CHANGELOG.md
MANIFEST.in
README.md
requirements-dev.txt
requirements.txt
setup.py
bionetgen/__init__.py
bionetgen/main.py
bionetgen.egg-info/PKG-INFO
bionetgen.egg-info/SOURCES.txt
bionetgen.egg-info/dependency_links.txt
bionetgen.egg-info/entry_points.txt
bionetgen.egg-info/not-zip-safe
bionetgen.egg-info/requires.txt
bionetgen.egg-info/top_level.txt
bionetgen/bng-linux/BNG2.pl
bionetgen/bng-linux/VERSION
bionetgen/bng-linux/Perl2/BNGAction.pm
bionetgen/bng-linux/Perl2/BNGMessages.pm
bionetgen/bng-linux/Perl2/BNGModel.pm
bionetgen/bng-linux/Perl2/BNGOptions.pm
bionetgen/bng-linux/Perl2/BNGOutput.pm
bionetgen/bng-linux/Perl2/BNGUtils.pm
bionetgen/bng-linux/Perl2/Cache.pm
bionetgen/bng-linux/Perl2/CartesianProduct.pm
bionetgen/bng-linux/Perl2/Compartment.pm
bionetgen/bng-linux/Perl2/CompartmentList.pm
bionetgen/bng-linux/Perl2/Component.pm
bionetgen/bng-linux/Perl2/ComponentType.pm
bionetgen/bng-linux/Perl2/Console.pm
bionetgen/bng-linux/Perl2/EnergyPattern.pm
bionetgen/bng-linux/Perl2/Expression.pm
bionetgen/bng-linux/Perl2/Function.pm
bionetgen/bng-linux/Perl2/HNauty.pm
bionetgen/bng-linux/Perl2/MacroBNG2.pl
bionetgen/bng-linux/Perl2/MacroBNGModel.pm
bionetgen/bng-linux/Perl2/Map.pm
bionetgen/bng-linux/Perl2/ModelWrapper.pm
bionetgen/bng-linux/Perl2/Molecule.pm
bionetgen/bng-linux/Perl2/MoleculeType.pm
bionetgen/bng-linux/Perl2/MoleculeTypesList.pm
bionetgen/bng-linux/Perl2/Observable.pm
bionetgen/bng-linux/Perl2/Param.pm
bionetgen/bng-linux/Perl2/ParamList.pm
bionetgen/bng-linux/Perl2/Population.pm
bionetgen/bng-linux/Perl2/PopulationList.pm
bionetgen/bng-linux/Perl2/RateLaw.pm
bionetgen/bng-linux/Perl2/RefineRule.pm
bionetgen/bng-linux/Perl2/Rxn.pm
bionetgen/bng-linux/Perl2/RxnList.pm
bionetgen/bng-linux/Perl2/RxnRule.pm
bionetgen/bng-linux/Perl2/SBMLMultiAux.pm
bionetgen/bng-linux/Perl2/Species.pm
bionetgen/bng-linux/Perl2/SpeciesGraph.pm
bionetgen/bng-linux/Perl2/SpeciesList.pm
bionetgen/bng-linux/Perl2/XMLReader.pm
bionetgen/bng-linux/Perl2/auto_hpp.pl
bionetgen/bng-linux/Perl2/diff_net.pl
bionetgen/bng-linux/Perl2/sample_vars_2.pl
bionetgen/bng-linux/Perl2/scan_var.pl
bionetgen/bng-linux/Perl2/test_cartesianproduct.pl
bionetgen/bng-linux/Perl2/verify.pl
bionetgen/bng-linux/Perl2/Aux2/MakeBin.pl
bionetgen/bng-linux/Perl2/Aux2/bnglstat.pl
bionetgen/bng-linux/Perl2/Aux2/count_blocks.pl
bionetgen/bng-linux/Perl2/Aux2/count_lines.pl
bionetgen/bng-linux/Perl2/Aux2/countdown.pl
bionetgen/bng-linux/Perl2/Aux2/diff_cdat.pl
bionetgen/bng-linux/Perl2/Aux2/express.pl
bionetgen/bng-linux/Perl2/Aux2/express_main.pl
bionetgen/bng-linux/Perl2/Aux2/group_size.pl
bionetgen/bng-linux/Perl2/Aux2/runBNG.pl
bionetgen/bng-linux/Perl2/Aux2/test.pl
bionetgen/bng-linux/Perl2/Aux2/test_compartment.pl
bionetgen/bng-linux/Perl2/Aux2/test_molorder.pl
bionetgen/bng-linux/Perl2/Aux2/test_redirect.pl
bionetgen/bng-linux/Perl2/Aux2/test_sub.pl
bionetgen/bng-linux/Perl2/Boolean2BNGL/ABC_example.txt
bionetgen/bng-linux/Perl2/Boolean2BNGL/Boolean2BNGL.pl
bionetgen/bng-linux/Perl2/Boolean2BNGL/Tcell_model_Nov2013_LAH.txt
bionetgen/bng-linux/Perl2/Boolean2BNGL/Tcell_model_Oct2013.txt
bionetgen/bng-linux/Perl2/Boolean2BNGL/Tcell_model_v16.txt
bionetgen/bng-linux/Perl2/Visualization/ContactMap.pm
bionetgen/bng-linux/Perl2/Visualization/GML.pm
bionetgen/bng-linux/Perl2/Visualization/NetworkGraph.pm
bionetgen/bng-linux/Perl2/Visualization/ProcessGraph.pm
bionetgen/bng-linux/Perl2/Visualization/README
bionetgen/bng-linux/Perl2/Visualization/RINF.pm
bionetgen/bng-linux/Perl2/Visualization/StructureGraph.pm
bionetgen/bng-linux/Perl2/Visualization/VisOptParse.pm
bionetgen/bng-linux/Perl2/Visualization/Viz.pm
bionetgen/bng-linux/Perl2/Visualization/analyze.pl
bionetgen/bng-linux/Perl2/Visualization/readGML.pl
bionetgen/bng-linux/Perl2/Visualization/visualize.pl
bionetgen/bng-linux/Perl2/XML/TreePP.pm
bionetgen/bng-linux/bin/NFsim
bionetgen/bng-linux/bin/run_network
bionetgen/bng-linux/bin/sundials-config
bionetgen/bng-mac/BNG2.pl
bionetgen/bng-mac/VERSION
bionetgen/bng-mac/Perl2/BNGAction.pm
bionetgen/bng-mac/Perl2/BNGMessages.pm
bionetgen/bng-mac/Perl2/BNGModel.pm
bionetgen/bng-mac/Perl2/BNGOptions.pm
bionetgen/bng-mac/Perl2/BNGOutput.pm
bionetgen/bng-mac/Perl2/BNGUtils.pm
bionetgen/bng-mac/Perl2/Cache.pm
bionetgen/bng-mac/Perl2/CartesianProduct.pm
bionetgen/bng-mac/Perl2/Compartment.pm
bionetgen/bng-mac/Perl2/CompartmentList.pm
bionetgen/bng-mac/Perl2/Component.pm
bionetgen/bng-mac/Perl2/ComponentType.pm
bionetgen/bng-mac/Perl2/Console.pm
bionetgen/bng-mac/Perl2/EnergyPattern.pm
bionetgen/bng-mac/Perl2/Expression.pm
bionetgen/bng-mac/Perl2/Function.pm
bionetgen/bng-mac/Perl2/HNauty.pm
bionetgen/bng-mac/Perl2/MacroBNG2.pl
bionetgen/bng-mac/Perl2/MacroBNGModel.pm
bionetgen/bng-mac/Perl2/Map.pm
bionetgen/bng-mac/Perl2/ModelWrapper.pm
bionetgen/bng-mac/Perl2/Molecule.pm
bionetgen/bng-mac/Perl2/MoleculeType.pm
bionetgen/bng-mac/Perl2/MoleculeTypesList.pm
bionetgen/bng-mac/Perl2/Observable.pm
bionetgen/bng-mac/Perl2/Param.pm
bionetgen/bng-mac/Perl2/ParamList.pm
bionetgen/bng-mac/Perl2/Population.pm
bionetgen/bng-mac/Perl2/PopulationList.pm
bionetgen/bng-mac/Perl2/RateLaw.pm
bionetgen/bng-mac/Perl2/RefineRule.pm
bionetgen/bng-mac/Perl2/Rxn.pm
bionetgen/bng-mac/Perl2/RxnList.pm
bionetgen/bng-mac/Perl2/RxnRule.pm
bionetgen/bng-mac/Perl2/SBMLMultiAux.pm
bionetgen/bng-mac/Perl2/Species.pm
bionetgen/bng-mac/Perl2/SpeciesGraph.pm
bionetgen/bng-mac/Perl2/SpeciesList.pm
bionetgen/bng-mac/Perl2/XMLReader.pm
bionetgen/bng-mac/Perl2/auto_hpp.pl
bionetgen/bng-mac/Perl2/diff_net.pl
bionetgen/bng-mac/Perl2/sample_vars_2.pl
bionetgen/bng-mac/Perl2/scan_var.pl
bionetgen/bng-mac/Perl2/test_cartesianproduct.pl
bionetgen/bng-mac/Perl2/verify.pl
bionetgen/bng-mac/Perl2/Aux2/MakeBin.pl
bionetgen/bng-mac/Perl2/Aux2/bnglstat.pl
bionetgen/bng-mac/Perl2/Aux2/count_blocks.pl
bionetgen/bng-mac/Perl2/Aux2/count_lines.pl
bionetgen/bng-mac/Perl2/Aux2/countdown.pl
bionetgen/bng-mac/Perl2/Aux2/diff_cdat.pl
bionetgen/bng-mac/Perl2/Aux2/express.pl
bionetgen/bng-mac/Perl2/Aux2/express_main.pl
bionetgen/bng-mac/Perl2/Aux2/group_size.pl
bionetgen/bng-mac/Perl2/Aux2/runBNG.pl
bionetgen/bng-mac/Perl2/Aux2/test.pl
bionetgen/bng-mac/Perl2/Aux2/test_compartment.pl
bionetgen/bng-mac/Perl2/Aux2/test_molorder.pl
bionetgen/bng-mac/Perl2/Aux2/test_redirect.pl
bionetgen/bng-mac/Perl2/Aux2/test_sub.pl
bionetgen/bng-mac/Perl2/Boolean2BNGL/ABC_example.txt
bionetgen/bng-mac/Perl2/Boolean2BNGL/Boolean2BNGL.pl
bionetgen/bng-mac/Perl2/Boolean2BNGL/Tcell_model_Nov2013_LAH.txt
bionetgen/bng-mac/Perl2/Boolean2BNGL/Tcell_model_Oct2013.txt
bionetgen/bng-mac/Perl2/Boolean2BNGL/Tcell_model_v16.txt
bionetgen/bng-mac/Perl2/Visualization/ContactMap.pm
bionetgen/bng-mac/Perl2/Visualization/GML.pm
bionetgen/bng-mac/Perl2/Visualization/NetworkGraph.pm
bionetgen/bng-mac/Perl2/Visualization/ProcessGraph.pm
bionetgen/bng-mac/Perl2/Visualization/README
bionetgen/bng-mac/Perl2/Visualization/RINF.pm
bionetgen/bng-mac/Perl2/Visualization/StructureGraph.pm
bionetgen/bng-mac/Perl2/Visualization/VisOptParse.pm
bionetgen/bng-mac/Perl2/Visualization/Viz.pm
bionetgen/bng-mac/Perl2/Visualization/analyze.pl
bionetgen/bng-mac/Perl2/Visualization/readGML.pl
bionetgen/bng-mac/Perl2/Visualization/visualize.pl
bionetgen/bng-mac/Perl2/XML/TreePP.pm
bionetgen/bng-mac/bin/NFsim
bionetgen/bng-mac/bin/run_network
bionetgen/bng-mac/bin/sundials-config
bionetgen/bng-win/BNG2.pl
bionetgen/bng-win/VERSION
bionetgen/bng-win/Perl2/BNGAction.pm
bionetgen/bng-win/Perl2/BNGMessages.pm
bionetgen/bng-win/Perl2/BNGModel.pm
bionetgen/bng-win/Perl2/BNGOptions.pm
bionetgen/bng-win/Perl2/BNGOutput.pm
bionetgen/bng-win/Perl2/BNGUtils.pm
bionetgen/bng-win/Perl2/Cache.pm
bionetgen/bng-win/Perl2/CartesianProduct.pm
bionetgen/bng-win/Perl2/Compartment.pm
bionetgen/bng-win/Perl2/CompartmentList.pm
bionetgen/bng-win/Perl2/Component.pm
bionetgen/bng-win/Perl2/ComponentType.pm
bionetgen/bng-win/Perl2/Console.pm
bionetgen/bng-win/Perl2/EnergyPattern.pm
bionetgen/bng-win/Perl2/Expression.pm
bionetgen/bng-win/Perl2/Function.pm
bionetgen/bng-win/Perl2/HNauty.pm
bionetgen/bng-win/Perl2/MacroBNG2.pl
bionetgen/bng-win/Perl2/MacroBNGModel.pm
bionetgen/bng-win/Perl2/Map.pm
bionetgen/bng-win/Perl2/ModelWrapper.pm
bionetgen/bng-win/Perl2/Molecule.pm
bionetgen/bng-win/Perl2/MoleculeType.pm
bionetgen/bng-win/Perl2/MoleculeTypesList.pm
bionetgen/bng-win/Perl2/Observable.pm
bionetgen/bng-win/Perl2/Param.pm
bionetgen/bng-win/Perl2/ParamList.pm
bionetgen/bng-win/Perl2/Population.pm
bionetgen/bng-win/Perl2/PopulationList.pm
bionetgen/bng-win/Perl2/RateLaw.pm
bionetgen/bng-win/Perl2/RefineRule.pm
bionetgen/bng-win/Perl2/Rxn.pm
bionetgen/bng-win/Perl2/RxnList.pm
bionetgen/bng-win/Perl2/RxnRule.pm
bionetgen/bng-win/Perl2/SBMLMultiAux.pm
bionetgen/bng-win/Perl2/Species.pm
bionetgen/bng-win/Perl2/SpeciesGraph.pm
bionetgen/bng-win/Perl2/SpeciesList.pm
bionetgen/bng-win/Perl2/XMLReader.pm
bionetgen/bng-win/Perl2/auto_hpp.pl
bionetgen/bng-win/Perl2/diff_net.pl
bionetgen/bng-win/Perl2/sample_vars_2.pl
bionetgen/bng-win/Perl2/scan_var.pl
bionetgen/bng-win/Perl2/test_cartesianproduct.pl
bionetgen/bng-win/Perl2/verify.pl
bionetgen/bng-win/Perl2/Aux2/MakeBin.pl
bionetgen/bng-win/Perl2/Aux2/bnglstat.pl
bionetgen/bng-win/Perl2/Aux2/count_blocks.pl
bionetgen/bng-win/Perl2/Aux2/count_lines.pl
bionetgen/bng-win/Perl2/Aux2/countdown.pl
bionetgen/bng-win/Perl2/Aux2/diff_cdat.pl
bionetgen/bng-win/Perl2/Aux2/express.pl
bionetgen/bng-win/Perl2/Aux2/express_main.pl
bionetgen/bng-win/Perl2/Aux2/group_size.pl
bionetgen/bng-win/Perl2/Aux2/runBNG.pl
bionetgen/bng-win/Perl2/Aux2/test.pl
bionetgen/bng-win/Perl2/Aux2/test_compartment.pl
bionetgen/bng-win/Perl2/Aux2/test_molorder.pl
bionetgen/bng-win/Perl2/Aux2/test_redirect.pl
bionetgen/bng-win/Perl2/Aux2/test_sub.pl
bionetgen/bng-win/Perl2/Boolean2BNGL/ABC_example.txt
bionetgen/bng-win/Perl2/Boolean2BNGL/Boolean2BNGL.pl
bionetgen/bng-win/Perl2/Boolean2BNGL/Tcell_model_Nov2013_LAH.txt
bionetgen/bng-win/Perl2/Boolean2BNGL/Tcell_model_Oct2013.txt
bionetgen/bng-win/Perl2/Boolean2BNGL/Tcell_model_v16.txt
bionetgen/bng-win/Perl2/Visualization/ContactMap.pm
bionetgen/bng-win/Perl2/Visualization/GML.pm
bionetgen/bng-win/Perl2/Visualization/NetworkGraph.pm
bionetgen/bng-win/Perl2/Visualization/ProcessGraph.pm
bionetgen/bng-win/Perl2/Visualization/README
bionetgen/bng-win/Perl2/Visualization/RINF.pm
bionetgen/bng-win/Perl2/Visualization/StructureGraph.pm
bionetgen/bng-win/Perl2/Visualization/VisOptParse.pm
bionetgen/bng-win/Perl2/Visualization/Viz.pm
bionetgen/bng-win/Perl2/Visualization/analyze.pl
bionetgen/bng-win/Perl2/Visualization/readGML.pl
bionetgen/bng-win/Perl2/Visualization/visualize.pl
bionetgen/bng-win/Perl2/XML/TreePP.pm
bionetgen/bng-win/bin/NFsim.exe
bionetgen/bng-win/bin/cyggcc_s-seh-1.dll
bionetgen/bng-win/bin/cygstdc++-6.dll
bionetgen/bng-win/bin/cygwin1.dll
bionetgen/bng-win/bin/cygz.dll
bionetgen/bng-win/bin/libgcc_s_dw2-1.dll
bionetgen/bng-win/bin/libstdc++-6.dll
bionetgen/bng-win/bin/run_network.exe
bionetgen/bng-win/bin/sundials-config
bionetgen/core/__init__.py
bionetgen/core/defaults.py
bionetgen/core/exc.py
bionetgen/core/main.py
bionetgen/core/notebook.py
bionetgen/core/plot.py
bionetgen/core/result.py
bionetgen/core/version.py
bionetgen/modelapi/__init__.py
bionetgen/modelapi/blocks.py
bionetgen/modelapi/bngfile.py
bionetgen/modelapi/bngparser.py
bionetgen/modelapi/model.py
bionetgen/modelapi/pattern.py
bionetgen/modelapi/runner.py
bionetgen/modelapi/structs.py
bionetgen/modelapi/utils.py
bionetgen/modelapi/xmlparsers.py
bionetgen/simulator/__init__.py
bionetgen/simulator/simulators.py