LICENSE.txt
MANIFEST.in
README.rst
ez_setup.py
setup.cfg
setup.py
versioneer.py
doc/Makefile
doc/conf.py
doc/faq.rst
doc/index.rst
doc/installation.rst
doc/make.bat
doc/requirements.txt
doc/tutorial.ipynb
doc/tutorial.md
doc/tutorial.rst
doc/useful_references.rst
doc/examples/fig_mymodel4.png
doc/examples/mymodel.dot
doc/examples/mymodel0.py
doc/examples/mymodel1.py
doc/examples/mymodel2.py
doc/examples/mymodel3.py
doc/examples/mymodel4.py
doc/examples/mymodel5.py
doc/examples/mymodel_fxns.py
doc/examples/robertson_standalone.py
doc/examples/test.png
doc/examples/__pycache__/mymodel4.cpython-37.pyc
doc/modules/bng.rst
doc/modules/core.rst
doc/modules/index.rst
doc/modules/integrate.rst
doc/modules/kappa.rst
doc/modules/macros.rst
doc/modules/modeltests.rst
doc/modules/pattern.rst
doc/modules/simulator.rst
doc/modules/export/bng_net.rst
doc/modules/export/bngl.rst
doc/modules/export/index.rst
doc/modules/export/kappa.rst
doc/modules/export/mathematica.rst
doc/modules/export/matlab.rst
doc/modules/export/potterswheel.rst
doc/modules/export/pysb_flat.rst
doc/modules/export/python.rst
doc/modules/export/sbml.rst
doc/modules/export/stochkit.rst
doc/modules/importers/index.rst
doc/modules/tools/render.rst
doc/modules/tools/render_reactions.rst
doc/modules/tools/render_species.rst
doc/modules/tools/robertson_reactions.png
doc/modules/tools/sensitivity_analysis.rst
pysb/__init__.py
pysb/_version.py
pysb/anneal_mod.py
pysb/annotation.py
pysb/bng.py
pysb/builder.py
pysb/core.py
pysb/integrate.py
pysb/jacobian.py
pysb/kappa.py
pysb/logging.py
pysb/macros.py
pysb/merge.py
pysb/pathfinder.py
pysb/pattern.py
pysb/util.py
pysb.egg-info/PKG-INFO
pysb.egg-info/SOURCES.txt
pysb.egg-info/dependency_links.txt
pysb.egg-info/requires.txt
pysb.egg-info/top_level.txt
pysb/examples/__init__.py
pysb/examples/bax_pore.py
pysb/examples/bax_pore_sequential.py
pysb/examples/bngwiki_egfr_simple.py
pysb/examples/bngwiki_enzymatic_cycle_mm.py
pysb/examples/bngwiki_simple.py
pysb/examples/earm_1_0.py
pysb/examples/earm_1_3.py
pysb/examples/explicit.py
pysb/examples/expression_observables.py
pysb/examples/fixed_initial.py
pysb/examples/fricker_2010_apoptosis.py
pysb/examples/hello_pysb.py
pysb/examples/kinase_cascade.py
pysb/examples/localfunc.py
pysb/examples/michment.py
pysb/examples/move_connected.py
pysb/examples/robertson.py
pysb/examples/run_bax_pore.py
pysb/examples/run_bax_pore_sequential.py
pysb/examples/run_bng_ssa_example.py
pysb/examples/run_earm_1_0.py
pysb/examples/run_earm_hpp.py
pysb/examples/run_earm_stochkit.py
pysb/examples/run_fixed_initial.py
pysb/examples/run_kinase_cascade.py
pysb/examples/run_michment.py
pysb/examples/run_robertson.py
pysb/examples/run_tutorial_a.py
pysb/examples/run_tyson_oscillator.py
pysb/examples/run_tyson_oscillator_stochkit.py
pysb/examples/synth_deg.py
pysb/examples/tutorial_a.py
pysb/examples/tutorial_b.py
pysb/examples/tutorial_c.py
pysb/examples/tyson_oscillator.py
pysb/export/__init__.py
pysb/export/__main__.py
pysb/export/bng_net.py
pysb/export/bngl.py
pysb/export/json.py
pysb/export/kappa.py
pysb/export/mathematica.py
pysb/export/matlab.py
pysb/export/potterswheel.py
pysb/export/pysb_flat.py
pysb/export/python.py
pysb/export/sbml.py
pysb/export/stochkit.py
pysb/generator/__init__.py
pysb/generator/bng.py
pysb/generator/kappa.py
pysb/importers/__init__.py
pysb/importers/bngl.py
pysb/importers/json.py
pysb/importers/kappa.py
pysb/importers/sbml.py
pysb/simulator/__init__.py
pysb/simulator/base.py
pysb/simulator/bng.py
pysb/simulator/cupsoda.py
pysb/simulator/kappa.py
pysb/simulator/scipyode.py
pysb/simulator/stochkit.py
pysb/testing/__init__.py
pysb/testing/modeltests.py
pysb/tests/__init__.py
pysb/tests/jacobian_runtimes.py
pysb/tests/test_bng.py
pysb/tests/test_core.py
pysb/tests/test_examples.py
pysb/tests/test_exporters.py
pysb/tests/test_expressions.py
pysb/tests/test_importer_kappa.py
pysb/tests/test_importers.py
pysb/tests/test_integrate.py
pysb/tests/test_kappa.py
pysb/tests/test_local_only.py
pysb/tests/test_macros.py
pysb/tests/test_merge.py
pysb/tests/test_pattern.py
pysb/tests/test_sensitivity_analysis.py
pysb/tests/test_simulationresult.py
pysb/tests/test_simulator_bng.py
pysb/tests/test_simulator_cupsoda.py
pysb/tests/test_simulator_kappa.py
pysb/tests/test_simulator_scipy.py
pysb/tests/test_simulator_stochkit.py
pysb/tests/test_util.py
pysb/tools/__init__.py
pysb/tools/render_reactions.py
pysb/tools/render_species.py
pysb/tools/sensitivity_analysis.py
pysb/tools/species_graph.py
scripts/pysb_export