.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/execute.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/services/__init__.py
biosimulator_processes/services/rest_service.py
biosimulator_processes/steps/__init__.py
biosimulator_processes/steps/comparator_step.py
biosimulator_processes/steps/ode_simulation.py
biosimulator_processes/steps/parameter_scan.py
biosimulator_processes/steps/viz.py
demos/compositions.ipynb
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
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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
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test_suite/examples/cellml/Elowitz-Nature-2000-Repressilator.omex
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test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE.omex
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test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/NaConductance.channel.nml
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test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/KConductance.channel.nml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/LeakConductance.channel.nml
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test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/NaConductance.channel.nml
test_suite/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/expected-results.json
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test_suite/examples/rba/Escherichia-coli-K12-WT.omex
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test_suite/examples/rba/Escherichia-coli-K12-WT/flux-map.vg.json
test_suite/examples/rba/Escherichia-coli-K12-WT/manifest.xml
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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
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test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/BIOMD0000000297_url.xml
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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
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test_suite/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/BIOMD0000000297_url.xml
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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
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test_suite/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/Figure_4b.vg.json
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test_suite/examples/sbml-core/Elowitz-Nature-2000-Repressilator/BIOMD0000000012_url.xml
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test_suite/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/BIOMD0000000734.xml
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test_suite/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/expected-results.json
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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
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test_suite/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/expected-results.json
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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
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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