├── .DS_Store ├── .github └── workflows │ └── validation.yml ├── .gitignore ├── .gitmodules ├── .readthedocs.yaml ├── Issues ├── 232 │ ├── comp_reversible_1.bngl │ ├── comp_reversible_1 │ │ ├── 2021_07_22__11_39_46 │ │ │ └── comp_reversible_1.bngl │ │ └── 2021_07_22__11_6_10 │ │ │ └── comp_reversible_1.bngl │ ├── comp_reversible_2.bngl │ └── comp_reversible_2 │ │ └── 2021_07_22__11_8_03 │ │ └── comp_reversible_2.bngl ├── 271 │ ├── run_sbml.ipynb │ ├── sbml_express.bngl │ ├── sbml_express │ │ ├── 2024_01_31__13_44_20 │ │ │ └── sbml_express.bngl │ │ ├── 2024_01_31__13_46_26 │ │ │ ├── sbml_express.bngl │ │ │ └── sbml_express_sbml.xml │ │ └── sim_sbml.ipynb │ ├── sbml_express_ratelaw.bngl │ ├── sbml_express_ratelaw │ │ ├── 2024_01_31__14_04_01 │ │ │ ├── sbml_express_ratelaw.bngl │ │ │ └── sbml_express_ratelaw_sbml.xml │ │ ├── 2024_01_31__17_29_33 │ │ │ ├── sbml_express_ratelaw.bngl │ │ │ └── sbml_express_ratelaw_sbml.xml │ │ └── 2024_01_31__17_36_33 │ │ │ ├── sbml_express_ratelaw.bngl │ │ │ └── sbml_express_ratelaw_sbml.xml │ ├── sbml_express_ratelaw_sbml.xml │ └── sbml_express_sbml.xml ├── 273 │ └── action_parameter.bngl ├── .DS_Store ├── Help with pyBNG │ ├── BNG_error.txt │ ├── FTC_A4_B4_20uM.bngl │ ├── FTC_A4_B4_20uM.species │ ├── FTC_A4_B4_20uM.xml │ ├── auto.bngl │ ├── run_bng.py │ └── timeDepFunction.bngl ├── nestedIF │ ├── BillsTest.bngl │ ├── BillsTest │ │ ├── 2024_05_09__17_36_20 │ │ │ ├── BillsTest.bngl │ │ │ ├── BillsTest_NF.species │ │ │ └── BillsTest_NF.xml │ │ └── 2024_05_09__17_37_20 │ │ │ └── BillsTest.bngl │ ├── BillsTest_NF.species │ ├── BillsTest_NF.xml │ ├── nestedIf.bngl │ ├── nestedIf │ │ ├── 2024_05_03__15_40_02 │ │ │ └── nestedIf.bngl │ │ ├── 2024_05_03__15_40_30 │ │ │ └── nestedIf.bngl │ │ └── 2024_05_03__15_41_01 │ │ │ └── nestedIf.bngl │ ├── nested_if.bngl │ ├── test.bngl │ ├── test.species │ ├── test.xml │ └── writeIf.ipynb ├── nfsim_indrani │ ├── .gitignore │ ├── deleteMolecules.bngl │ ├── deleteMolecules │ │ └── 2024_02_07__16_11_07 │ │ │ ├── deleteMolecules.bngl │ │ │ └── deleteMolecules │ │ │ └── 2024_02_07__16_11_47 │ │ │ ├── deleteMolecules.bngl │ │ │ ├── deleteMolecules.net │ │ │ └── deleteMolecules_test.bngl │ ├── deleteMolecules_changed.bngl │ ├── run_nf.ipynb │ ├── run_pybng.ipynb │ ├── run_pybng.py │ ├── test_deleteMolecules.bngl │ ├── test_deleteMolecules.xml │ ├── test_deleteMolecules_changed.bngl │ ├── test_deleteMolecules_simple.bngl │ ├── test_totalRate.bngl │ ├── test_totalRate.xml │ └── test_totalRate_changed.bngl ├── paramchange_rama │ ├── param_change.ipynb │ ├── simple.bngl │ ├── simple │ │ └── 2024_02_13__09_14_02 │ │ │ └── simple.bngl │ └── simple_sbml.xml └── ringOpening_pawel │ ├── .gitignore │ ├── run_sbml.ipynb │ ├── xyz_01.bngl │ ├── xyz_01.net │ ├── xyz_02.bngl │ ├── xyz_02.gdat │ ├── xyz_02.species │ ├── xyz_02.xml │ ├── xyz_03.bngl │ ├── xyz_03.gdat │ ├── xyz_03.species │ ├── xyz_03.xml │ ├── xyz_04.bngl │ ├── xyz_04.gdat │ ├── xyz_04.net │ ├── xyz_04.species │ ├── xyz_04.xml │ ├── xyz_04_sbml.xml │ ├── xyz_04b.bngl │ ├── xyz_04b.gdat │ ├── xyz_04b.net │ ├── xyz_04b.species │ ├── xyz_04b.xml │ ├── xyz_04b_sbml.xml │ ├── xyz_05.bngl │ ├── xyz_05.gdat │ ├── xyz_05.net │ ├── xyz_05.species │ └── xyz_05.xml ├── LICENSE ├── PhiBPlot ├── PhiBPlot.jar ├── README.md └── lib │ ├── jcommon-1.0.0.jar │ ├── jfreechart-1.0.1.jar │ └── swing-layout-1.0.jar ├── README.md ├── bng-graph ├── BNGcore │ ├── BNGcore.hpp │ ├── BNGcore.i │ ├── BNGcore.pm │ ├── BNGcore.so │ ├── BNGcore_wrap.cxx │ ├── CartesianProduct.hpp │ ├── List.hpp │ ├── Makefile │ ├── Map.cpp │ ├── Node.cpp │ ├── NodeType.cpp │ ├── PatternGraph.cpp │ ├── ReactionRule.hpp │ ├── State.cpp │ ├── StateType.cpp │ ├── Transformation.cpp │ ├── Ullmann.cpp │ ├── Ullmann.hpp │ └── Vector.hpp ├── blbr ├── blbr.cpp ├── nauty │ ├── nausparse.c │ ├── nausparse.h │ ├── nautil.c │ ├── nauty.c │ ├── nauty.h │ ├── nauty24.tar.gz │ └── nauty24 │ │ ├── NRswitchg.c │ │ ├── README │ │ ├── addedgeg.c │ │ ├── amtog.c │ │ ├── biplabg.c │ │ ├── callgeng.c │ │ ├── catg.c │ │ ├── checks6.c │ │ ├── complg.c │ │ ├── config.guess │ │ ├── config.sub │ │ ├── config.txt │ │ ├── configure │ │ ├── configure.ac │ │ ├── copyg.c │ │ ├── deledgeg.c │ │ ├── directg.c │ │ ├── dreadnaut.c │ │ ├── dreadtest.c │ │ ├── dretog.c │ │ ├── formats.txt │ │ ├── genbg.c │ │ ├── geng.c │ │ ├── genrang.c │ │ ├── gentourng.c │ │ ├── gread.me │ │ ├── gtnauty.c │ │ ├── gtools-h.in │ │ ├── gtools.c │ │ ├── gtools.h │ │ ├── gutil1.c │ │ ├── gutil2.c │ │ ├── gutils.h │ │ ├── install-sh │ │ ├── labelg.c │ │ ├── listg.c │ │ ├── makefile │ │ ├── makefile.basic │ │ ├── makefile.in │ │ ├── multig.c │ │ ├── naugraph.c │ │ ├── naugroup.c │ │ ├── naugroup.h │ │ ├── nausparse.c │ │ ├── nausparse.h │ │ ├── nautaux.c │ │ ├── nautaux.h │ │ ├── nautest.c │ │ ├── nautest2.c │ │ ├── nautil.c │ │ ├── nautinv.c │ │ ├── nautinv.h │ │ ├── naututil-h.in │ │ ├── naututil.c │ │ ├── naututil.h │ │ ├── nauty-h.in │ │ ├── nauty.c │ │ ├── nauty.h │ │ ├── nautyex1.c │ │ ├── nautyex2.c │ │ ├── nautyex3.c │ │ ├── nautyex4.c │ │ ├── nautyex5.c │ │ ├── newedgeg.c │ │ ├── nug.pdf │ │ ├── planarg.c │ │ ├── planarity.c │ │ ├── planarity.h │ │ ├── rng.c │ │ ├── rng.h │ │ ├── shortg.c │ │ ├── showg.c │ │ ├── splay.c │ │ ├── sumlines.c │ │ ├── testB.dre │ │ ├── testL.dre │ │ ├── testM.dre │ │ ├── testS.dre │ │ ├── testW.dre │ │ ├── testa.dre │ │ ├── testg.c │ │ └── testlab.c └── test.pl ├── bng2 ├── BNG2.pl ├── BooleanConverter │ ├── BioNetGen Logic.doc │ ├── BoolExpr.cpp │ ├── BoolExpr.h │ ├── BoolExprParser.cpp │ ├── BoolExprParser.h │ ├── CompileInstructions.txt │ ├── c-api.cpp │ ├── c-api.h │ ├── final_v0.0.0.cpp │ ├── final_v0.0.1.cpp │ ├── final_v0.0.2.cpp │ ├── final_v0.0.3.cpp │ ├── final_v0.0.4.cpp │ ├── final_v0.0.5.cpp │ ├── final_v0.0.6.cpp │ ├── final_v0.0.7.cpp │ ├── final_v0.0.8.cpp │ ├── final_v0.1.0.cpp │ ├── final_v0.1.1.cpp │ └── test_v0.1.bngb ├── CHANGES.txt ├── CREDITS.txt ├── Makefile ├── Models2 │ ├── BIOMD0000000010.xml │ ├── ButcherTableau.txt │ ├── CaOscillate_Func.bngl │ ├── CaOscillate_Sat.bngl │ ├── EnergyModels │ │ ├── Kiefhaber_emodel.bngl │ │ ├── energy_example1.bngl │ │ ├── mwc.bngl │ │ └── wofsy-goldstein.bngl │ ├── FceriModels │ │ ├── MODELS.txt │ │ ├── fceri_fyn.bngl │ │ ├── fceri_fyn.net │ │ ├── fceri_fyn_lig.bngl │ │ ├── fceri_fyn_trimer.bngl │ │ ├── fceri_gamma2.bngl │ │ ├── fceri_gamma2_asym.bngl │ │ ├── fceri_ji.bngl │ │ ├── fceri_ji_red.bngl │ │ ├── fceri_lyn_745.bngl │ │ └── fceri_trimer.bngl │ ├── Haugh2b.bngl │ ├── LV.bngl │ ├── MCell │ │ ├── README.pdf │ │ ├── default.geometry.mdl │ │ ├── fceri_ji.bngl │ │ ├── fceri_ji_comp.bngl │ │ ├── fceri_ji_comp.geometry.mdl │ │ ├── rec_dim.bngl │ │ ├── rec_dim_comp.bngl │ │ └── rec_dim_comp.geometry.mdl │ ├── Motivating_example.bngl │ ├── Motivating_example_cBNGL.bngl │ ├── Repressilator.bngl │ ├── SHP2_base_model.bngl │ ├── blbr.bngl │ ├── catalysis.bngl │ ├── egfr_net.bngl │ ├── egfr_net_red.bngl │ ├── egfr_path.bngl │ ├── energy_example1.bngl │ ├── fceri_ji.bngl │ ├── gene_expr_func.bngl │ ├── localfunc.bngl │ ├── nfkb.bngl │ ├── nfkb_illustrating_protocols.bngl │ ├── nfkb_illustrating_protocols_R │ │ ├── nfkb_illustrating_protocols_R_00001.cdat │ │ ├── nfkb_illustrating_protocols_R_00001.gdat │ │ ├── nfkb_illustrating_protocols_R_00001.net │ │ ├── nfkb_illustrating_protocols_R_00002.cdat │ │ ├── nfkb_illustrating_protocols_R_00002.gdat │ │ ├── nfkb_illustrating_protocols_R_00002.net │ │ ├── nfkb_illustrating_protocols_R_00003.cdat │ │ ├── nfkb_illustrating_protocols_R_00003.gdat │ │ ├── nfkb_illustrating_protocols_R_00003.net │ │ ├── nfkb_illustrating_protocols_R_00004.cdat │ │ ├── nfkb_illustrating_protocols_R_00004.gdat │ │ └── nfkb_illustrating_protocols_R_00004.net │ ├── parameter_scan_with_protocol.ipynb │ ├── partial_dynamical_scaling.bngl │ ├── run_all.pl │ ├── simargs.txt │ ├── simple_nfsim.bngl │ ├── simple_sbml_import.bngl │ ├── test_continue.bngl │ ├── test_fixed.bngl │ ├── tlbr.bngl │ ├── toy-jim.bngl │ ├── visualize.bngl │ ├── visualize_opts1.txt │ └── visualize_opts2.txt ├── Network3 │ ├── CMakeLists.txt │ ├── INSTALL │ ├── LICENSE │ ├── Makefile.am │ ├── Makefile.cmake │ ├── configure.ac │ └── src │ │ ├── Makefile.am │ │ ├── model │ │ ├── function.cpp │ │ ├── function.hh │ │ ├── observable.cpp │ │ ├── observable.hh │ │ ├── rateExpression.cpp │ │ ├── rateExpression.hh │ │ ├── rateExpressions │ │ │ ├── rateElementary.cpp │ │ │ ├── rateHill.cpp │ │ │ ├── rateMM.cpp │ │ │ ├── rateMuParser.cpp │ │ │ ├── rateMuParser.hh │ │ │ └── rateSaturation.cpp │ │ ├── reaction.cpp │ │ ├── reaction.hh │ │ ├── reactions │ │ │ ├── bioNetGenRxn.cpp │ │ │ ├── bioNetGenRxn.hh │ │ │ ├── elementaryRxn.cpp │ │ │ ├── functionalRxn.cpp │ │ │ ├── hillRxn.cpp │ │ │ ├── michaelisMentenRxn.cpp │ │ │ └── saturationRxn.cpp │ │ ├── simpleSpecies.cpp │ │ ├── simpleSpecies.hh │ │ └── species.hh │ │ ├── network.cpp │ │ ├── network.h │ │ ├── network3.cpp │ │ ├── network3.hh │ │ ├── pla │ │ ├── PLA.cpp │ │ ├── PLA.hh │ │ ├── base │ │ │ ├── firingGenerator.cpp │ │ │ ├── firingGenerator.hh │ │ │ ├── postleapChecker.cpp │ │ │ ├── postleapChecker.hh │ │ │ ├── rxnClassifier.cpp │ │ │ ├── rxnClassifier.hh │ │ │ ├── tauCalculator.cpp │ │ │ └── tauCalculator.hh │ │ ├── eRungeKutta │ │ │ ├── base │ │ │ │ ├── eRungeKutta_BASE.hh │ │ │ │ ├── eRungeKutta_TC_RC_FG_PL.cpp │ │ │ │ ├── eRungeKutta_TC_RC_FG_rbPL.cpp │ │ │ │ └── eRungeKutta_TC_RC_FG_sbPL.cpp │ │ │ ├── eRungeKutta.hh │ │ │ ├── eRungeKutta_postTC_RC_FG_rbPL.cpp │ │ │ ├── eRungeKutta_postTC_RC_FG_sbPL.cpp │ │ │ ├── eRungeKutta_preTC_RC_FG_negPL.cpp │ │ │ ├── eRungeKutta_preTC_RC_FG_rbPL.cpp │ │ │ ├── eRungeKutta_preTC_RC_FG_sbPL.cpp │ │ │ ├── extra │ │ │ │ ├── eRK_FG.cpp │ │ │ │ ├── eRK_FG.hh │ │ │ │ ├── eRK_RC.cpp │ │ │ │ ├── eRK_RC.hh │ │ │ │ ├── eRungeKutta_EXTRA.hh │ │ │ │ ├── eRungeKutta_FG.cpp │ │ │ │ ├── eRungeKutta_FG_rbPL.cpp │ │ │ │ ├── eRungeKutta_FG_sbPL.cpp │ │ │ │ ├── eRungeKutta_RC_FG.cpp │ │ │ │ ├── eRungeKutta_RC_FG_PL.cpp │ │ │ │ ├── eRungeKutta_TC_FG_rbPL.cpp │ │ │ │ └── eRungeKutta_TC_FG_sbPL.cpp │ │ │ └── util │ │ │ │ ├── aEff_Calculator.cpp │ │ │ │ ├── aEff_Calculator.hh │ │ │ │ ├── binomialCorrector_RK.cpp │ │ │ │ ├── binomialCorrector_RK.hh │ │ │ │ ├── butcherTableau.cpp │ │ │ │ └── butcherTableau.hh │ │ ├── fEuler │ │ │ ├── fEuler.hh │ │ │ ├── fEulerPreleapRB_TC.cpp │ │ │ ├── fEulerPreleapSB_TC.cpp │ │ │ ├── fEulerRB_PL.cpp │ │ │ ├── fEulerRB_TC_PL.cpp │ │ │ ├── fEulerSB_PL.cpp │ │ │ ├── fEulerSB_TC_PL.cpp │ │ │ ├── fEuler_FG.cpp │ │ │ └── fEuler_RC.cpp │ │ ├── midpoint │ │ │ ├── midpoint.hh │ │ │ ├── midpoint_FG.cpp │ │ │ └── midpoint_RC_FG.cpp │ │ └── util │ │ │ ├── fixed_TC.cpp │ │ │ ├── fixed_TC.hh │ │ │ ├── g_Getter.cpp │ │ │ ├── g_Getter.hh │ │ │ ├── negPopChecker.cpp │ │ │ ├── plCheckers.hh │ │ │ ├── preleap_TC.cpp │ │ │ ├── preleap_TC.hh │ │ │ ├── rbChecker.cpp │ │ │ └── sbChecker.cpp │ │ ├── run_network.cpp │ │ ├── std_include.hh │ │ └── util │ │ ├── MTrand │ │ ├── mtrand.cpp │ │ ├── mtrand.h │ │ └── mtreadme.txt │ │ ├── constants.hh │ │ ├── conversion.cpp │ │ ├── conversion.hh │ │ ├── mathutils │ │ ├── Makefile │ │ ├── allocate.c │ │ ├── cabs.c │ │ ├── cadd.c │ │ ├── cconj.c │ │ ├── cmult.c │ │ ├── complex_zero.c │ │ ├── copy_vector.c │ │ ├── cprob.c │ │ ├── csub.c │ │ ├── dotp.c │ │ ├── eigensystem.c │ │ ├── expi.c │ │ ├── gram_schmidt.c │ │ ├── herm_matrix_mult.c │ │ ├── herm_matrix_vector_mult.c │ │ ├── icmult.c │ │ ├── init.c │ │ ├── integration.c │ │ ├── linsolve.c │ │ ├── matherr.c │ │ ├── mathutils.h │ │ ├── matrix_add.c │ │ ├── matrix_elt.c │ │ ├── matrix_mult.c │ │ ├── matrix_sub.c │ │ ├── matrix_transpose.c │ │ ├── matrix_vector_mult.c │ │ ├── matrixexp.c │ │ ├── minimum.c │ │ ├── norm.c │ │ ├── normsq.c │ │ ├── project.c │ │ ├── random.c │ │ ├── rcmult.c │ │ ├── rect_transpose.c │ │ ├── roots.c │ │ ├── runge-kutta.c │ │ ├── scale_vector.c │ │ ├── splines.c │ │ ├── sum_vector.c │ │ ├── svd.c │ │ ├── sym_linsolve.c │ │ ├── sym_matrix_mult.c │ │ ├── sym_matrix_vector_mult.c │ │ ├── sympos_linsolve.c │ │ ├── test_transpose.c │ │ ├── testdummy.c │ │ ├── testgram.c │ │ ├── testspline.c │ │ ├── testsvd.c │ │ ├── testutils.c │ │ ├── vector_add.c │ │ ├── vector_dist.c │ │ ├── zcopy_vector.c │ │ ├── zdotc.c │ │ ├── zdotu.c │ │ ├── zmatrix_add.c │ │ ├── zmatrix_mult.c │ │ ├── zmatrix_sub.c │ │ ├── zmatrix_transpose.c │ │ ├── zmatrix_vector_mult.c │ │ ├── znorm.c │ │ ├── znormsq.c │ │ ├── zrscale_vector.c │ │ ├── zscale_vector.c │ │ ├── zsum_vector.c │ │ └── zsym_linsolve.c │ │ ├── misc.cpp │ │ ├── misc.hh │ │ ├── rand.cpp │ │ ├── rand.hh │ │ ├── rand2 │ │ ├── rand2.cpp │ │ └── rand2.hh │ │ └── util.hh ├── Perl2 │ ├── Aux2 │ │ ├── MakeBin.pl │ │ ├── bnglstat.pl │ │ ├── count_blocks.pl │ │ ├── count_lines.pl │ │ ├── countdown.pl │ │ ├── diff_cdat.pl │ │ ├── express.pl │ │ ├── express_main.pl │ │ ├── group_size.pl │ │ ├── runBNG.pl │ │ ├── test.pl │ │ ├── test_compartment.pl │ │ ├── test_molorder.pl │ │ ├── test_redirect.pl │ │ └── test_sub.pl │ ├── BNGAction.pm │ ├── BNGMessages.pm │ ├── BNGModel.pm │ ├── BNGOptions.pm │ ├── BNGOutput.pm │ ├── BNGUtils.pm │ ├── Boolean2BNGL │ │ ├── ABC_example.txt │ │ ├── Boolean2BNGL.pl │ │ ├── Tcell_model_Nov2013_LAH.txt │ │ ├── Tcell_model_Oct2013.txt │ │ └── Tcell_model_v16.txt │ ├── Cache.pm │ ├── CartesianProduct.pm │ ├── Compartment.pm │ ├── CompartmentList.pm │ ├── Component.pm │ ├── ComponentType.pm │ ├── Console.pm │ ├── EnergyPattern.pm │ ├── Expression.pm │ ├── Function.pm │ ├── HNauty.pm │ ├── MacroBNG2.pl │ ├── MacroBNGModel.pm │ ├── Map.pm │ ├── ModelWrapper.pm │ ├── Molecule.pm │ ├── MoleculeType.pm │ ├── MoleculeTypesList.pm │ ├── Observable.pm │ ├── Param.pm │ ├── ParamList.pm │ ├── Population.pm │ ├── PopulationList.pm │ ├── RateLaw.pm │ ├── RefineRule.pm │ ├── Rxn.pm │ ├── RxnList.pm │ ├── RxnRule.pm │ ├── SBMLMultiAux.pm │ ├── Species.pm │ ├── SpeciesGraph.pm │ ├── SpeciesList.pm │ ├── Visualization │ │ ├── ContactMap.pm │ │ ├── GML.pm │ │ ├── NetworkGraph.pm │ │ ├── ProcessGraph.pm │ │ ├── README │ │ ├── RINF.pm │ │ ├── StructureGraph.pm │ │ ├── VisOptParse.pm │ │ ├── Viz.pm │ │ ├── analyze.pl │ │ ├── readGML.pl │ │ └── visualize.pl │ ├── XML │ │ └── TreePP.pm │ ├── XMLReader.pm │ ├── auto_hpp.pl │ ├── diff_net.pl │ ├── sample_vars_2.pl │ ├── scan_var.pl │ ├── test_cartesianproduct.pl │ └── verify.pl ├── RuleBuilder │ ├── Examples │ │ └── toy-jim.bng │ ├── INSTALL_RB.pdf │ ├── RuleBuilder-beta-1.51.jar │ ├── RuleBuilder_GettingStarted.pdf │ └── rulebuilder.cfg ├── Tutorial │ ├── example1.bngl │ ├── example1.cdat │ ├── example1.gdat │ ├── example1.log │ ├── example1.net │ └── tutorial.txt ├── VERSION ├── Validate │ ├── ANx.bngl │ ├── CaOscillate_Func.bngl │ ├── CaOscillate_Sat.bngl │ ├── DAT_validate │ │ ├── ANx.xml │ │ ├── CaOscillate_Func.cdat │ │ ├── CaOscillate_Func.gdat │ │ ├── CaOscillate_Func.net │ │ ├── CaOscillate_Sat.cdat │ │ ├── CaOscillate_Sat.gdat │ │ ├── CaOscillate_Sat.net │ │ ├── Haugh2b.cdat │ │ ├── Haugh2b.gdat │ │ ├── Haugh2b.net │ │ ├── Haugh2b.xml │ │ ├── Motivating_example.cdat │ │ ├── Motivating_example.gdat │ │ ├── Motivating_example.net │ │ ├── Motivating_example_cBNGL.cdat │ │ ├── Motivating_example_cBNGL.gdat │ │ ├── Motivating_example_cBNGL.net │ │ ├── Motivating_example_cBNGL_sbml.xml │ │ ├── Motivating_example_sbml.xml │ │ ├── Repressilator.cdat │ │ ├── Repressilator.gdat │ │ ├── Repressilator.net │ │ ├── SHP2_base_model.cdat │ │ ├── SHP2_base_model.gdat │ │ ├── SHP2_base_model.net │ │ ├── blbr.net │ │ ├── continue.cdat │ │ ├── continue.gdat │ │ ├── continue.net │ │ ├── deleteMolecules.net │ │ ├── egfr_net.cdat │ │ ├── egfr_net.gdat │ │ ├── empty_compartments_block.net │ │ ├── fceri_ji.cdat │ │ ├── fceri_ji.gdat │ │ ├── gene_expr_func_nf_equil.stats │ │ ├── gene_expr_func_ssa_equil.stats │ │ ├── gene_expr_nf_equil.stats │ │ ├── gene_expr_sbml.xml │ │ ├── gene_expr_simple_nf_equil.stats │ │ ├── gene_expr_simple_ssa_equil.stats │ │ ├── gene_expr_ssa_equil.stats │ │ ├── heise.cdat │ │ ├── heise.gdat │ │ ├── heise.net │ │ ├── hybrid_test_hpp.bngl │ │ ├── hybrid_test_hpp.xml │ │ ├── isingspin_energy.net │ │ ├── isingspin_energy_ssa_equil.stats │ │ ├── isingspin_localfcn.net │ │ ├── isingspin_localfcn_nf_equil.stats │ │ ├── isingspin_localfcn_ssa_equil.stats │ │ ├── isomerization_ssa_equil.stats │ │ ├── issue_198_short.gdat │ │ ├── issue_198_short.net │ │ ├── localfunc.cdat │ │ ├── localfunc.gdat │ │ ├── localfunc.m │ │ ├── localfunc.net │ │ ├── localfunc_mex.m │ │ ├── localfunc_mex_cvode.c │ │ ├── michment.cdat │ │ ├── michment.gdat │ │ ├── michment.net │ │ ├── michment_cont.cdat │ │ ├── michment_cont.gdat │ │ ├── michment_cont.net │ │ ├── motor.cdat │ │ ├── motor.gdat │ │ ├── motor.net │ │ ├── nfkb_illustrating_protocols.scan │ │ ├── reformat.pl │ │ ├── reformat_all.pl │ │ ├── simple_system.cdat │ │ ├── simple_system.gdat │ │ ├── simple_system.net │ │ ├── simple_system.xml │ │ ├── statfactor.net │ │ ├── statfactor_R1_StatFactorCalculation.txt │ │ ├── statfactor_R2_StatFactorCalculation.txt │ │ ├── statfactor_R3_StatFactorCalculation.txt │ │ ├── statfactor__reverse_R1_StatFactorCalculation.txt │ │ ├── statfactor__reverse_R2_StatFactorCalculation.txt │ │ ├── statfactor__reverse_R3_StatFactorCalculation.txt │ │ ├── test.dat │ │ ├── test_ANG_SSA_synthesis_simple.net │ │ ├── test_ANG_parscan_synthesis_simple.net │ │ ├── test_ANG_synthesis_simple.cdat │ │ ├── test_ANG_synthesis_simple.gdat │ │ ├── test_ANG_synthesis_simple.net │ │ ├── test_MM.cdat │ │ ├── test_assignment.net │ │ ├── test_compartment_XML.net │ │ ├── test_compartment_XML.xml │ │ ├── test_fixed.cdat │ │ ├── test_fixed.gdat │ │ ├── test_fixed.net │ │ ├── test_heterogeneous_adaptive_scaling.cdat │ │ ├── test_heterogeneous_adaptive_scaling.gdat │ │ ├── test_heterogeneous_adaptive_scaling.net │ │ ├── test_mratio.cdat │ │ ├── test_mratio.gdat │ │ ├── test_mratio.net │ │ ├── test_network_gen.cdat │ │ ├── test_network_gen.gdat │ │ ├── test_network_gen.net │ │ ├── test_paramname.cdat │ │ ├── test_sat.cdat │ │ ├── test_sat_cont.cdat │ │ ├── test_sbml_flat.cdat │ │ ├── test_sbml_flat.gdat │ │ ├── test_sbml_flat.net │ │ ├── test_sbml_flat_SBML.bngl │ │ ├── test_sbml_structured.cdat │ │ ├── test_sbml_structured.gdat │ │ ├── test_sbml_structured.net │ │ ├── test_sbml_structured_SBML.bngl │ │ ├── test_setconc.cdat │ │ ├── test_setconc.gdat │ │ ├── test_setconc.m │ │ ├── test_setconc.net │ │ ├── test_setconc.xml │ │ ├── test_synthesis_cBNGL_simple.cdat │ │ ├── test_synthesis_cBNGL_simple.gdat │ │ ├── test_synthesis_cBNGL_simple.net │ │ ├── test_synthesis_complex.cdat │ │ ├── test_synthesis_complex.gdat │ │ ├── test_synthesis_complex.net │ │ ├── test_synthesis_complex_0_cBNGL.cdat │ │ ├── test_synthesis_complex_0_cBNGL.gdat │ │ ├── test_synthesis_complex_0_cBNGL.net │ │ ├── test_synthesis_complex_source_cBNGL.cdat │ │ ├── test_synthesis_complex_source_cBNGL.gdat │ │ ├── test_synthesis_complex_source_cBNGL.net │ │ ├── test_synthesis_simple.cdat │ │ ├── test_synthesis_simple.gdat │ │ ├── test_synthesis_simple.net │ │ ├── test_write_sbml_multi_sbml_sbmlmulti.xml │ │ ├── tlbr.cdat │ │ ├── tlbr.gdat │ │ ├── tlbr.net │ │ ├── tlmr.cdat │ │ ├── toy-jim.cdat │ │ ├── toy-jim.gdat │ │ ├── toy-jim.net │ │ ├── toy-jim_equil.cdat │ │ ├── toy-jim_equil.gdat │ │ ├── toy-jim_equil.net │ │ ├── univ_synth.cdat │ │ ├── univ_synth.gdat │ │ ├── univ_synth.net │ │ ├── visualize_contactmap.gml │ │ ├── visualize_regulatory_1.gml │ │ ├── visualize_regulatory_2.gml │ │ ├── visualize_regulatory_3.gml │ │ └── visualize_regulatory_4.gml │ ├── Haugh2b.bngl │ ├── INPUT_FILES │ │ ├── test_sbml_flat_SBML.xml │ │ └── test_sbml_structured_SBML.xml │ ├── Motivating_example.bngl │ ├── Motivating_example_cBNGL.bngl │ ├── Repressilator.bngl │ ├── SHP2_base_model.bngl │ ├── blbr.bngl │ ├── compare_rxn.pl │ ├── compare_species.pl │ ├── continue.bngl │ ├── deleteMolecules.bngl │ ├── egfr_net.bngl │ ├── empty_compartments_block.bngl │ ├── fceri_ji.bngl │ ├── gene_expr.bngl │ ├── gene_expr_func.bngl │ ├── gene_expr_simple.bngl │ ├── heise.bngl │ ├── hybrid_test.bngl │ ├── isingspin_energy.bngl │ ├── isingspin_localfcn.bngl │ ├── isomerization.bngl │ ├── issue_198_short.bngl │ ├── localfunc.bngl │ ├── michment.bngl │ ├── michment_cont.bngl │ ├── motor.bngl │ ├── nfkb_illustrating_protocols.bngl │ ├── simple_system.bngl │ ├── statfactor.bngl │ ├── test_ANG_SSA_synthesis_simple.bngl │ ├── test_ANG_parscan_synthesis_simple.bngl │ ├── test_ANG_parscan_synthesis_simple_dummy.scan │ ├── test_ANG_parscan_synthesis_simple_dummy │ │ ├── test_ANG_parscan_synthesis_simple_dummy_00001.cdat │ │ ├── test_ANG_parscan_synthesis_simple_dummy_00001.gdat │ │ ├── test_ANG_parscan_synthesis_simple_dummy_00001.net │ │ ├── test_ANG_parscan_synthesis_simple_dummy_00002.cdat │ │ ├── test_ANG_parscan_synthesis_simple_dummy_00002.gdat │ │ └── test_ANG_parscan_synthesis_simple_dummy_00002.net │ ├── test_ANG_synthesis_simple.bngl │ ├── test_MM.bngl │ ├── test_assignment.bngl │ ├── test_compartment_XML.bngl │ ├── test_fixed.bngl │ ├── test_mratio.bngl │ ├── test_network_gen.bngl │ ├── test_paramname.bngl │ ├── test_partial_dynamical_scaling.bngl │ ├── test_sat.bngl │ ├── test_sat_cont.bngl │ ├── test_sbml_flat.bngl │ ├── test_sbml_structured.bngl │ ├── test_setconc.bngl │ ├── test_synthesis_cBNGL_simple.bngl │ ├── test_synthesis_complex.bngl │ ├── test_synthesis_complex_0_cBNGL.bngl │ ├── test_synthesis_complex_source_cBNGL.bngl │ ├── test_synthesis_simple.bngl │ ├── test_tfun.bngl │ ├── test_tfun.species │ ├── test_tfun.xml │ ├── test_write_sbml_multi.bngl │ ├── tlbr.bngl │ ├── tlmr.bngl │ ├── toy-jim.bngl │ ├── univ_synth.bngl │ ├── validate_examples.pl │ ├── visualize.bngl │ ├── visualize_opts1.txt │ └── visualize_opts2.txt ├── libsource │ ├── Mathutils.tar.gz │ ├── cvode-2.6.0.tar.gz │ ├── gsl-1.9.tar.gz │ ├── muparser_v2_2_4.tar.gz │ └── muparser_v2_2_4.zip └── make_dist.pl ├── compilation_instructions.md ├── docs ├── Makefile ├── assets │ ├── SIR.bngl │ ├── SIR.png │ ├── SIR_example.png │ ├── bmd19.jpg │ ├── bmd48.jpg │ ├── featured.gif │ ├── flagman.png │ ├── for_plotly_dark.svg │ ├── for_plotly_light.svg │ ├── lib_bngmodel_tutorial.ipynb │ ├── library_tutorial.ipynb │ ├── network.svg │ ├── plot_icon_dark.svg │ ├── plot_icon_light.svg │ ├── plotting.gif │ ├── plotting_cli.gif │ ├── runner.gif │ ├── snippets.gif │ └── visualize.gif ├── conf.py ├── make.bat ├── requirements.txt ├── source │ ├── conf.py │ ├── index.rst │ ├── install.rst │ ├── pybng.rst │ ├── pybng_atomizer.rst │ ├── pybng_cli.rst │ ├── pybng_cli_tutorial.rst │ ├── pybng_lib_tutorial.rst │ ├── pybng_library.rst │ ├── pybng_quickstart.rst │ ├── pybng_tutorials.rst │ ├── vsc_devs.rst │ ├── vsc_ext.rst │ ├── vsc_options.rst │ └── vsc_usage.rst └── unused │ ├── .BioNetGen_Beta.html │ ├── BNG-distributions.md │ ├── BNG_Build_Instructions.html │ ├── Gemfile │ ├── Gemfile.lock │ ├── Published_BioNetGen_Models.md │ ├── QRG-30Mar2016.pdf │ ├── _config.yml │ ├── _site │ ├── assets │ │ ├── css │ │ │ └── style.css │ │ ├── fonts │ │ │ ├── Noto-Sans-700 │ │ │ │ ├── Noto-Sans-700.eot │ │ │ │ ├── Noto-Sans-700.svg │ │ │ │ ├── Noto-Sans-700.ttf │ │ │ │ ├── Noto-Sans-700.woff │ │ │ │ └── Noto-Sans-700.woff2 │ │ │ ├── Noto-Sans-700italic │ │ │ │ ├── Noto-Sans-700italic.eot │ │ │ │ ├── Noto-Sans-700italic.svg │ │ │ │ ├── Noto-Sans-700italic.ttf │ │ │ │ ├── Noto-Sans-700italic.woff │ │ │ │ └── Noto-Sans-700italic.woff2 │ │ │ ├── Noto-Sans-italic │ │ │ │ ├── Noto-Sans-italic.eot │ │ │ │ ├── Noto-Sans-italic.svg │ │ │ │ ├── Noto-Sans-italic.ttf │ │ │ │ ├── Noto-Sans-italic.woff │ │ │ │ └── Noto-Sans-italic.woff2 │ │ │ └── Noto-Sans-regular │ │ │ │ ├── Noto-Sans-regular.eot │ │ │ │ ├── Noto-Sans-regular.svg │ │ │ │ ├── Noto-Sans-regular.ttf │ │ │ │ ├── Noto-Sans-regular.woff │ │ │ │ └── Noto-Sans-regular.woff2 │ │ └── js │ │ │ └── scale.fix.js │ ├── index.html │ └── index.md │ └── index.md ├── flow ├── LAH_Jan2014 │ ├── Arterial.bngl │ ├── Brain.bngl │ ├── Fat.bngl │ ├── Gut.bngl │ ├── Heart.bngl │ ├── Kidney.bngl │ ├── Liver.bngl │ ├── Lung.bngl │ ├── Muscle.bngl │ ├── Other.bngl │ ├── RBC_Art.bngl │ ├── RBC_Ven.bngl │ ├── Spleen.bngl │ ├── Tumor.bngl │ ├── Venous.bngl │ ├── physio.flow │ └── univ.bngl └── concept │ ├── Arterial.bngl │ ├── BNGflowDeleteDuplicate.pl │ ├── BNGflowSort.pl │ ├── BNGflowSortOutput.bngl │ ├── Brain.bngl │ ├── Fat.bngl │ ├── Gut.bngl │ ├── Heart.bngl │ ├── Kidney.bngl │ ├── Liver.bngl │ ├── Lung.bngl │ ├── Muscle.bngl │ ├── Organ.bngl │ ├── Other.bngl │ ├── OutBNGflow.pl.bac │ ├── Spleen.bngl │ ├── Tumor.bngl │ ├── Venous.bngl │ ├── heartJH.bngl │ ├── liverJH.bngl │ ├── output.bngl │ ├── output.pl │ ├── physio.flow │ └── physiological_man.bngl ├── make_bundles ├── matlab ├── classes │ ├── bng │ │ ├── bngData.m │ │ ├── bngEnsemble.m │ │ ├── bngExperiment.m │ │ ├── bngLabels.m │ │ ├── bngModel.m │ │ ├── bngObs.m │ │ ├── bngParam.m │ │ ├── bngParamActions.m │ │ ├── bngSampler.m │ │ ├── bngSpecies.m │ │ ├── bngSpeciesActions.m │ │ └── bngTraj.m │ └── dist │ │ ├── distConstant.m │ │ ├── distDiscrete.m │ │ ├── distDiscreteInterval.m │ │ ├── distDiscreteUniform.m │ │ ├── distGeneric.m │ │ ├── distNormal.m │ │ ├── distUniform.m │ │ └── distUniformLog.m ├── examples │ ├── bngModel_Name.m │ ├── example_000.m │ ├── example_001.m │ ├── fitter.m │ ├── initSpecies_Name.m │ ├── model.bngl │ ├── model.m │ ├── model.net │ ├── model_1.gdat │ ├── model_2.gdat │ └── model_3.gdat └── temp │ └── fitting_ensemble │ ├── bestfit.mat │ ├── bngModel_model.m │ ├── fitter.m │ ├── initSpecies_model.m │ ├── mh.mat │ ├── model.bngl │ ├── model.m │ ├── model_1.gdat │ ├── model_2.gdat │ ├── model_3.gdat │ ├── runthis_ens.m │ └── runthis_fit.m └── parsers ├── BNGParser ├── .settings │ ├── org.eclipse.jdt.core.prefs │ └── org.eclipse.ltk.core.refactoring.prefs ├── commons-lang3-3.1.jar ├── compartments.net ├── input.bngl ├── input.txt ├── json.stg ├── lab42c.net ├── mapk.net ├── mcell.stg ├── nfsim1.bngl ├── output.json ├── outputTest.xml ├── s_build ├── schema.xsd ├── src │ ├── BNGGrammar.tokens │ ├── BNGLexer.tokens │ ├── BNGTree.tokens │ ├── antlr-3.3-complete.jar │ └── bngparser │ │ ├── BNGParseData.java │ │ ├── BNGParserUtility.java │ │ ├── MCellTranslatorTester.java │ │ ├── ParserCommands.java │ │ ├── Tester.java │ │ ├── dataType │ │ ├── BondList.java │ │ ├── ChangeableChannelTokenStream.java │ │ ├── Compartments.java │ │ ├── MoleculeBond.java │ │ ├── MoleculeSites.java │ │ ├── MoleculeType.java │ │ ├── ReactionRegister.java │ │ ├── Register.java │ │ └── SingleMoleculeType.java │ │ ├── exceptions │ │ ├── BNGSemanticException.java │ │ └── VariableNotFoundException.java │ │ ├── grammars │ │ ├── BNGGrammar.g │ │ ├── BNGGrammar_Actions.g │ │ ├── BNGGrammar_Expression.g │ │ ├── BNGGrammar_MoleculeDef.g │ │ ├── BNGGrammar_Observables.g │ │ ├── BNGGrammar_Parameters.g │ │ ├── BNGGrammar_ReactionRules.g │ │ ├── BNGGrammar_SeedSpecies.g │ │ ├── BNGLexer.g │ │ ├── BNGTree.g │ │ └── outputGeneration.py │ │ ├── methods │ │ ├── GenericMethods.java │ │ ├── InvertBidirectional.java │ │ ├── ReactionAction.java │ │ └── Singleton.java │ │ └── models │ │ ├── compartment.bngl │ │ ├── egfr_net.bngl │ │ ├── egfr_simple.bngl │ │ └── toy-jim.bngl ├── temp ├── test │ └── eq_Bound_prom1_0.dat ├── testModels │ ├── BP.bngl │ ├── CaOscillate_Func.bngl │ ├── CaOscillate_Sat.bngl │ ├── ExampleModel4_v7.bngl │ ├── ExampleModel4_v8.bngl │ ├── Flabel.bngl │ ├── FullModelBurstSeconds.bngl │ ├── HIV1.bngl │ ├── LR.bngl │ ├── MM_exact.bngl │ ├── MWC.bngl │ ├── Parente.bngl │ ├── SHP2_base_model.bngl │ ├── ST.bngl │ ├── ST_cBNGL.bngl │ ├── S_p_simple.bngl │ ├── TCell_GA.bngl │ ├── TCell_ROA.bngl │ ├── blbr.bngl │ ├── cellcycle.bngl │ ├── cellcycle_mod.bngl │ ├── compartments.bngl │ ├── egfr_net.bngl │ ├── egfr_path.bngl │ ├── egfr_simple.bngl │ ├── fceri_ji.bngl │ ├── fceri_stub.bngl │ ├── geneExpr.bngl │ ├── invivo_reduced_model.bngl │ ├── oscSystem.bngl │ ├── simple.bngl │ ├── simple_system_bng.bngl │ ├── simple_system_nfsim.bngl │ ├── specialSpecies.bngl │ ├── test.bngl │ ├── testTLR4.bngl │ ├── test_sbml_translator.bngl │ ├── testrun.bngl │ ├── toy-jim.bngl │ ├── twoObservableBlock.bngl │ └── visualize.bngl ├── toy-jim.bngl └── xml.stg ├── BipartiteGraph ├── bipartiteGraph.py ├── bpgActions.py ├── bpgAnnotate.py ├── bpgMaps.py ├── bpgModel.py ├── modelviz │ ├── index.html │ └── js │ │ ├── d3.js │ │ ├── data.js │ │ └── viz_engine.js ├── readBNGXML.py └── structures.py ├── ContactMap ├── BM48.xml ├── collapsedContactMap.py ├── createGraph.py ├── fceri.xml ├── networkx_reference.pdf ├── networkx_tutorial.pdf ├── readBNGXML.py ├── server.py ├── structures.py └── structures.pyc ├── annotations ├── YAML │ └── Tiny.pm ├── annotations.pm ├── sample.bngl └── sample.yml ├── gml2sbgn ├── libsbgn.py └── readGML.py └── utils ├── consoleCommands.py ├── extractAtomic.py ├── readBNGXML.py └── smallStructures.py /.DS_Store: -------------------------------------------------------------------------------- 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