra_process.py
test_suite/test_processes/test_comparator_process.py
test_suite/test_processes/test_copasi_process.py
test_suite/test_processes/test_process.py
test_suite/test_processes/test_smoldyn_process.py
test_suite/test_processes/test_tellurium_process.py
test_suite/test_steps/__init__.py