├── .coveragerc ├── .gitignore ├── .nojekyll ├── .travis.yml ├── COPYING ├── Dockerfile ├── LICENSE.txt ├── Makefile ├── README.md ├── conda ├── Makefile ├── bld.bat ├── build.sh ├── meta.yaml └── run_test.sh ├── conda_test.sh ├── dipde ├── __init__.py ├── examples │ ├── ExponentialSolver.py │ ├── __init__.py │ ├── cortical_column.png │ ├── cortical_column.py │ ├── excitatory_inhibitory.png │ ├── excitatory_inhibitory.py │ ├── feedforward_exponential_distribution.py │ ├── singlepop.png │ ├── singlepop.py │ ├── singlepop_exponential_distribution.png │ ├── singlepop_exponential_distribution.py │ ├── singlepop_recurrent.png │ ├── singlepop_recurrent.py │ ├── singlepop_sine.png │ ├── singlepop_sine.py │ └── twopop.png ├── experimental │ ├── distributed │ │ ├── __init__.py │ │ ├── distributedconfiguration.py │ │ └── synchronizationharness.py │ ├── distributed_mongo.py │ ├── distributed_sandbox.py │ ├── distributed_zmq.py │ ├── fixed_point_analysis │ │ ├── J.npy │ │ ├── nullspace_intuition.py │ │ ├── parameter_jacobian_ei.py │ │ ├── recurrent_excitatory.py │ │ ├── recurrent_excitatory_nest.py │ │ ├── recurrent_inhibitory.py │ │ ├── recurrent_inhibitory_nest.py │ │ ├── sandbox.py │ │ ├── simple_external.py │ │ ├── simple_external_nest.py │ │ └── tmp.mat │ ├── launch.sh │ ├── mongodistributedconfiguration.py │ ├── pynest │ │ └── __init__.py │ └── xtest_distributed.py ├── interfaces │ ├── __init__.py │ ├── access_matrices.py │ ├── mpi │ │ ├── __init__.py │ │ ├── benchmark.py │ │ ├── run_benchmark.py │ │ └── synchronizationharness.py │ ├── networkx │ │ └── __init__.py │ ├── neuroml │ │ ├── __init__.py │ │ ├── dipde_2.net.nml │ │ └── sandbox.py │ ├── nwb │ │ └── __init__.py │ ├── pandas │ │ └── __init__.py │ └── zmq │ │ └── __init__.py ├── internals │ ├── __init__.py │ ├── connection.py │ ├── connectiondistribution.py │ ├── connectiondistributioncollection.py │ ├── externalpopulation.py │ ├── firingrateorganizer.py │ ├── internalpopulation.py │ ├── network.py │ ├── simulation.py │ ├── simulationconfiguration.py │ └── utilities.py ├── profiling │ └── __init__.py ├── test │ ├── __init__.py │ ├── test_analysis.py │ ├── test_basic.py │ ├── test_copy.py │ ├── test_delay.py │ ├── test_distribution_constuctor.py │ ├── test_examples.py │ ├── test_interfaces.py │ ├── test_marshal.py │ ├── test_matrices.py │ ├── test_mpi.py │ ├── test_pandas.py │ ├── test_profiling.py │ ├── test_propogation_methods.py │ ├── test_singlepop.py │ └── test_utilities.py └── visualization │ ├── __init__.py │ └── sandbox.py ├── doc ├── Makefile ├── build │ ├── doctrees │ │ ├── dipde.column.doctree │ │ ├── dipde.doctree │ │ ├── dipde.examples.doctree │ │ ├── dipde.internals.doctree │ │ ├── environment.pickle │ │ ├── index.doctree │ │ └── user.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _images │ │ └── Dipde_Nick_final.png │ │ ├── _sources │ │ ├── dipde.column.rst.txt │ │ ├── dipde.examples.rst.txt │ │ ├── dipde.internals.rst.txt │ │ ├── dipde.rst.txt │ │ ├── index.rst.txt │ │ └── user.rst.txt │ │ ├── _static │ │ ├── aibs_sphinx.css │ │ ├── ajax-loader.gif │ │ ├── alabaster.css │ │ ├── basic.css │ │ ├── ccf_v3_sdk.png │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── custom.css │ │ ├── doctools.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── external_assets │ │ │ ├── images │ │ │ │ ├── AIBS_Logo.png │ │ │ │ ├── Brain_Atlas_Logotype_SDK.png │ │ │ │ ├── arrow_off.gif │ │ │ │ ├── arrow_on.gif │ │ │ │ ├── arrow_over.gif │ │ │ │ ├── close_x.png │ │ │ │ ├── logo_AIBS.gif │ │ │ │ ├── logo_aibs_footer.png │ │ │ │ ├── progress_indicator.gif │ │ │ │ └── tab_blue.gif │ │ │ ├── javascript │ │ │ │ ├── AC_RunActiveContent.js │ │ │ │ ├── appConfig.js │ │ │ │ ├── browserVersions.js │ │ │ │ ├── portal.js │ │ │ │ ├── portalFooter.js │ │ │ │ ├── portalHeader.js │ │ │ │ └── relatedData.js │ │ │ └── stylesheets │ │ │ │ ├── animation.css │ │ │ │ ├── bebasneue-webfont.eot │ │ │ │ ├── bebasneue-webfont.svg │ │ │ │ ├── bebasneue-webfont.ttf │ │ │ │ ├── bebasneue-webfont.woff │ │ │ │ ├── common_layout.css │ │ │ │ ├── portal.css │ │ │ │ ├── portal_icon_font.css │ │ │ │ ├── portal_icon_font.eot │ │ │ │ ├── portal_icon_font.svg │ │ │ │ ├── portal_icon_font.ttf │ │ │ │ └── portal_icon_font.woff │ │ ├── file.png │ │ ├── jquery-3.1.0.js │ │ ├── jquery.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ │ ├── dipde.column.html │ │ ├── dipde.examples.html │ │ ├── dipde.html │ │ ├── dipde.internals.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ ├── searchindex.js │ │ └── user.html ├── dipde.examples.rst ├── make.bat └── source │ ├── .DS_Store │ ├── Dipde_Nick_final.png │ ├── _static │ ├── aibs_sphinx.css_t │ ├── ccf_v3_sdk.png │ └── external_assets │ │ ├── images │ │ ├── AIBS_Logo.png │ │ ├── Brain_Atlas_Logotype_SDK.png │ │ ├── arrow_off.gif │ │ ├── arrow_on.gif │ │ ├── arrow_over.gif │ │ ├── close_x.png │ │ ├── logo_AIBS.gif │ │ ├── logo_aibs_footer.png │ │ ├── progress_indicator.gif │ │ └── tab_blue.gif │ │ ├── javascript │ │ ├── AC_RunActiveContent.js │ │ ├── appConfig.js │ │ ├── browserVersions.js │ │ ├── portal.js │ │ ├── portalFooter.js │ │ ├── portalHeader.js │ │ └── relatedData.js │ │ └── stylesheets │ │ ├── animation.css │ │ ├── bebasneue-webfont.eot │ │ ├── bebasneue-webfont.svg │ │ ├── bebasneue-webfont.ttf │ │ ├── bebasneue-webfont.woff │ │ ├── common_layout.css │ │ ├── portal.css │ │ ├── portal_icon_font.css │ │ ├── portal_icon_font.eot │ │ ├── portal_icon_font.svg │ │ ├── portal_icon_font.ttf │ │ └── portal_icon_font.woff │ ├── conf.py │ ├── conf.py~ │ ├── dipde.column.rst │ ├── dipde.examples.rst │ ├── dipde.internals.rst │ ├── dipde.rst │ ├── index.rst │ ├── templates │ ├── globaltoc.html │ ├── layout.html │ ├── portalFooter.html │ └── portalHeader.html │ └── user.rst ├── doc_template ├── .nojekyll ├── Dipde_Nick_final.png ├── aibs_sphinx │ ├── static │ │ ├── aibs_sphinx.css_t │ │ ├── ccf_v3_sdk.png │ │ └── external_assets │ │ │ ├── images │ │ │ ├── AIBS_Logo.png │ │ │ ├── Brain_Atlas_Logotype_SDK.png │ │ │ ├── arrow_off.gif │ │ │ ├── arrow_on.gif │ │ │ ├── arrow_over.gif │ │ │ ├── close_x.png │ │ │ ├── logo_AIBS.gif │ │ │ ├── logo_aibs_footer.png │ │ │ ├── progress_indicator.gif │ │ │ └── tab_blue.gif │ │ │ ├── javascript │ │ │ ├── AC_RunActiveContent.js │ │ │ ├── appConfig.js │ │ │ ├── browserVersions.js │ │ │ ├── portal.js │ │ │ ├── portalFooter.js │ │ │ ├── portalHeader.js │ │ │ └── relatedData.js │ │ │ └── stylesheets │ │ │ ├── animation.css │ │ │ ├── bebasneue-webfont.eot │ │ │ ├── bebasneue-webfont.svg │ │ │ ├── bebasneue-webfont.ttf │ │ │ ├── bebasneue-webfont.woff │ │ │ ├── common_layout.css │ │ │ ├── portal.css │ │ │ ├── portal_icon_font.css │ │ │ ├── portal_icon_font.eot │ │ │ ├── portal_icon_font.svg │ │ │ ├── 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