├── .github └── workflows │ ├── build-conda.yml │ ├── cibuildwheel.yml │ └── release-biosimulators.yml ├── .gitignore ├── .gitmodules ├── .readthedocs.yaml ├── .zenodo.json ├── ADDITIONAL_LICENCES.md ├── CHANGES.md ├── CITATION.cff ├── CONTRIBUTORS.md ├── DESCRIPTION.md ├── INSTALL.md ├── LATEST.md ├── LICENSE.txt ├── README.md ├── config.py ├── devtest ├── models │ ├── BIOMD0000000012_url.xml │ ├── BIOMD0000000126.xml │ ├── BIOMD0000000860.xml │ └── rohwer_sucrose2.psc ├── out │ ├── BIOMD0000000012_url.xml │ │ └── BIOMD0000000012_url.xml-ref.png │ ├── BIOMD0000000126.xml │ │ └── BIOMD0000000126.xml-ref.png │ ├── BIOMD0000000860.xml │ │ └── BIOMD0000000860.xml-ref.png │ └── rohwer_sucrose2 │ │ ├── rohwer_sucrose2_fluxes-ref.png │ │ ├── rohwer_sucrose2_mca-ref.png │ │ └── rohwer_sucrose2_species-ref.png ├── ref_data │ ├── BIOMD0000000012_url.xml │ │ └── simdata.pkl │ ├── BIOMD0000000126.xml │ │ └── simdata.pkl │ ├── BIOMD0000000860.xml │ │ └── simdata.pkl │ └── rohwer_sucrose2 │ │ ├── mcadata.pkl │ │ ├── scandata.pkl │ │ └── ssdata.pkl ├── run_tests.py ├── test_sbml_log_ln.py ├── test_sbml_rules_functions.py ├── test_sbml_time_events.py └── test_state_mca_scans.py ├── meson.build ├── packaging ├── cibuildwheel │ └── macos_arm64.toml ├── conda-macos-arm64 │ ├── conda_build_config.yaml │ └── meta.yaml ├── conda-scripts │ ├── README.md │ ├── VS2019_gfortran8_build.md │ ├── build_conda_linux.sh │ ├── build_conda_macos.sh │ ├── build_conda_windows.bat │ └── conda_build.txt ├── conda │ ├── conda_build_config.yaml │ └── meta.yaml ├── many_linux │ ├── README.md │ ├── build_pysces.sh │ ├── build_script.sh │ └── run_pysces.sh ├── wheels_win │ ├── Instructions.txt │ ├── README.md │ ├── VS2017_gfortran8_build.md │ ├── create_environment.bat │ └── fix_environment.bat └── windows_libs │ ├── build_export_lib.md │ ├── dlltool.exe │ └── gendef.exe ├── pyproject.toml ├── pysces ├── PyscesConfig.py ├── PyscesContrib.py ├── PyscesContribUser.py ├── PyscesInterfaces.py ├── PyscesJWSParse.py ├── PyscesLink.py ├── PyscesMiniModel.py ├── PyscesModel.py ├── PyscesModelMap.py ├── PyscesParScan.py ├── PyscesParse.py ├── PyscesPlot.py ├── PyscesPlot2.py ├── PyscesRandom.py ├── PyscesSBML.py ├── PyscesSED.py ├── PyscesScan.py ├── PyscesStoich.py ├── PyscesTest.py ├── PyscesUtils.py ├── PyscesWeb.py ├── RateChar.py ├── __init__.py ├── _multicorescan.py ├── contrib │ ├── __init__.py │ ├── demo │ │ ├── __init__.py │ │ └── demotest.py │ ├── sbw │ │ ├── __init__.py │ │ └── sbw_func.py │ └── visualise │ │ ├── VisualiseClasses.py │ │ ├── VisualiseNodeClasses.py │ │ ├── VisualiseSBML.py │ │ └── __init__.py ├── core2 │ ├── InfixParser.py │ ├── PyscesCore2.py │ ├── PyscesCore2Interfaces.py │ ├── PyscesCore2Modules.py │ ├── __init__.py │ ├── lex.py │ ├── version.py │ └── yacc.py ├── docs │ ├── DOCS.txt │ ├── HISTORY.txt │ └── userguide.pdf ├── examples │ ├── benchmark.ipy │ ├── parallelscan.ipy │ ├── pysces_stochpy.py │ ├── testRunScatter.py │ ├── testinvalidstate.py │ ├── testparscanner.py │ └── testratechar.py ├── kraken │ ├── Kraken.py │ ├── KrakenDataTools.py │ ├── KrakenNET.py │ ├── KrakenServer.py │ ├── __init__.py │ ├── controllers │ │ ├── kill_tentacles.py │ │ ├── kraken_continuation.py │ │ ├── kraken_continuation_eigen.py │ │ ├── kraken_continuation_eigen2.py │ │ ├── kraken_intersect.py │ │ └── kraken_scanner2.py │ ├── server_list │ └── startup.py ├── lib │ ├── FirstDerivatives.py │ ├── __init__.py │ ├── lex.py │ ├── miriamids.py │ ├── pyparsing.py │ └── yacc.py ├── meson.build ├── metatool │ └── __init__.py ├── nleq2 │ ├── 4.2 │ │ ├── __init__.py │ │ ├── nleq2.f │ │ ├── nleq2.pyf │ │ ├── nleq2.tar.gz │ │ ├── nleq2_big.f │ │ ├── nleq2_gfortran.f │ │ ├── nleq2_little.f │ │ └── nleq2_little_pre-gcc41.f │ ├── __init__.py │ ├── linalg_nleq2.f │ ├── meson.build │ ├── nleq2-4.3.tar.gz │ ├── nleq2.f │ ├── nleq2.pyf │ ├── nleq2_readme.txt │ ├── readme.txt │ ├── wnorm.f │ ├── zibconst.f │ ├── zibmon.f │ └── zibsec.f ├── pitcon │ ├── __init__.py │ ├── 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