├── .dockerignore ├── .github ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── auto-tag.yml │ ├── auto-update.yml │ ├── dockerimage-next.yml │ ├── docs.yml │ ├── for-next.yml │ ├── mirror-ghcr.yml │ ├── mirror-zenodo.yml │ ├── monthly-merge.yml │ ├── release.yml │ └── validate-pr.yml ├── .gitignore ├── CONTRIBUTING.md ├── Dockerfile ├── MANIFEST.in ├── Makefile ├── README.md ├── TROUBLESHOOTING.md ├── bin ├── colomoto-env └── colomoto-nb ├── docs ├── Makefile ├── _config.yml ├── _toc.yml ├── contact.md ├── logo-dark.png ├── logo.png ├── materials.md ├── requirements.txt ├── usage.md ├── usecases.md └── versions.md ├── hooks ├── build ├── release_changes.json ├── release_changes.py ├── requirements.txt └── tools_metadata.py ├── tools ├── ActoNet.md ├── AstroLogics.md ├── TEMPLATE.md ├── aeon.md ├── biolqm.md ├── bns.md ├── bonesis.md ├── booleannet.md ├── boolsim.md ├── boon.md ├── cabean.md ├── caspo.md ├── casq.md ├── cellcollective.md ├── erode.md ├── ginsim.md ├── index.md ├── maboss.md ├── minibn.md ├── mpbn.md ├── nordic.md ├── nusmv.md ├── optboolnet.md ├── pint.md ├── pyboolnet.md ├── pydruglogics.md ├── pystablemotifs.md ├── r-boolnet.md └── scboolseq.md ├── tutorials ├── ActoNet │ ├── ActoNet_Bladder.ipynb │ └── Bladder_Model.zginml ├── AstroLogics │ ├── Analysis_BonesisTutorial.ipynb │ └── ensemble.zip ├── BoNesis │ ├── Marker reprogramming.ipynb │ └── Synthesis of Boolean networks.ipynb ├── BooN │ ├── BooN-demo.ipynb │ └── Th_17.zginml ├── BooleanNet │ └── introduction_to_boleannet.ipynb ├── CABEAN │ ├── CABEAN_Myeloid_reprogramming.ipynb │ └── MyeloidRules.txt ├── CaSQ │ ├── Apoptosis_VS_SSA_AN.sbml │ ├── Apoptosis_VS_SSA_AN.xml │ └── CaSQ_from_CellDesigner_to_GINsim.ipynb ├── Caspo │ ├── Bladder_Model.zginml │ └── Caspo-control_Bladder.ipynb ├── CellCollective │ ├── CellCollective - Knowledge Base.ipynb │ └── cellcollective-2329-1.sbml ├── ERODE │ ├── CAD.bnet │ ├── Reduction of synchronous BNs by Backward Boolean Equivalence.ipynb │ ├── SignallinginMacrophageActivation.bnet │ ├── TCRsig40.zginml │ └── ap-1_else-0_wt.bnet ├── GINsim │ ├── GINsim - visualization.ipynb │ └── SuppMat_Model_Master_Model.zginml ├── MaBoSS │ ├── Four_cycle.bnd │ ├── Four_cycle_FEscape.cfg │ ├── MaBoSS - Quick tutorial.ipynb │ ├── Predict mutations with Pint, refine with MaBoSS.ipynb │ ├── SuppMat_Model_Master_Model.zginml │ ├── Toy Example.ipynb │ ├── example.zginml │ └── tuto.zginml ├── NORDic │ └── NORDic-demo.ipynb ├── NuSMV │ ├── NuSMV with GINsim.ipynb │ └── phageLambda4.zginml ├── Pint │ ├── .gitignore │ ├── SuppMat_Model_Master_Model.zginml │ ├── Th_17.zginml │ ├── cellcollective-2329-1.sbml │ ├── drosophilaCellCycleVariants.zginml │ ├── models │ │ ├── ERBB_G1-S.an │ │ └── metazoan.an │ ├── phageLambda4.zginml │ └── quick-tutorial.ipynb ├── PyBoolNet │ └── PyBoolNet_tutorial.ipynb ├── PyDrugLogics │ ├── modeloutputs │ ├── network.bnet │ ├── network.sif │ ├── pydruglogics_tutorial.ipynb │ └── training ├── R-BoolNet │ └── Random BN generation, loading with biolqm or minibn.ipynb ├── Reproducibility - fixpoints.ipynb ├── Reproducibility - model checking.ipynb ├── Th_17.zginml ├── aeon │ ├── AEON.py Tutorial.ipynb │ ├── Partially specified networks in AEON.ipynb │ ├── Symbolic Computation in AEON.ipynb │ ├── cellcollective-36604-1.sbml │ └── g2a.sbml ├── bioLQM │ ├── Fixpoints (interactive).ipynb │ ├── Layout for regulatory graph.ipynb │ ├── SuppMat_Model_Master_Model.zginml │ ├── bioLQM_tutorial.ipynb │ ├── boolean_cell_cycle.zginml │ ├── cellcollective-2171-1.sbml │ └── phageLambda4.zginml ├── bns │ ├── bns tutorial.ipynb │ ├── boolean_cell_cycle.zginml │ └── cellcycle.cnet ├── boolSim │ ├── SuppMat_Model_Master_Model.zginml │ ├── boolSim - attractors.ipynb │ ├── boolSim - reachable.ipynb │ └── drosophilaCellCycleVariants.zginml ├── minibn │ ├── Computing dynamics with minibn.ipynb │ ├── Model creation and edition with minibn.ipynb │ ├── ModelT2DM_0.zginml │ ├── Simulations with minibn.ipynb │ └── phageLambda4.zginml ├── models │ ├── Apoptosis_VS_SSA_AN.sbml │ ├── Bladder_Model.zginml │ ├── ModelT2DM_0.zginml │ ├── SuppMat_Model_Master_Model.zginml │ ├── Th_17.zginml │ ├── boolean_cell_cycle.zginml │ ├── cellcollective-2171-1.sbml │ ├── cellcollective-2329-1.sbml │ ├── drosophilaCellCycleVariants.zginml │ └── phageLambda4.zginml ├── mpbn │ ├── Bladder_Model.zginml │ ├── Bladder_Remy2015.ipynb │ ├── Quick_example.ipynb │ ├── Simulation.ipynb │ ├── SuppMat_Model_Master_Model.zginml │ └── TumourInvasion_Cohen2015.ipynb ├── optboolnet │ ├── Bladder_Model.zginml │ └── bladder_example.ipynb ├── phageLambda4.zginml ├── pystablemotifs │ ├── 2018_zanudo_proliferation.zginml │ ├── Basic Usage Tutorial.ipynb │ ├── Control Tutorial.ipynb │ └── simple_model.txt └── scBoolSeq │ ├── .gitignore │ ├── scBoolSeq - scRNA-Seq binarization.ipynb │ └── scBoolSeq - synthetic scRNA-Seq generation from Boolean dynamics.ipynb ├── update-n-freeze.json ├── update-n-freeze.py ├── usecases ├── Frontiers-Th-Full-model-annotated.zginml ├── Population-level Cell Fate with UpPMaBoSS │ ├── CellFateModel_uppmaboss.bnd │ ├── CellFateModel_uppmaboss.cfg │ ├── CellFateModel_uppmaboss.ipynb │ ├── CellFateModel_uppmaboss.upp │ └── TimeStepDependency.ipynb ├── SuppMat_Model_Master_Model.zginml ├── Usecase - Balance of Th17 vs Treg cell populations.ipynb ├── Usecase - Mutations enabling tumour invasion.ipynb └── snakemake │ ├── Models │ └── 2016_CellCycle_Traynard │ │ ├── Traynard_MultiLevel_MamCC_Apr2016.zginml │ │ └── Traynard_MultiLevel_MamCC_Apr2016_property.smv │ ├── README.md │ ├── Scripts │ ├── ginsim_export_as_NuSMV.py │ └── nusmv_report_all_tests.py │ └── SnakeMake │ └── Snakefile_GINsim-SS_NuSMV ├── validate.sh └── zenodo_template.json /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/colomoto/colomoto-docker/HEAD/.dockerignore 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