├── debian ├── install ├── compat ├── README.Debian ├── rules └── changelog ├── DockerFiles ├── chamcham └── chennapoda ├── moose-core ├── tests │ ├── python │ │ ├── mus │ │ │ ├── ee │ │ │ ├── passive │ │ │ ├── README │ │ │ └── nmda.py │ │ ├── _neuroml │ │ │ ├── __init__.py │ │ │ └── README │ │ ├── test_files │ │ ├── test_pyrun.py │ │ ├── chem_models │ │ │ └── 19085.cspace │ │ ├── two_cells_nml_1.8 │ │ │ ├── simulations │ │ │ │ └── README │ │ │ ├── morphologies │ │ │ │ ├── cellA.java.ser │ │ │ │ ├── cellB.java.ser │ │ │ │ └── SampleCell.java.ser │ │ │ └── cellMechanisms │ │ │ │ └── README │ │ ├── mpi │ │ │ ├── launch.sh │ │ │ └── .gdbinit │ │ ├── test_vec.py │ │ ├── Rallpacks │ │ │ ├── moose_vs_neuron │ │ │ │ └── rallpack3 │ │ │ │ │ ├── moose_vs_neuron0.png │ │ │ │ │ ├── moose_vs_neuron1.png │ │ │ │ │ ├── data │ │ │ │ │ ├── compare_neuron0.png │ │ │ │ │ └── compare_neuron1.png │ │ │ │ │ ├── profile_neuron.sh │ │ │ │ │ ├── compare.hs │ │ │ │ │ └── neuron.log │ │ │ └── data │ │ │ │ └── run_data.dat │ │ ├── test_import.py │ │ ├── soma.p │ │ ├── test_all.sh │ │ ├── run_mumble.sh │ │ ├── benchmark.py │ │ └── test_docs.py │ └── issues │ │ ├── issue_47.py │ │ ├── issue_69.py │ │ └── hsolve │ │ └── README ├── cmake_modules │ ├── Pinfo.plist │ └── FindSIP.py ├── python │ ├── rdesigneur │ │ ├── .gitignore │ │ ├── __init__.py │ │ └── chans │ │ │ ├── Glu.xml │ │ │ └── NMDA.xml │ └── moose │ │ ├── chemMerge │ │ └── __init__.py │ │ ├── genesis │ │ └── __init__.py │ │ ├── chemUtil │ │ └── __init__.py │ │ ├── SBML │ │ └── __init__.py │ │ ├── neuroml │ │ └── __init__.py │ │ └── __init__.py ├── external │ ├── boost-numeric-bindings │ │ ├── .gitignore │ │ └── boost │ │ │ └── numeric │ │ │ └── bindings │ │ │ ├── blas │ │ │ └── blas.hpp │ │ │ ├── mumps │ │ │ └── mumps_driver.hpp │ │ │ ├── traits │ │ │ ├── transpose.hpp │ │ │ └── traits.hpp │ │ │ └── atlas │ │ │ └── cblas.hpp │ ├── muparser │ │ ├── src │ │ │ ├── muParserTest.cpp │ │ │ └── muParserTokenReader.cpp │ │ └── CMakeLists.txt │ └── README ├── intfire │ └── CMakeLists.txt ├── examples │ ├── CMakeLists.txt │ ├── Ex.h │ └── Example.h ├── signeur │ └── CMakeLists.txt ├── CONTRIBUTING.md ├── device │ └── CMakeLists.txt ├── randnum │ └── CMakeLists.txt ├── msg │ └── CMakeLists.txt ├── diffusion │ └── CMakeLists.txt ├── mpi │ ├── CMakeLists.txt │ └── testMpi.cpp ├── .pre-commit-config.yaml ├── builtins │ ├── MooseParser.cpp │ └── Group.h ├── hsolve │ ├── CTestTestfile.cmake │ ├── README.txt │ └── CMakeLists.txt ├── mesh │ └── CMakeLists.txt ├── synapse │ └── CMakeLists.txt ├── kinetics │ └── CMakeLists.txt ├── scheduling │ └── CMakeLists.txt ├── utility │ ├── CMakeLists.txt │ ├── fileutils.cpp │ └── simple_test.hpp ├── AUTHORS ├── basecode │ ├── doubleEq.h │ ├── CMakeLists.txt │ ├── EpFunc.cpp │ └── ProcInfo.h ├── shell │ ├── LoadModels.h │ └── CMakeLists.txt └── .travis │ └── deploy_pypi.sh ├── docs ├── _config.yml ├── source │ ├── user │ │ └── py │ │ │ ├── references │ │ │ ├── Melement.rst │ │ │ ├── LIF.rst │ │ │ ├── Leakage.rst │ │ │ ├── Compartment.rst │ │ │ ├── ZombieCompartment.rst │ │ │ ├── Group.rst │ │ │ ├── testSched.rst │ │ │ ├── CaConc.rst │ │ │ ├── ZombieCaConc.rst │ │ │ ├── HHChannel.rst │ │ │ ├── InputVariable.rst │ │ │ ├── Enz.rst │ │ │ ├── OneToAllMsg.rst │ │ │ ├── Pool.rst │ │ │ ├── PoissonRng.rst │ │ │ ├── SimpleSynHandler.rst │ │ │ ├── DiagonalMsg.rst │ │ │ ├── Variable.rst │ │ │ ├── Cinfo.rst │ │ │ ├── MarkovSolver.rst │ │ │ ├── index_ref.rst │ │ │ └── STDPSynapse.rst │ │ │ ├── graphics │ │ │ ├── index_graphics.rst │ │ │ └── content_g.rst │ │ │ ├── cookbook │ │ │ ├── network.rst │ │ │ ├── multiscale.rst │ │ │ ├── chem.rst │ │ │ ├── elec.rst │ │ │ └── index_ckbk.rst │ │ │ ├── rdesigneur │ │ │ └── index_rd.rst │ │ │ ├── quickstart │ │ │ ├── index_qs.rst │ │ │ ├── qs_inter.rst │ │ │ └── demos.rst │ │ │ └── tutorials │ │ │ └── index_tut.rst │ ├── images │ │ ├── FB.png │ │ ├── sV1.png │ │ ├── sV2.png │ │ ├── sV3.png │ │ ├── sV4.png │ │ ├── sV5.png │ │ ├── sV6.png │ │ ├── sV7.png │ │ ├── Help.png │ │ ├── Pool.png │ │ ├── clone.png │ │ ├── doseR.png │ │ ├── findS.png │ │ ├── func.png │ │ ├── grid.png │ │ ├── move.png │ │ ├── plot.png │ │ ├── relax.png │ │ ├── Addgraph.png │ │ ├── BufPool.png │ │ ├── Chemical.png │ │ ├── Moose1.png │ │ ├── RunView.png │ │ ├── delete.png │ │ ├── delgraph.png │ │ ├── ex7.6_A.png │ │ ├── ex7.6_C.png │ │ ├── function.png │ │ ├── mapkFB.png │ │ ├── mapkFB2.png │ │ ├── propBis.gif │ │ ├── propBis.png │ │ ├── repris.png │ │ ├── simpleB.png │ │ ├── strongB.png │ │ ├── turing.png │ │ ├── twoCells.png │ │ ├── MM_EnzIcon.png │ │ ├── MM_EnzReac.png │ │ ├── Moose_Run.png │ │ ├── Moose_edit.png │ │ ├── PlotConfig.png │ │ ├── moose_logo.png │ │ ├── rdes4_osc.png │ │ ├── squid_demo.png │ │ ├── strongBis.png │ │ ├── Chemical_run.png │ │ ├── KkitPoolIcon.png │ │ ├── KkitReacIcon.png │ │ ├── KkitReaction.png │ │ ├── KkitSumTotal.png │ │ ├── MatPlotLibPan.png │ │ ├── MooseGuiImage.png │ │ ├── chemical_CS.png │ │ ├── classIcon │ │ │ ├── Enz.png │ │ │ ├── MMenz.png │ │ │ ├── Pool.png │ │ │ ├── Reac.png │ │ │ ├── BufPool.png │ │ │ ├── CubeMesh.png │ │ │ ├── CylMesh.png │ │ │ ├── FuncPool.png │ │ │ ├── Function.png │ │ │ ├── SumFunc.png │ │ │ └── StimulusTable.png │ │ ├── pythonshell.png │ │ ├── randomSpike.png │ │ ├── rdes3.1_axon.png │ │ ├── rdes3_squid.png │ │ ├── rdes7_passive.png │ │ ├── rdes8_active.png │ │ ├── relaxOsc_tut.png │ │ ├── Electrical_sim.png │ │ ├── Electrical_vis.png │ │ ├── Kholodenko_tut.png │ │ ├── KkitModelWindow.png │ │ ├── KkitPlotWindow.png │ │ ├── MOOSE_threading.gif │ │ ├── MatPlotLibSave.png │ │ ├── MatPlotLibZoom.png │ │ ├── NeurokitEditor.png │ │ ├── NeurokitRunner.png │ │ ├── NkitModelWindow.png │ │ ├── PlotWindowIcons.png │ │ ├── PropertyEditor.png │ │ ├── rdes10_CaSpread.png │ │ ├── rdes5_reacdiff.png │ │ ├── MassActionEnzIcon.png │ │ ├── MassActionEnzReac.png │ │ ├── MatPlotLibDoUndo.png │ │ ├── MatPlotLibHomeIcon.png │ │ ├── MooseGuiMenuImage.png │ │ ├── SimulationControl.png │ │ ├── chemDoseResponse.png │ │ ├── neuroncompartment.png │ │ ├── rdes6_multiscale.png │ │ ├── rdes9_spiny_active.png │ │ ├── repressillatorOsc.png │ │ ├── testWigglySpines3.png │ │ ├── turingPatternTut.png │ │ ├── tweakingParameters.png │ │ ├── CompartmentalEditor.png │ │ ├── MOOSE_MPI_threading.gif │ │ ├── neuronalcompartment.jpg │ │ ├── rdes10_CaTimecourse.png │ │ ├── rdes2_passive_squid.png │ │ ├── rdes3.2_myelinated_axon.png │ │ ├── reacDiffBranchingNeuron.png │ │ ├── ChemicalSignallingEditor.png │ │ ├── Gallery_Moose_Multiscale.png │ │ └── MatPlotLibConfigureSubplots.png │ ├── install │ │ └── index_install.rst │ ├── release_notes │ │ └── index.rst │ ├── introduction │ │ └── index_introduction.rst │ ├── doxygen │ │ └── doxy.rst │ ├── changes │ │ └── index.rst │ └── known_issues │ │ └── index.rst ├── readthedocs-pip-requirements.txt ├── images │ ├── Pool.png │ ├── clone.png │ ├── func.png │ ├── grid.png │ ├── move.png │ ├── plot.png │ ├── BufPool.png │ ├── Moose1.png │ ├── RunView.png │ ├── delete.png │ ├── ex7.3_1.png │ ├── ex7.3_2.png │ ├── ex7.3_3.png │ ├── ex7.3_4.png │ ├── ex7.3_5.png │ ├── ex7.3_6.png │ ├── ex7.5_a.png │ ├── ex7.5_b.png │ ├── ex7.5_s.png │ ├── ex7.6_A.png │ ├── ex7.6_C.png │ ├── Addgraph.png │ ├── Chemical.png │ ├── MM_EnzIcon.png │ ├── MM_EnzReac.png │ ├── Moose_Run.png │ ├── Moose_edit.png │ ├── PlotConfig.png │ ├── delgraph.png │ ├── ex8.2_Vm.png │ ├── ex8.3_Vm.png │ ├── ex8.3_gluR.png │ ├── function.png │ ├── moose_logo.png │ ├── rdes4_osc.png │ ├── squid_demo.png │ ├── twoCells.png │ ├── Chemical_run.png │ ├── KkitPoolIcon.png │ ├── KkitReacIcon.png │ ├── KkitReaction.png │ ├── KkitSumTotal.png │ ├── chemical_CS.png │ ├── ex8.1_ER_Ca.png │ ├── ex8.3_chan_p.png │ ├── pythonshell.png │ ├── randomSpike.png │ ├── rdes3.1_axon.png │ ├── rdes3_squid.png │ ├── rdes8_active.png │ ├── Electrical_sim.png │ ├── Electrical_vis.png │ ├── KkitModelWindow.png │ ├── KkitPlotWindow.png │ ├── MOOSE_threading.gif │ ├── MatPlotLibPan.png │ ├── MatPlotLibSave.png │ ├── MatPlotLibZoom.png │ ├── MooseGuiImage.png │ ├── NeurokitEditor.png │ ├── NeurokitRunner.png │ ├── NkitModelWindow.png │ ├── PlotWindowIcons.png │ ├── PropertyEditor.png │ ├── classIcon │ │ ├── Enz.png │ │ ├── MMenz.png │ │ ├── Pool.png │ │ ├── Reac.png │ │ ├── BufPool.png │ │ ├── CylMesh.png │ │ ├── SumFunc.png │ │ ├── CubeMesh.png │ │ ├── FuncPool.png │ │ ├── Function.png │ │ └── StimulusTable.png │ ├── ex2.1_vclamp_a.png │ ├── ex2.1_vclamp_b.png │ ├── ex4.2_sine_stim.png │ ├── ex4.2_spiking.png │ ├── ex7.5_a_later.png │ ├── ex8.1_dend_Ca.png │ ├── ex8.2_Ca_dend.png │ ├── ex8.2_Ca_spine.png │ ├── rdes10_CaSpread.png │ ├── rdes5_reacdiff.png │ ├── rdes7_passive.png │ ├── MassActionEnzIcon.png │ ├── MassActionEnzReac.png │ ├── MatPlotLibDoUndo.png │ ├── MooseGuiMenuImage.png │ ├── SimulationControl.png │ ├── chemDoseResponse.png │ ├── ex4.0_scaledSoma.png │ ├── ex7.2_CICR_static.png │ ├── neuroncompartment.png │ ├── rdes6_multiscale.png │ ├── testWigglySpines3.png │ ├── CompartmentalEditor.png │ ├── MOOSE_MPI_threading.gif │ ├── MatPlotLibHomeIcon.png │ ├── ex3.1_squid_vclamp.png │ ├── ex3.3_AP_collision.png │ ├── ex4.1_ballAndStick.png │ ├── ex7.4_travelling_osc.png │ ├── ex8.0_multiscale_Ca.png │ ├── ex8.2_active_CaMKII.png │ ├── ex8.3_CaMKII_spine.png │ ├── neuronalcompartment.jpg │ ├── rdes10_CaTimecourse.png │ ├── rdes2_passive_squid.png │ ├── rdes9_spiny_active.png │ ├── tweakingParameters.png │ ├── ex5.0_random_syn_input.png │ ├── ex7.0_spatial_chem_osc.png │ ├── ChemicalSignallingEditor.png │ ├── Gallery_Moose_Multiscale.png │ ├── ex3.2_axon_propagating_AP.png │ ├── ex5.1_periodic_syn_input.png │ ├── ex7.1_diffusive_gradient.png │ ├── ex7.2_CICR_wave_lastFrame.png │ ├── ex8.0_multiscale_KA_conc.png │ ├── ex8.0_multiscale_currInj.png │ ├── ex9.0_passive_cell_morpho.png │ ├── rdes3.2_myelinated_axon.png │ ├── reacDiffBranchingNeuron.png │ ├── MatPlotLibConfigureSubplots.png │ └── ex8.0_multiscale_cell_spiking.png ├── markdown │ └── images │ │ └── purkinje.png ├── user │ ├── tutorials │ │ ├── _static │ │ │ ├── h10_CNG_swc.png │ │ │ ├── rdes5_reacdiff.png │ │ │ ├── Neuro_Morophy_a.png │ │ │ ├── Neuro_Morophy_b.png │ │ │ ├── Neuro_Morophy_activeChanA.png │ │ │ └── Neuro_Morophy_activeChanB.png │ │ └── index.rst │ └── py │ │ ├── cookbook │ │ └── README.txt │ │ ├── quickstart │ │ └── README.txt │ │ └── builtins_classes │ │ └── index.rst ├── doxygen │ └── doxy_1.4.6 │ │ └── docgen ├── README.txt └── Makefile ├── moose-examples ├── .travis │ ├── .ignore_on_travis │ └── matplotlibrc ├── squid │ ├── .gitignore │ ├── images │ │ └── navigationtoolbar.jpg │ └── README.txt ├── _config.yml ├── genesis │ ├── acc68.png │ ├── Kholodenko.png │ ├── EGFR_MAPK_58.png │ ├── traff_nn_diff_TRI.png │ ├── Osc_cspace_ref_model.png │ └── M1719.cspace ├── tutorials │ ├── ChemicalBistables │ │ ├── 19085.cspace │ │ ├── mapkFB.png │ │ ├── propBis.png │ │ ├── strongBis.png │ │ └── simple_bistab.png │ ├── Electrophys │ │ ├── EI_input.png │ │ ├── RallsLaw.png │ │ ├── SeqSummation.png │ │ ├── synapticSummation.png │ │ └── CableInjectEquivCkt.png │ ├── ChemicalOscillators │ │ ├── relaxOsc_tut.png │ │ ├── Kholodenko_tut.png │ │ ├── repressillatorOsc.png │ │ └── turingPatternTut.png │ └── Rdesigneur │ │ ├── ex1_minimalModel.py │ │ ├── ex2.0_currentPulse.py │ │ ├── ex2.1_vclamp.py │ │ ├── ex3.0_squid_currentPulse.py │ │ ├── ex6_chem_osc.py │ │ ├── ex9.0_load_neuronal_morphology_file.py │ │ ├── chans │ │ ├── Glu.xml │ │ └── NMDA.xml │ │ └── ex7.0_spatial_chem_osc.py ├── neuroml │ ├── lobster_pyloric │ │ ├── STG.png │ │ └── synapses │ │ │ └── load_synapses.py │ ├── PurkinjeCellPassivePulseInput │ │ └── README │ └── OlfactoryBulbPassive │ │ └── README ├── snippets │ ├── Osc.cspace │ ├── timetable.txt │ └── soma.p ├── traub_2005 │ ├── py │ │ ├── proto │ │ │ ├── SupPyrFRB.depths │ │ │ ├── SupPyrRS.depths │ │ │ ├── NontuftedRS.depths │ │ │ ├── NontuftedRS.levels │ │ │ ├── nRT.levels │ │ │ ├── DeepLTS.levels │ │ │ ├── SpinyStellate.levels │ │ │ ├── SupLTS.levels │ │ │ ├── DeepAxoaxonic.levels │ │ │ ├── DeepBasket.levels │ │ │ ├── SupBasket.levels │ │ │ ├── TuftedIB.levels │ │ │ ├── TuftedRS.levels │ │ │ ├── SupPyrFRB.levels │ │ │ ├── SupPyrRS.levels │ │ │ └── SupAxoaxonic.levels │ │ └── benchmark.sh │ └── nrn │ │ ├── test_ka.hoc │ │ ├── test_cal.hoc │ │ ├── test_cat.hoc │ │ ├── test_kdr.hoc │ │ ├── test_km.hoc │ │ ├── test_nap.hoc │ │ ├── test_napf.hoc │ │ ├── test_cat_a.hoc │ │ ├── test_ka_ib.hoc │ │ ├── test_kdr_fs.hoc │ │ ├── test_napf_tcr.hoc │ │ ├── test_k2.hoc │ │ ├── test_naf2_nRT.hoc │ │ ├── test_ar.hoc │ │ ├── test_naf.hoc │ │ ├── test_naf2.hoc │ │ ├── test_naf_tcr.hoc │ │ └── test_napf_ss.hoc ├── hopfield │ ├── input.csv │ ├── memory1.csv │ └── memory2.csv ├── cuda │ └── check_error.py ├── README.md ├── run_pylint.sh ├── unsorted │ └── test_function.py ├── symcomp │ └── symcomp.p ├── parallelSolver │ └── README └── paper-2015 │ ├── Fig2_elecModels │ └── chans │ │ ├── Glu.xml │ │ └── NMDA.xml │ ├── Fig5_CellMultiscale │ └── chans │ │ ├── Glu.xml │ │ └── NMDA.xml │ └── Fig6_NetMultiscale │ └── cells_channels │ ├── Glu.xml │ ├── NMDA.xml │ └── GABA.xml ├── moose-gui ├── __init__.py ├── plugins │ ├── list.txt │ ├── README │ ├── defines.py │ └── constants.py ├── icons │ ├── add.png │ ├── run.png │ ├── arrow.png │ ├── grid.png │ ├── hand.png │ ├── help.png │ ├── list.png │ ├── reset.png │ ├── squid.png │ ├── stop.png │ ├── wrench.png │ ├── continue.png │ ├── hopfield.png │ ├── runtime.png │ ├── add_graph.png │ ├── arrow_undo.png │ ├── connection.png │ ├── moose_icon.png │ ├── classIcon │ │ ├── Enz.png │ │ ├── MMenz.png │ │ ├── Pool.png │ │ ├── Reac.png │ │ ├── BufPool.png │ │ ├── CubeMesh.png │ │ ├── CylMesh.png │ │ ├── FuncPool.png │ │ ├── Function.png │ │ ├── SumFunc.png │ │ └── StimulusTable.png │ ├── delete_graph.png │ ├── QMdiBackground.png │ ├── moose_icon_64x64.png │ ├── moose_icon_large.png │ ├── straight_connector_with_filled_circles.png │ ├── delete.svg │ └── clone.svg ├── global_constants.py └── README.md ├── .gitignore ├── data ├── moosegui ├── matplotlibrc └── Makefile ├── scripts ├── build-moose ├── build_mac_bundle.sh ├── build-moogli ├── build-moose-core └── install-dependencies-on-debian ├── cmake ├── moosegui.in └── build_moose-core.sh.in ├── packaging_scripts ├── moose_icon_64x64.png ├── moose_icon_large.png ├── build_using_xcode.sh └── HOWTO_MAC.md ├── INSTALL.md ├── .gitattributes ├── .travis_build_osx.sh ├── macosx ├── port_moose.sh ├── brew_moose.sh ├── brew_moogli.sh └── moogli.rb ├── .travis_build_linux.sh ├── _travis ├── prepare_linux.sh ├── prepare_osx.sh └── build_on_osx.sh ├── .travis_prepare_linux.sh └── .travis.yml /debian/install: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /DockerFiles/chamcham: -------------------------------------------------------------------------------- 1 | 3.2 -------------------------------------------------------------------------------- /debian/compat: -------------------------------------------------------------------------------- 1 | 9 2 | -------------------------------------------------------------------------------- /DockerFiles/chennapoda: -------------------------------------------------------------------------------- 1 | 3.3 -------------------------------------------------------------------------------- /moose-core/tests/python/mus/ee: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /moose-core/tests/python/mus/passive: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docs/_config.yml: -------------------------------------------------------------------------------- 1 | theme: jekyll-theme-minimal -------------------------------------------------------------------------------- /docs/source/user/py/references/Melement.rst: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /moose-examples/.travis/.ignore_on_travis: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /moose-examples/squid/.gitignore: -------------------------------------------------------------------------------- 1 | *.dat 2 | -------------------------------------------------------------------------------- /moose-core/tests/python/_neuroml/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /moose-examples/_config.yml: -------------------------------------------------------------------------------- 1 | theme: jekyll-theme-minimal -------------------------------------------------------------------------------- /moose-gui/__init__.py: -------------------------------------------------------------------------------- 1 | all = [ "plugins", 'suds' ] 2 | -------------------------------------------------------------------------------- /moose-gui/plugins/list.txt: -------------------------------------------------------------------------------- 1 | kkit 2 | NeuroKit 3 | 4 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.png 2 | *.*~ 3 | *~ 4 | *.html 5 | /moose 6 | -------------------------------------------------------------------------------- /docs/readthedocs-pip-requirements.txt: -------------------------------------------------------------------------------- 1 | numpydoc 2 | mock 3 | -------------------------------------------------------------------------------- /moose-core/cmake_modules/Pinfo.plist: -------------------------------------------------------------------------------- 1 | # Currently empty. 2 | -------------------------------------------------------------------------------- /moose-core/tests/python/test_files: -------------------------------------------------------------------------------- 1 | ../../python/moose/neuroml2/test_files -------------------------------------------------------------------------------- /data/moosegui: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ( cd /usr/lib/moose/gui && python mgui.py ) 3 | -------------------------------------------------------------------------------- /moose-core/python/rdesigneur/.gitignore: -------------------------------------------------------------------------------- 1 | test*.py 2 | foo.py 3 | old.py 4 | NOTES 5 | -------------------------------------------------------------------------------- /scripts/build-moose: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | sh ./build-moose-core 4 | sh ./build-moogli 5 | -------------------------------------------------------------------------------- /docs/images/Pool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/Pool.png -------------------------------------------------------------------------------- /docs/images/clone.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/clone.png -------------------------------------------------------------------------------- /docs/images/func.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/func.png -------------------------------------------------------------------------------- /docs/images/grid.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/grid.png -------------------------------------------------------------------------------- /docs/images/move.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/move.png -------------------------------------------------------------------------------- /docs/images/plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/plot.png -------------------------------------------------------------------------------- /docs/images/BufPool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/BufPool.png -------------------------------------------------------------------------------- /docs/images/Moose1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/Moose1.png -------------------------------------------------------------------------------- /docs/images/RunView.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/RunView.png -------------------------------------------------------------------------------- /docs/images/delete.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/delete.png -------------------------------------------------------------------------------- /docs/images/ex7.3_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.3_1.png -------------------------------------------------------------------------------- /docs/images/ex7.3_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.3_2.png -------------------------------------------------------------------------------- /docs/images/ex7.3_3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.3_3.png -------------------------------------------------------------------------------- /docs/images/ex7.3_4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.3_4.png -------------------------------------------------------------------------------- /docs/images/ex7.3_5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.3_5.png -------------------------------------------------------------------------------- /docs/images/ex7.3_6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.3_6.png -------------------------------------------------------------------------------- /docs/images/ex7.5_a.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.5_a.png -------------------------------------------------------------------------------- /docs/images/ex7.5_b.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.5_b.png -------------------------------------------------------------------------------- /docs/images/ex7.5_s.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.5_s.png -------------------------------------------------------------------------------- /docs/images/ex7.6_A.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.6_A.png -------------------------------------------------------------------------------- /docs/images/ex7.6_C.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.6_C.png -------------------------------------------------------------------------------- /moose-core/python/moose/chemMerge/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | from .merge import * 3 | -------------------------------------------------------------------------------- /moose-gui/icons/add.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/add.png -------------------------------------------------------------------------------- /moose-gui/icons/run.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/run.png -------------------------------------------------------------------------------- /docs/images/Addgraph.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/Addgraph.png -------------------------------------------------------------------------------- /docs/images/Chemical.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/Chemical.png -------------------------------------------------------------------------------- /docs/images/MM_EnzIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/MM_EnzIcon.png -------------------------------------------------------------------------------- /docs/images/MM_EnzReac.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/MM_EnzReac.png -------------------------------------------------------------------------------- /docs/images/Moose_Run.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/Moose_Run.png -------------------------------------------------------------------------------- /docs/images/Moose_edit.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/Moose_edit.png -------------------------------------------------------------------------------- /docs/images/PlotConfig.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/PlotConfig.png -------------------------------------------------------------------------------- /docs/images/delgraph.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/delgraph.png -------------------------------------------------------------------------------- /docs/images/ex8.2_Vm.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex8.2_Vm.png -------------------------------------------------------------------------------- /docs/images/ex8.3_Vm.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex8.3_Vm.png -------------------------------------------------------------------------------- /docs/images/ex8.3_gluR.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex8.3_gluR.png -------------------------------------------------------------------------------- /docs/images/function.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/function.png -------------------------------------------------------------------------------- /docs/images/moose_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/moose_logo.png -------------------------------------------------------------------------------- /docs/images/rdes4_osc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/rdes4_osc.png -------------------------------------------------------------------------------- /docs/images/squid_demo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/squid_demo.png -------------------------------------------------------------------------------- /docs/images/twoCells.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/twoCells.png -------------------------------------------------------------------------------- /docs/source/images/FB.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/FB.png -------------------------------------------------------------------------------- /docs/source/images/sV1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/sV1.png -------------------------------------------------------------------------------- /docs/source/images/sV2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/sV2.png -------------------------------------------------------------------------------- /docs/source/images/sV3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/sV3.png -------------------------------------------------------------------------------- /docs/source/images/sV4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/sV4.png -------------------------------------------------------------------------------- /docs/source/images/sV5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/sV5.png -------------------------------------------------------------------------------- /docs/source/images/sV6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/sV6.png -------------------------------------------------------------------------------- /docs/source/images/sV7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/sV7.png -------------------------------------------------------------------------------- /moose-gui/icons/arrow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/arrow.png -------------------------------------------------------------------------------- /moose-gui/icons/grid.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/grid.png -------------------------------------------------------------------------------- /moose-gui/icons/hand.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/hand.png -------------------------------------------------------------------------------- /moose-gui/icons/help.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/help.png -------------------------------------------------------------------------------- /moose-gui/icons/list.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/list.png -------------------------------------------------------------------------------- /moose-gui/icons/reset.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/reset.png -------------------------------------------------------------------------------- /moose-gui/icons/squid.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/squid.png -------------------------------------------------------------------------------- /moose-gui/icons/stop.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/stop.png -------------------------------------------------------------------------------- /moose-gui/icons/wrench.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/wrench.png -------------------------------------------------------------------------------- /moose-gui/plugins/README: -------------------------------------------------------------------------------- 1 | This directory will contain python scripts implementing moose plugins. 2 | -------------------------------------------------------------------------------- /cmake/moosegui.in: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | cd @CMAKE_INSTALL_PREFIX@/lib/moose/gui && @PYTHON_EXECUTABLE@ mgui.py 3 | -------------------------------------------------------------------------------- /docs/images/Chemical_run.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/Chemical_run.png -------------------------------------------------------------------------------- /docs/images/KkitPoolIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/KkitPoolIcon.png -------------------------------------------------------------------------------- /docs/images/KkitReacIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/KkitReacIcon.png -------------------------------------------------------------------------------- /docs/images/KkitReaction.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/KkitReaction.png -------------------------------------------------------------------------------- /docs/images/KkitSumTotal.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/KkitSumTotal.png -------------------------------------------------------------------------------- /docs/images/chemical_CS.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/chemical_CS.png -------------------------------------------------------------------------------- /docs/images/ex8.1_ER_Ca.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex8.1_ER_Ca.png -------------------------------------------------------------------------------- /docs/images/ex8.3_chan_p.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex8.3_chan_p.png -------------------------------------------------------------------------------- /docs/images/pythonshell.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/pythonshell.png -------------------------------------------------------------------------------- /docs/images/randomSpike.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/randomSpike.png -------------------------------------------------------------------------------- /docs/images/rdes3.1_axon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/rdes3.1_axon.png -------------------------------------------------------------------------------- /docs/images/rdes3_squid.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/rdes3_squid.png -------------------------------------------------------------------------------- /docs/images/rdes8_active.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/rdes8_active.png -------------------------------------------------------------------------------- /docs/source/images/Help.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/Help.png -------------------------------------------------------------------------------- /docs/source/images/Pool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/Pool.png -------------------------------------------------------------------------------- /docs/source/images/clone.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/clone.png -------------------------------------------------------------------------------- /docs/source/images/doseR.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/doseR.png -------------------------------------------------------------------------------- /docs/source/images/findS.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/findS.png -------------------------------------------------------------------------------- /docs/source/images/func.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/func.png -------------------------------------------------------------------------------- /docs/source/images/grid.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/grid.png -------------------------------------------------------------------------------- /docs/source/images/move.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/move.png -------------------------------------------------------------------------------- /docs/source/images/plot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/plot.png -------------------------------------------------------------------------------- /docs/source/images/relax.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/relax.png -------------------------------------------------------------------------------- /moose-core/tests/python/test_pyrun.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | import moose 3 | moose.PyRun('/p') 4 | -------------------------------------------------------------------------------- /moose-gui/icons/continue.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/continue.png -------------------------------------------------------------------------------- /moose-gui/icons/hopfield.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/hopfield.png -------------------------------------------------------------------------------- /moose-gui/icons/runtime.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/runtime.png -------------------------------------------------------------------------------- /docs/images/Electrical_sim.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/Electrical_sim.png -------------------------------------------------------------------------------- /docs/images/Electrical_vis.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/Electrical_vis.png -------------------------------------------------------------------------------- /docs/images/KkitModelWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/KkitModelWindow.png -------------------------------------------------------------------------------- /docs/images/KkitPlotWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/KkitPlotWindow.png -------------------------------------------------------------------------------- /docs/images/MOOSE_threading.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/MOOSE_threading.gif -------------------------------------------------------------------------------- /docs/images/MatPlotLibPan.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/MatPlotLibPan.png -------------------------------------------------------------------------------- /docs/images/MatPlotLibSave.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/MatPlotLibSave.png -------------------------------------------------------------------------------- /docs/images/MatPlotLibZoom.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/MatPlotLibZoom.png -------------------------------------------------------------------------------- /docs/images/MooseGuiImage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/MooseGuiImage.png -------------------------------------------------------------------------------- /docs/images/NeurokitEditor.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/NeurokitEditor.png -------------------------------------------------------------------------------- /docs/images/NeurokitRunner.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/NeurokitRunner.png -------------------------------------------------------------------------------- /docs/images/NkitModelWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/NkitModelWindow.png -------------------------------------------------------------------------------- /docs/images/PlotWindowIcons.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/PlotWindowIcons.png -------------------------------------------------------------------------------- /docs/images/PropertyEditor.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/PropertyEditor.png -------------------------------------------------------------------------------- /docs/images/classIcon/Enz.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/classIcon/Enz.png -------------------------------------------------------------------------------- /docs/images/classIcon/MMenz.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/classIcon/MMenz.png -------------------------------------------------------------------------------- /docs/images/classIcon/Pool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/classIcon/Pool.png -------------------------------------------------------------------------------- /docs/images/classIcon/Reac.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/classIcon/Reac.png -------------------------------------------------------------------------------- /docs/images/ex2.1_vclamp_a.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex2.1_vclamp_a.png -------------------------------------------------------------------------------- /docs/images/ex2.1_vclamp_b.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex2.1_vclamp_b.png -------------------------------------------------------------------------------- /docs/images/ex4.2_sine_stim.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex4.2_sine_stim.png -------------------------------------------------------------------------------- /docs/images/ex4.2_spiking.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex4.2_spiking.png -------------------------------------------------------------------------------- /docs/images/ex7.5_a_later.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.5_a_later.png -------------------------------------------------------------------------------- /docs/images/ex8.1_dend_Ca.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex8.1_dend_Ca.png -------------------------------------------------------------------------------- /docs/images/ex8.2_Ca_dend.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex8.2_Ca_dend.png -------------------------------------------------------------------------------- /docs/images/ex8.2_Ca_spine.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex8.2_Ca_spine.png -------------------------------------------------------------------------------- /docs/images/rdes10_CaSpread.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/rdes10_CaSpread.png -------------------------------------------------------------------------------- /docs/images/rdes5_reacdiff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/rdes5_reacdiff.png -------------------------------------------------------------------------------- /docs/images/rdes7_passive.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/rdes7_passive.png -------------------------------------------------------------------------------- /docs/source/images/Addgraph.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/Addgraph.png -------------------------------------------------------------------------------- /docs/source/images/BufPool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/BufPool.png -------------------------------------------------------------------------------- /docs/source/images/Chemical.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/Chemical.png -------------------------------------------------------------------------------- /docs/source/images/Moose1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/Moose1.png -------------------------------------------------------------------------------- /docs/source/images/RunView.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/RunView.png -------------------------------------------------------------------------------- /docs/source/images/delete.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/delete.png -------------------------------------------------------------------------------- /docs/source/images/delgraph.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/delgraph.png -------------------------------------------------------------------------------- /docs/source/images/ex7.6_A.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/ex7.6_A.png -------------------------------------------------------------------------------- /docs/source/images/ex7.6_C.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/ex7.6_C.png -------------------------------------------------------------------------------- /docs/source/images/function.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/function.png -------------------------------------------------------------------------------- /docs/source/images/mapkFB.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/mapkFB.png -------------------------------------------------------------------------------- /docs/source/images/mapkFB2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/mapkFB2.png -------------------------------------------------------------------------------- /docs/source/images/propBis.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/propBis.gif -------------------------------------------------------------------------------- /docs/source/images/propBis.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/propBis.png -------------------------------------------------------------------------------- /docs/source/images/repris.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/repris.png -------------------------------------------------------------------------------- /docs/source/images/simpleB.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/simpleB.png -------------------------------------------------------------------------------- /docs/source/images/strongB.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/strongB.png -------------------------------------------------------------------------------- /docs/source/images/turing.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/turing.png -------------------------------------------------------------------------------- /docs/source/images/twoCells.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/twoCells.png -------------------------------------------------------------------------------- /moose-gui/icons/add_graph.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/add_graph.png -------------------------------------------------------------------------------- /moose-gui/icons/arrow_undo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/arrow_undo.png -------------------------------------------------------------------------------- /moose-gui/icons/connection.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/connection.png -------------------------------------------------------------------------------- /moose-gui/icons/moose_icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/moose_icon.png -------------------------------------------------------------------------------- /docs/images/MassActionEnzIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/MassActionEnzIcon.png -------------------------------------------------------------------------------- /docs/images/MassActionEnzReac.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/MassActionEnzReac.png -------------------------------------------------------------------------------- /docs/images/MatPlotLibDoUndo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/MatPlotLibDoUndo.png -------------------------------------------------------------------------------- /docs/images/MooseGuiMenuImage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/MooseGuiMenuImage.png -------------------------------------------------------------------------------- /docs/images/SimulationControl.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/SimulationControl.png -------------------------------------------------------------------------------- /docs/images/chemDoseResponse.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/chemDoseResponse.png -------------------------------------------------------------------------------- /docs/images/classIcon/BufPool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/classIcon/BufPool.png -------------------------------------------------------------------------------- /docs/images/classIcon/CylMesh.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/classIcon/CylMesh.png -------------------------------------------------------------------------------- /docs/images/classIcon/SumFunc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/classIcon/SumFunc.png -------------------------------------------------------------------------------- /docs/images/ex4.0_scaledSoma.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex4.0_scaledSoma.png -------------------------------------------------------------------------------- /docs/images/ex7.2_CICR_static.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.2_CICR_static.png -------------------------------------------------------------------------------- /docs/images/neuroncompartment.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/neuroncompartment.png -------------------------------------------------------------------------------- /docs/images/rdes6_multiscale.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/rdes6_multiscale.png -------------------------------------------------------------------------------- /docs/images/testWigglySpines3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/testWigglySpines3.png -------------------------------------------------------------------------------- /docs/markdown/images/purkinje.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/markdown/images/purkinje.png -------------------------------------------------------------------------------- /docs/source/images/MM_EnzIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/MM_EnzIcon.png -------------------------------------------------------------------------------- /docs/source/images/MM_EnzReac.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/MM_EnzReac.png -------------------------------------------------------------------------------- /docs/source/images/Moose_Run.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/Moose_Run.png -------------------------------------------------------------------------------- /docs/source/images/Moose_edit.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/Moose_edit.png -------------------------------------------------------------------------------- /docs/source/images/PlotConfig.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/PlotConfig.png -------------------------------------------------------------------------------- /docs/source/images/moose_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/moose_logo.png -------------------------------------------------------------------------------- /docs/source/images/rdes4_osc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/rdes4_osc.png -------------------------------------------------------------------------------- /docs/source/images/squid_demo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/squid_demo.png -------------------------------------------------------------------------------- /docs/source/images/strongBis.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/strongBis.png -------------------------------------------------------------------------------- /moose-core/python/moose/genesis/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | from .writeKkit import mooseWriteKkit 3 | -------------------------------------------------------------------------------- /moose-examples/genesis/acc68.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/genesis/acc68.png -------------------------------------------------------------------------------- /moose-gui/icons/classIcon/Enz.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/classIcon/Enz.png -------------------------------------------------------------------------------- /moose-gui/icons/delete_graph.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/delete_graph.png -------------------------------------------------------------------------------- /docs/images/CompartmentalEditor.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/CompartmentalEditor.png -------------------------------------------------------------------------------- /docs/images/MOOSE_MPI_threading.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/MOOSE_MPI_threading.gif -------------------------------------------------------------------------------- /docs/images/MatPlotLibHomeIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/MatPlotLibHomeIcon.png -------------------------------------------------------------------------------- /docs/images/classIcon/CubeMesh.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/classIcon/CubeMesh.png -------------------------------------------------------------------------------- /docs/images/classIcon/FuncPool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/classIcon/FuncPool.png -------------------------------------------------------------------------------- /docs/images/classIcon/Function.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/classIcon/Function.png -------------------------------------------------------------------------------- /docs/images/ex3.1_squid_vclamp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex3.1_squid_vclamp.png -------------------------------------------------------------------------------- /docs/images/ex3.3_AP_collision.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex3.3_AP_collision.png -------------------------------------------------------------------------------- /docs/images/ex4.1_ballAndStick.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex4.1_ballAndStick.png -------------------------------------------------------------------------------- /docs/images/ex7.4_travelling_osc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.4_travelling_osc.png -------------------------------------------------------------------------------- /docs/images/ex8.0_multiscale_Ca.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex8.0_multiscale_Ca.png -------------------------------------------------------------------------------- /docs/images/ex8.2_active_CaMKII.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex8.2_active_CaMKII.png -------------------------------------------------------------------------------- /docs/images/ex8.3_CaMKII_spine.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex8.3_CaMKII_spine.png -------------------------------------------------------------------------------- /docs/images/neuronalcompartment.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/neuronalcompartment.jpg -------------------------------------------------------------------------------- /docs/images/rdes10_CaTimecourse.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/rdes10_CaTimecourse.png -------------------------------------------------------------------------------- /docs/images/rdes2_passive_squid.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/rdes2_passive_squid.png -------------------------------------------------------------------------------- /docs/images/rdes9_spiny_active.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/rdes9_spiny_active.png -------------------------------------------------------------------------------- /docs/images/tweakingParameters.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/tweakingParameters.png -------------------------------------------------------------------------------- /docs/source/images/Chemical_run.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/Chemical_run.png -------------------------------------------------------------------------------- /docs/source/images/KkitPoolIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/KkitPoolIcon.png -------------------------------------------------------------------------------- /docs/source/images/KkitReacIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/KkitReacIcon.png -------------------------------------------------------------------------------- /docs/source/images/KkitReaction.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/KkitReaction.png -------------------------------------------------------------------------------- /docs/source/images/KkitSumTotal.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/KkitSumTotal.png -------------------------------------------------------------------------------- /docs/source/images/MatPlotLibPan.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/MatPlotLibPan.png -------------------------------------------------------------------------------- /docs/source/images/MooseGuiImage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/MooseGuiImage.png -------------------------------------------------------------------------------- /docs/source/images/chemical_CS.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/chemical_CS.png -------------------------------------------------------------------------------- /docs/source/images/classIcon/Enz.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/classIcon/Enz.png -------------------------------------------------------------------------------- /docs/source/images/pythonshell.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/pythonshell.png -------------------------------------------------------------------------------- /docs/source/images/randomSpike.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/randomSpike.png -------------------------------------------------------------------------------- /docs/source/images/rdes3.1_axon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/rdes3.1_axon.png -------------------------------------------------------------------------------- /docs/source/images/rdes3_squid.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/rdes3_squid.png -------------------------------------------------------------------------------- /docs/source/images/rdes7_passive.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/rdes7_passive.png -------------------------------------------------------------------------------- /docs/source/images/rdes8_active.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/rdes8_active.png -------------------------------------------------------------------------------- /docs/source/images/relaxOsc_tut.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/relaxOsc_tut.png -------------------------------------------------------------------------------- /docs/source/user/py/graphics/index_graphics.rst: -------------------------------------------------------------------------------- 1 | Graphics 2 | ======== 3 | 4 | .. toctree:: 5 | 6 | content_g 7 | -------------------------------------------------------------------------------- /moose-gui/icons/QMdiBackground.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/QMdiBackground.png -------------------------------------------------------------------------------- /moose-gui/icons/classIcon/MMenz.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/classIcon/MMenz.png -------------------------------------------------------------------------------- /moose-gui/icons/classIcon/Pool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/classIcon/Pool.png -------------------------------------------------------------------------------- /moose-gui/icons/classIcon/Reac.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/classIcon/Reac.png -------------------------------------------------------------------------------- /moose-gui/icons/moose_icon_64x64.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/moose_icon_64x64.png -------------------------------------------------------------------------------- /moose-gui/icons/moose_icon_large.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/moose_icon_large.png -------------------------------------------------------------------------------- /docs/images/ex5.0_random_syn_input.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex5.0_random_syn_input.png -------------------------------------------------------------------------------- /docs/images/ex7.0_spatial_chem_osc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.0_spatial_chem_osc.png -------------------------------------------------------------------------------- /docs/source/images/Electrical_sim.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/Electrical_sim.png -------------------------------------------------------------------------------- /docs/source/images/Electrical_vis.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/Electrical_vis.png -------------------------------------------------------------------------------- /docs/source/images/Kholodenko_tut.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/Kholodenko_tut.png -------------------------------------------------------------------------------- /docs/source/images/KkitModelWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/KkitModelWindow.png -------------------------------------------------------------------------------- /docs/source/images/KkitPlotWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/KkitPlotWindow.png -------------------------------------------------------------------------------- /docs/source/images/MOOSE_threading.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/MOOSE_threading.gif -------------------------------------------------------------------------------- /docs/source/images/MatPlotLibSave.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/MatPlotLibSave.png -------------------------------------------------------------------------------- /docs/source/images/MatPlotLibZoom.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/MatPlotLibZoom.png -------------------------------------------------------------------------------- /docs/source/images/NeurokitEditor.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/NeurokitEditor.png -------------------------------------------------------------------------------- /docs/source/images/NeurokitRunner.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/NeurokitRunner.png -------------------------------------------------------------------------------- /docs/source/images/NkitModelWindow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/NkitModelWindow.png -------------------------------------------------------------------------------- /docs/source/images/PlotWindowIcons.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/PlotWindowIcons.png -------------------------------------------------------------------------------- /docs/source/images/PropertyEditor.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/PropertyEditor.png -------------------------------------------------------------------------------- /docs/source/images/classIcon/MMenz.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/classIcon/MMenz.png -------------------------------------------------------------------------------- /docs/source/images/classIcon/Pool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/classIcon/Pool.png -------------------------------------------------------------------------------- /docs/source/images/classIcon/Reac.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/classIcon/Reac.png -------------------------------------------------------------------------------- /docs/source/images/rdes10_CaSpread.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/rdes10_CaSpread.png -------------------------------------------------------------------------------- /docs/source/images/rdes5_reacdiff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/rdes5_reacdiff.png -------------------------------------------------------------------------------- /docs/source/user/py/references/LIF.rst: -------------------------------------------------------------------------------- 1 | LIF 2 | --- 3 | 4 | .. py:class:: LIF 5 | 6 | Leaky Integrate-and-Fire neuron 7 | -------------------------------------------------------------------------------- /moose-core/external/boost-numeric-bindings/.gitignore: -------------------------------------------------------------------------------- 1 | *~ 2 | Makefile 3 | *.swp 4 | *.patch 5 | .svn 6 | *.orig 7 | *.rej 8 | -------------------------------------------------------------------------------- /moose-core/tests/python/chem_models/19085.cspace: -------------------------------------------------------------------------------- 1 | M101: |DabX|Jbca| 5.59269 0.0157641 0.172865 0.361005 4.72728 1.08558 0.0982933 -------------------------------------------------------------------------------- /moose-examples/genesis/Kholodenko.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/genesis/Kholodenko.png -------------------------------------------------------------------------------- /moose-gui/icons/classIcon/BufPool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/classIcon/BufPool.png -------------------------------------------------------------------------------- /moose-gui/icons/classIcon/CubeMesh.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/classIcon/CubeMesh.png -------------------------------------------------------------------------------- /moose-gui/icons/classIcon/CylMesh.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/classIcon/CylMesh.png -------------------------------------------------------------------------------- /moose-gui/icons/classIcon/FuncPool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/classIcon/FuncPool.png -------------------------------------------------------------------------------- /moose-gui/icons/classIcon/Function.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/classIcon/Function.png -------------------------------------------------------------------------------- /moose-gui/icons/classIcon/SumFunc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/classIcon/SumFunc.png -------------------------------------------------------------------------------- /packaging_scripts/moose_icon_64x64.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/packaging_scripts/moose_icon_64x64.png -------------------------------------------------------------------------------- /packaging_scripts/moose_icon_large.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/packaging_scripts/moose_icon_large.png -------------------------------------------------------------------------------- /docs/images/ChemicalSignallingEditor.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ChemicalSignallingEditor.png -------------------------------------------------------------------------------- /docs/images/Gallery_Moose_Multiscale.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/Gallery_Moose_Multiscale.png -------------------------------------------------------------------------------- /docs/images/classIcon/StimulusTable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/classIcon/StimulusTable.png -------------------------------------------------------------------------------- /docs/images/ex3.2_axon_propagating_AP.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex3.2_axon_propagating_AP.png -------------------------------------------------------------------------------- /docs/images/ex5.1_periodic_syn_input.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex5.1_periodic_syn_input.png -------------------------------------------------------------------------------- /docs/images/ex7.1_diffusive_gradient.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.1_diffusive_gradient.png -------------------------------------------------------------------------------- /docs/images/ex7.2_CICR_wave_lastFrame.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex7.2_CICR_wave_lastFrame.png -------------------------------------------------------------------------------- /docs/images/ex8.0_multiscale_KA_conc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex8.0_multiscale_KA_conc.png -------------------------------------------------------------------------------- /docs/images/ex8.0_multiscale_currInj.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex8.0_multiscale_currInj.png -------------------------------------------------------------------------------- /docs/images/ex9.0_passive_cell_morpho.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex9.0_passive_cell_morpho.png -------------------------------------------------------------------------------- /docs/images/rdes3.2_myelinated_axon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/rdes3.2_myelinated_axon.png -------------------------------------------------------------------------------- /docs/images/reacDiffBranchingNeuron.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/reacDiffBranchingNeuron.png -------------------------------------------------------------------------------- /docs/source/images/MassActionEnzIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/MassActionEnzIcon.png -------------------------------------------------------------------------------- /docs/source/images/MassActionEnzReac.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/MassActionEnzReac.png -------------------------------------------------------------------------------- /docs/source/images/MatPlotLibDoUndo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/MatPlotLibDoUndo.png -------------------------------------------------------------------------------- /docs/source/images/MatPlotLibHomeIcon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/MatPlotLibHomeIcon.png -------------------------------------------------------------------------------- /docs/source/images/MooseGuiMenuImage.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/MooseGuiMenuImage.png -------------------------------------------------------------------------------- /docs/source/images/SimulationControl.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/SimulationControl.png -------------------------------------------------------------------------------- /docs/source/images/chemDoseResponse.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/chemDoseResponse.png -------------------------------------------------------------------------------- /docs/source/images/classIcon/BufPool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/classIcon/BufPool.png -------------------------------------------------------------------------------- /docs/source/images/classIcon/CubeMesh.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/classIcon/CubeMesh.png -------------------------------------------------------------------------------- /docs/source/images/classIcon/CylMesh.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/classIcon/CylMesh.png -------------------------------------------------------------------------------- /docs/source/images/classIcon/FuncPool.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/classIcon/FuncPool.png -------------------------------------------------------------------------------- /docs/source/images/classIcon/Function.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/classIcon/Function.png -------------------------------------------------------------------------------- /docs/source/images/classIcon/SumFunc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/classIcon/SumFunc.png -------------------------------------------------------------------------------- /docs/source/images/neuroncompartment.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/neuroncompartment.png -------------------------------------------------------------------------------- /docs/source/images/rdes6_multiscale.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/rdes6_multiscale.png -------------------------------------------------------------------------------- /docs/source/images/rdes9_spiny_active.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/rdes9_spiny_active.png -------------------------------------------------------------------------------- /docs/source/images/repressillatorOsc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/repressillatorOsc.png -------------------------------------------------------------------------------- /docs/source/images/testWigglySpines3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/testWigglySpines3.png -------------------------------------------------------------------------------- /docs/source/images/turingPatternTut.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/turingPatternTut.png -------------------------------------------------------------------------------- /docs/source/images/tweakingParameters.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/tweakingParameters.png -------------------------------------------------------------------------------- /moose-examples/genesis/EGFR_MAPK_58.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/genesis/EGFR_MAPK_58.png -------------------------------------------------------------------------------- /moose-gui/global_constants.py: -------------------------------------------------------------------------------- 1 | from PreferencesPresenter import PreferencesPresenter 2 | 3 | preferences = PreferencesPresenter() 4 | -------------------------------------------------------------------------------- /INSTALL.md: -------------------------------------------------------------------------------- 1 | Installation instructions are available here 2 | 3 | - http://moose.readthedocs.io/en/latest/install/index_install.html 4 | -------------------------------------------------------------------------------- /docs/images/MatPlotLibConfigureSubplots.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/MatPlotLibConfigureSubplots.png -------------------------------------------------------------------------------- /docs/source/images/CompartmentalEditor.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/CompartmentalEditor.png -------------------------------------------------------------------------------- /docs/source/images/MOOSE_MPI_threading.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/MOOSE_MPI_threading.gif -------------------------------------------------------------------------------- /docs/source/images/neuronalcompartment.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/neuronalcompartment.jpg -------------------------------------------------------------------------------- /docs/source/images/rdes10_CaTimecourse.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/rdes10_CaTimecourse.png -------------------------------------------------------------------------------- /docs/source/images/rdes2_passive_squid.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/rdes2_passive_squid.png -------------------------------------------------------------------------------- /docs/source/install/index_install.rst: -------------------------------------------------------------------------------- 1 | Installation 2 | ============= 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | install 8 | -------------------------------------------------------------------------------- /docs/source/release_notes/index.rst: -------------------------------------------------------------------------------- 1 | Release Notes 2 | ============= 3 | 4 | .. todo:: 5 | 6 | Collect release notes from github. 7 | -------------------------------------------------------------------------------- /docs/user/tutorials/_static/h10_CNG_swc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/user/tutorials/_static/h10_CNG_swc.png -------------------------------------------------------------------------------- /moose-core/tests/python/two_cells_nml_1.8/simulations/README: -------------------------------------------------------------------------------- 1 | This is the directory for the simulation data associated with the project 2 | -------------------------------------------------------------------------------- /moose-examples/tutorials/ChemicalBistables/19085.cspace: -------------------------------------------------------------------------------- 1 | M101: |DabX|Jbca| 5.59269 0.0157641 0.172865 0.361005 4.72728 1.08558 0.0982933 -------------------------------------------------------------------------------- /moose-gui/icons/classIcon/StimulusTable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/classIcon/StimulusTable.png -------------------------------------------------------------------------------- /docs/images/ex8.0_multiscale_cell_spiking.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/images/ex8.0_multiscale_cell_spiking.png -------------------------------------------------------------------------------- /docs/source/images/classIcon/StimulusTable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/classIcon/StimulusTable.png -------------------------------------------------------------------------------- /docs/source/images/rdes3.2_myelinated_axon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/rdes3.2_myelinated_axon.png -------------------------------------------------------------------------------- /docs/source/images/reacDiffBranchingNeuron.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/reacDiffBranchingNeuron.png -------------------------------------------------------------------------------- /docs/source/user/py/references/Leakage.rst: -------------------------------------------------------------------------------- 1 | Leakage 2 | ------- 3 | 4 | .. py:class:: Leakage 5 | 6 | Leakage: Passive leakage channel. 7 | -------------------------------------------------------------------------------- /docs/user/tutorials/_static/rdes5_reacdiff.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/user/tutorials/_static/rdes5_reacdiff.png -------------------------------------------------------------------------------- /moose-core/tests/python/mpi/launch.sh: -------------------------------------------------------------------------------- 1 | mpirun -np 1 xterm -e gdb --args python recurrentIntFire.py : -np 1 xterm -e gdb ../../../moose 2 | 3 | -------------------------------------------------------------------------------- /moose-examples/genesis/traff_nn_diff_TRI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/genesis/traff_nn_diff_TRI.png -------------------------------------------------------------------------------- /moose-examples/neuroml/lobster_pyloric/STG.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/neuroml/lobster_pyloric/STG.png -------------------------------------------------------------------------------- /docs/source/images/ChemicalSignallingEditor.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/ChemicalSignallingEditor.png -------------------------------------------------------------------------------- /docs/source/images/Gallery_Moose_Multiscale.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/Gallery_Moose_Multiscale.png -------------------------------------------------------------------------------- /docs/source/introduction/index_introduction.rst: -------------------------------------------------------------------------------- 1 | Introduction 2 | ============ 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | introduction 8 | -------------------------------------------------------------------------------- /docs/user/tutorials/_static/Neuro_Morophy_a.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/user/tutorials/_static/Neuro_Morophy_a.png -------------------------------------------------------------------------------- /docs/user/tutorials/_static/Neuro_Morophy_b.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/user/tutorials/_static/Neuro_Morophy_b.png -------------------------------------------------------------------------------- /moose-core/tests/python/mus/README: -------------------------------------------------------------------------------- 1 | TO RUN 2 | 3 | python rc19.py type solver 4 | 5 | type: active or passive 6 | solve: hsolve or ee 7 | 8 | -------------------------------------------------------------------------------- /moose-examples/genesis/Osc_cspace_ref_model.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/genesis/Osc_cspace_ref_model.png -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | *.deb filter=lfs diff=lfs merge=lfs -text 2 | *.rpm filter=lfs diff=lfs merge=lfs -text 3 | *.dmg filter=lfs diff=lfs merge=lfs -text 4 | -------------------------------------------------------------------------------- /docs/source/images/MatPlotLibConfigureSubplots.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/source/images/MatPlotLibConfigureSubplots.png -------------------------------------------------------------------------------- /moose-core/external/muparser/src/muParserTest.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-core/external/muparser/src/muParserTest.cpp -------------------------------------------------------------------------------- /moose-examples/snippets/Osc.cspace: -------------------------------------------------------------------------------- 1 | |AabX|DabX|Jbca|AdeX|DdeX|Jefd|AadX|AbeX| 3.5 0 0.1 0 0 0.1 0.01 0 0.5 1 1 0.05 0.01 0 0.5 1 1 0.05 0.01 0 0 0.005 2 | -------------------------------------------------------------------------------- /moose-examples/squid/images/navigationtoolbar.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/squid/images/navigationtoolbar.jpg -------------------------------------------------------------------------------- /moose-examples/tutorials/Electrophys/EI_input.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/tutorials/Electrophys/EI_input.png -------------------------------------------------------------------------------- /moose-examples/tutorials/Electrophys/RallsLaw.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/tutorials/Electrophys/RallsLaw.png -------------------------------------------------------------------------------- /moose-examples/tutorials/ChemicalBistables/mapkFB.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/tutorials/ChemicalBistables/mapkFB.png -------------------------------------------------------------------------------- /moose-examples/tutorials/Electrophys/SeqSummation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/tutorials/Electrophys/SeqSummation.png -------------------------------------------------------------------------------- /moose-core/external/README: -------------------------------------------------------------------------------- 1 | This folder contains third party software required for MOOSE. The copyright information should be available in the file headers. 2 | -------------------------------------------------------------------------------- /moose-core/external/muparser/src/muParserTokenReader.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-core/external/muparser/src/muParserTokenReader.cpp -------------------------------------------------------------------------------- /moose-examples/genesis/M1719.cspace: -------------------------------------------------------------------------------- 1 | M1719: |DabX|DacX|Jbca|Jcba| 0.550553 2.24249 0.0641231 0.820999 4.27648 8.64488 1.18389 4.11567 0.131328 1.43907 0.221104 2 | -------------------------------------------------------------------------------- /moose-examples/tutorials/ChemicalBistables/propBis.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/tutorials/ChemicalBistables/propBis.png -------------------------------------------------------------------------------- /moose-examples/tutorials/ChemicalBistables/strongBis.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/tutorials/ChemicalBistables/strongBis.png -------------------------------------------------------------------------------- /docs/user/tutorials/_static/Neuro_Morophy_activeChanA.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/user/tutorials/_static/Neuro_Morophy_activeChanA.png -------------------------------------------------------------------------------- /docs/user/tutorials/_static/Neuro_Morophy_activeChanB.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/docs/user/tutorials/_static/Neuro_Morophy_activeChanB.png -------------------------------------------------------------------------------- /moose-examples/tutorials/Electrophys/synapticSummation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/tutorials/Electrophys/synapticSummation.png -------------------------------------------------------------------------------- /moose-gui/README.md: -------------------------------------------------------------------------------- 1 | [![Build Status](https://travis-ci.org/BhallaLab/moose-gui.svg?branch=master)](https://travis-ci.org/BhallaLab/moose-gui) 2 | 3 | # moose-gui 4 | -------------------------------------------------------------------------------- /moose-gui/icons/straight_connector_with_filled_circles.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-gui/icons/straight_connector_with_filled_circles.png -------------------------------------------------------------------------------- /moose-core/tests/python/test_vec.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | import moose 3 | foo = moose.Pool('/foo1', 500) 4 | bar = moose.vec('/foo1') 5 | assert len(bar) == 500 6 | -------------------------------------------------------------------------------- /moose-examples/tutorials/ChemicalBistables/simple_bistab.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/tutorials/ChemicalBistables/simple_bistab.png -------------------------------------------------------------------------------- /moose-examples/tutorials/ChemicalOscillators/relaxOsc_tut.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/tutorials/ChemicalOscillators/relaxOsc_tut.png -------------------------------------------------------------------------------- /moose-examples/tutorials/Electrophys/CableInjectEquivCkt.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/tutorials/Electrophys/CableInjectEquivCkt.png -------------------------------------------------------------------------------- /docs/source/user/py/cookbook/network.rst: -------------------------------------------------------------------------------- 1 | ********** 2 | Networking 3 | ********** 4 | 5 | .. toctree:: 6 | :maxdepth: 2 7 | 8 | net_sim_eg 9 | net_tut 10 | -------------------------------------------------------------------------------- /docs/source/user/py/references/Compartment.rst: -------------------------------------------------------------------------------- 1 | Compartment 2 | ----------- 3 | 4 | .. py:class:: Compartment 5 | 6 | Compartment object, for branching neuron models. 7 | -------------------------------------------------------------------------------- /moose-examples/tutorials/ChemicalOscillators/Kholodenko_tut.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/tutorials/ChemicalOscillators/Kholodenko_tut.png -------------------------------------------------------------------------------- /moose-core/tests/python/mpi/.gdbinit: -------------------------------------------------------------------------------- 1 | set environment PYTHONPATH ../../python VERBOSITY 2 2 | set breakpoint pending on 3 | break PostMaster.cpp:193 4 | #break Shell::doCreate 5 | 6 | -------------------------------------------------------------------------------- /moose-examples/tutorials/ChemicalOscillators/repressillatorOsc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/tutorials/ChemicalOscillators/repressillatorOsc.png -------------------------------------------------------------------------------- /moose-examples/tutorials/ChemicalOscillators/turingPatternTut.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-examples/tutorials/ChemicalOscillators/turingPatternTut.png -------------------------------------------------------------------------------- /moose-examples/tutorials/Rdesigneur/ex1_minimalModel.py: -------------------------------------------------------------------------------- 1 | import moose 2 | import rdesigneur as rd 3 | rdes = rd.rdesigneur() 4 | rdes.buildModel() 5 | moose.showfields( rdes.soma ) 6 | -------------------------------------------------------------------------------- /docs/source/doxygen/doxy.rst: -------------------------------------------------------------------------------- 1 | Doxygen 2 | ------- 3 | 4 | Here you can find all the references necessary for MOOSE. 5 | 6 | `Click here <../../../source/doxygen/cpp/html/index.html>`_ 7 | 8 | -------------------------------------------------------------------------------- /moose-core/tests/python/two_cells_nml_1.8/morphologies/cellA.java.ser: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-core/tests/python/two_cells_nml_1.8/morphologies/cellA.java.ser -------------------------------------------------------------------------------- /moose-core/tests/python/two_cells_nml_1.8/morphologies/cellB.java.ser: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-core/tests/python/two_cells_nml_1.8/morphologies/cellB.java.ser -------------------------------------------------------------------------------- /docs/source/user/py/references/ZombieCompartment.rst: -------------------------------------------------------------------------------- 1 | ZombieCompartment 2 | ----------------- 3 | 4 | .. py:class:: ZombieCompartment 5 | 6 | Compartment object, for branching neuron models. 7 | -------------------------------------------------------------------------------- /moose-core/intfire/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake) 3 | file(GLOB SRC *.cpp) 4 | add_library(intfire ${SRC}) 5 | -------------------------------------------------------------------------------- /moose-core/python/moose/chemUtil/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | from .add_Delete_ChemicalSolver import * 3 | from .chemConnectUtil import * 4 | from .graphUtils import autoCoordinates 5 | -------------------------------------------------------------------------------- /moose-core/tests/python/two_cells_nml_1.8/morphologies/SampleCell.java.ser: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-core/tests/python/two_cells_nml_1.8/morphologies/SampleCell.java.ser -------------------------------------------------------------------------------- /moose-core/python/moose/SBML/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | from .writeSBML import mooseWriteSBML 3 | from .readSBML import mooseReadSBML 4 | 5 | __all__ = ["mooseWriteSBML","mooseReadSBML"] 6 | -------------------------------------------------------------------------------- /docs/source/user/py/cookbook/multiscale.rst: -------------------------------------------------------------------------------- 1 | ******************* 2 | MultiScale Modeling 3 | ******************* 4 | 5 | .. toctree:: 6 | :maxdepth: 2 7 | 8 | multi_sim_eg 9 | 10 | 11 | 12 | -------------------------------------------------------------------------------- /moose-core/tests/python/Rallpacks/moose_vs_neuron/rallpack3/moose_vs_neuron0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-core/tests/python/Rallpacks/moose_vs_neuron/rallpack3/moose_vs_neuron0.png -------------------------------------------------------------------------------- /moose-core/tests/python/Rallpacks/moose_vs_neuron/rallpack3/moose_vs_neuron1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-core/tests/python/Rallpacks/moose_vs_neuron/rallpack3/moose_vs_neuron1.png -------------------------------------------------------------------------------- /debian/README.Debian: -------------------------------------------------------------------------------- 1 | moose for Debian 2 | ---------------- 3 | 4 | 5 | 6 | -- Dilawar Thu, 24 Jul 2014 16:41:58 +0530 7 | -------------------------------------------------------------------------------- /moose-core/examples/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake) 3 | ADD_LIBRARY(examples 4 | Example.cpp 5 | Ex.cpp 6 | ) 7 | 8 | -------------------------------------------------------------------------------- /docs/source/user/py/references/Group.rst: -------------------------------------------------------------------------------- 1 | Group 2 | ----- 3 | 4 | .. py:class:: Group 5 | 6 | 7 | .. py:attribute:: group 8 | 9 | void (*source message field*) Handle for grouping Elements 10 | -------------------------------------------------------------------------------- /moose-core/signeur/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake) 3 | add_library(signeur 4 | Adaptor.cpp 5 | testSigNeur.cpp 6 | ) 7 | -------------------------------------------------------------------------------- /moose-core/tests/python/Rallpacks/moose_vs_neuron/rallpack3/data/compare_neuron0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-core/tests/python/Rallpacks/moose_vs_neuron/rallpack3/data/compare_neuron0.png -------------------------------------------------------------------------------- /moose-core/tests/python/Rallpacks/moose_vs_neuron/rallpack3/data/compare_neuron1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BhallaLab/moose/HEAD/moose-core/tests/python/Rallpacks/moose_vs_neuron/rallpack3/data/compare_neuron1.png -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/SupPyrFRB.depths: -------------------------------------------------------------------------------- 1 | 1 850e-6 2 | 2 885e-6 3 | 3 920e-6 4 | 4 955e-6 5 | 5 825e-6 6 | 6 775e-6 7 | 7 725e-6 8 | 8 690e-6 9 | 9 655e-6 10 | 10 620e-6 11 | 11 585e-6 12 | 12 550e-6 13 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/SupPyrRS.depths: -------------------------------------------------------------------------------- 1 | 1 850e-6 2 | 2 885e-6 3 | 3 920e-6 4 | 4 955e-6 5 | 5 825e-6 6 | 6 775e-6 7 | 7 725e-6 8 | 8 690e-6 9 | 9 655e-6 10 | 10 620e-6 11 | 11 585e-6 12 | 12 550e-6 13 | -------------------------------------------------------------------------------- /docs/source/user/py/references/testSched.rst: -------------------------------------------------------------------------------- 1 | testSched 2 | --------- 3 | 4 | .. py:class:: testSched 5 | 6 | 7 | .. py:method:: process 8 | 9 | (*destination message field*) handles process call 10 | -------------------------------------------------------------------------------- /scripts/build_mac_bundle.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | echo "Create a bundle on MAC" 3 | mkdir -p _build 4 | ( 5 | cd _build 6 | cmake -DCMAKE_INSTALL_PREFIX=_install .. 7 | make -j4 8 | cpack -G Bundle 9 | ) 10 | -------------------------------------------------------------------------------- /docs/source/user/py/cookbook/chem.rst: -------------------------------------------------------------------------------- 1 | **************** 2 | Chemical Aspects 3 | **************** 4 | 5 | .. toctree:: 6 | :maxdepth: 2 7 | 8 | chem_GUI 9 | chem_load_save 10 | chem_sim_eg 11 | chem_tut 12 | -------------------------------------------------------------------------------- /moose-core/python/rdesigneur/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | from __future__ import print_function, absolute_import 3 | 4 | from rdesigneur.rdesigneur import * 5 | from rdesigneur.rdesigneur import rdesigneur 6 | 7 | 8 | 9 | -------------------------------------------------------------------------------- /.travis_build_osx.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | brew tap BhallaLab/moose 3 | brew install --HEAD moose-nightly 4 | python -m pip install networkx python-libsbml pyNeuroML matplotlib 5 | python -c 'import moose; print( moose.__version__ )' 6 | -------------------------------------------------------------------------------- /moose-core/tests/python/test_import.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # Script to test all import modules. 3 | 4 | import moose 5 | from moose.genesis import * 6 | from moose.SBML import * 7 | import moose.chemMerge 8 | import moose.utils as mu 9 | -------------------------------------------------------------------------------- /docs/source/user/py/references/CaConc.rst: -------------------------------------------------------------------------------- 1 | CaConc 2 | ------ 3 | 4 | .. py:class:: CaConc 5 | 6 | CaConc: Calcium concentration pool. Takes current from a channel and keeps track of calcium buildup and depletion by a single exponential process. 7 | -------------------------------------------------------------------------------- /moose-core/CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | To contribute, fork this repo and submit your changes via a pull-request. 2 | Before sending pull-request, check the following: 3 | 4 | - [ ] Software builds locally 5 | - [ ] `ctest --output-on-failure` passes all tests. 6 | -------------------------------------------------------------------------------- /moose-core/device/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake) 3 | add_library(device 4 | PulseGen.cpp 5 | DiffAmp.cpp 6 | PIDController.cpp 7 | RC.cpp 8 | ) 9 | -------------------------------------------------------------------------------- /moose-core/tests/python/Rallpacks/data/run_data.dat: -------------------------------------------------------------------------------- 1 | ; Compartments SimTimeInMoose 2 | 10 1.1 3 | 100 2.95 4 | 200 4.85 5 | 300 7.14 6 | 400 9.27 7 | 500 11.96 8 | 600 14.29 9 | 700 17.65 10 | 1000 28 11 | 2000 66 12 | 3000 124 13 | 4000 200 14 | 5000 276 15 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/NontuftedRS.depths: -------------------------------------------------------------------------------- 1 | 1 2200e-6 2 | 2 2245e-6 3 | 3 2290e-6 4 | 4 2335e-6 5 | 5 2175e-6 6 | 6 2125e-6 7 | 7 2075e-6 8 | 8 2025e-6 9 | 9 1975e-6 10 | 10 1925e-6 11 | 11 1875e-6 12 | 12 1825e-6 13 | 13 1775e-6 14 | 14 1725e-6 15 | -------------------------------------------------------------------------------- /moose-gui/icons/delete.svg: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /moose-examples/hopfield/input.csv: -------------------------------------------------------------------------------- 1 | 1 0 0 0 0 1 1 0 1 1 2 | 1 0 1 0 1 0 0 1 0 1 3 | 1 1 0 1 0 0 1 0 1 0 4 | 1 0 1 0 1 0 0 1 0 1 5 | 0 1 0 1 0 1 1 1 1 0 6 | 0 1 1 0 0 0 0 0 1 1 7 | 0 0 1 1 1 1 0 1 0 1 8 | 0 1 1 1 0 0 1 0 0 0 9 | 0 1 1 0 1 1 0 1 0 1 10 | 0 1 1 1 0 1 1 0 1 1 -------------------------------------------------------------------------------- /docs/source/user/py/references/ZombieCaConc.rst: -------------------------------------------------------------------------------- 1 | ZombieCaConc 2 | ------------ 3 | 4 | .. py:class:: ZombieCaConc 5 | 6 | ZombieCaConc: Calcium concentration pool. Takes current from a channel and keeps track of calcium buildup and depletion by a single exponential process. 7 | -------------------------------------------------------------------------------- /moose-core/tests/python/mus/nmda.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | """ 3 | Created on Sun Jun 1 15:35:13 2014 4 | 5 | @author: subhasis ray 6 | """ 7 | 8 | import moose 9 | 10 | def make_nmda(path): 11 | nmda = moose.MarkovChannel(path) 12 | return nmda 13 | 14 | -------------------------------------------------------------------------------- /moose-examples/hopfield/memory1.csv: -------------------------------------------------------------------------------- 1 | 1 1 0 1 1 1 1 0 1 1 2 | 1 0 1 0 1 1 0 1 0 1 3 | 0 1 0 1 0 0 1 0 1 0 4 | 1 0 1 0 1 1 0 1 0 1 5 | 1 1 0 1 0 1 1 0 1 0 6 | 1 1 0 1 1 1 1 0 1 1 7 | 1 0 1 0 1 1 0 1 0 1 8 | 0 1 0 1 0 0 1 0 1 0 9 | 1 0 1 0 1 1 0 1 0 1 10 | 1 1 0 1 0 1 1 0 1 0 -------------------------------------------------------------------------------- /moose-examples/hopfield/memory2.csv: -------------------------------------------------------------------------------- 1 | 0 0 0 0 0 0 0 0 0 0 2 | 1 1 1 1 1 1 1 1 1 1 3 | 0 0 0 0 0 0 0 0 0 0 4 | 1 1 1 1 1 1 1 1 1 1 5 | 0 0 0 0 0 0 0 0 0 0 6 | 1 1 1 1 1 1 1 1 1 1 7 | 0 0 0 0 0 0 0 0 0 0 8 | 1 1 1 1 1 1 1 1 1 1 9 | 0 0 0 0 0 0 0 0 0 0 10 | 1 1 1 1 1 1 1 1 1 1 -------------------------------------------------------------------------------- /docs/source/user/py/references/HHChannel.rst: -------------------------------------------------------------------------------- 1 | HHChannel 2 | --------- 3 | 4 | .. py:class:: HHChannel 5 | 6 | HHChannel: Hodgkin-Huxley type voltage-gated Ion channel. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS. 7 | -------------------------------------------------------------------------------- /moose-examples/neuroml/lobster_pyloric/synapses/load_synapses.py: -------------------------------------------------------------------------------- 1 | 2 | # -*- coding: utf-8 -*- 3 | 4 | from GluSyn_STG import GluSyn_STG 5 | from AchSyn_STG import AchSyn_STG 6 | 7 | def load_synapses(): 8 | GluSyn_STG("/library/DoubExpSyn_Glu") 9 | AchSyn_STG("/library/DoubExpSyn_Ach") 10 | -------------------------------------------------------------------------------- /docs/source/user/py/cookbook/elec.rst: -------------------------------------------------------------------------------- 1 | ********************************************* 2 | Single Neuron Electrical Aspects (BioPhysics) 3 | ********************************************* 4 | 5 | .. toctree:: 6 | :maxdepth: 2 7 | 8 | elec_mod 9 | elec_GUI 10 | elec_load_run 11 | elec_sim_eg 12 | -------------------------------------------------------------------------------- /moose-core/randnum/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | 3 | add_executable( normal_dist 4 | ${CMAKE_CURRENT_SOURCE_DIR}/test_normal_dist.cpp 5 | ) 6 | 7 | add_library(randnum RNG.cpp) 8 | 9 | enable_testing() 10 | add_test( NAME test_normal_dist COMMAND $ ) 11 | -------------------------------------------------------------------------------- /docs/source/changes/index.rst: -------------------------------------------------------------------------------- 1 | Series `chennapoda` 2 | =================== 3 | 4 | Version 3.2.0 5 | ------------- 6 | 7 | - Improved SBML support. 8 | - NeuroML2 support (Thanks to Padraig Glesson) 9 | - Various bugfixes. 10 | 11 | Series `chamcham` 12 | ================= 13 | 14 | Version 3.1.3 15 | ------------- 16 | -------------------------------------------------------------------------------- /moose-examples/snippets/timetable.txt: -------------------------------------------------------------------------------- 1 | 5.396058372591854280e+00 2 | 1.813731090272489865e+01 3 | 1.813845471631132966e+01 4 | 2.173858226485052114e+01 5 | 2.332567821679726094e+01 6 | 2.429451693333459517e+01 7 | 2.635566327415540044e+01 8 | 3.059542809222615034e+01 9 | 3.564995350933363483e+01 10 | 4.338955125794120704e+01 11 | -------------------------------------------------------------------------------- /debian/rules: -------------------------------------------------------------------------------- 1 | #!/usr/bin/make -f 2 | 3 | export MAKEOPTS=-j5 4 | 5 | export DH_VERBOSE=1 6 | 7 | %: 8 | dh "$@" --buildsystem=cmake --with-python2 9 | 10 | override_dh_auto_configure: 11 | dh_auto_configure -- -DVERSION_MOOSE=3.2.0-dev -DCMAKE_SKIP_RPATH=ON 12 | 13 | override_dh_python2: 14 | dh_numpy 15 | dh_python2 16 | -------------------------------------------------------------------------------- /moose-core/python/moose/neuroml/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | 3 | from __future__ import absolute_import, division, print_function 4 | 5 | import moose.utils as mu 6 | 7 | from .NeuroML import NeuroML, loadNeuroML_L123 8 | from .NetworkML import NetworkML 9 | from .MorphML import MorphML 10 | from .ChannelML import ChannelML 11 | -------------------------------------------------------------------------------- /moose-core/tests/python/soma.p: -------------------------------------------------------------------------------- 1 | 2 | *relative 3 | *cartesian 4 | *asymmetric 5 | 6 | *set_global RA 4.0 7 | //change Cm to account for no spines - make 3x higher? 8 | *set_global CM 0.03 9 | *set_global RM 2.8 10 | *set_global EREST_ACT -80e-3 11 | *set_global ELEAK -50e-3 12 | 13 | *start_cell 14 | soma none 16.000 0 0 16.000 15 | 16 | -------------------------------------------------------------------------------- /docs/source/user/py/references/InputVariable.rst: -------------------------------------------------------------------------------- 1 | InputVariable 2 | ------------- 3 | 4 | .. py:class:: InputVariable 5 | 6 | Variable for capturing incoming values and updating them in owner object. 7 | 8 | .. py:method:: input 9 | 10 | (*destination message field*) Handles input message, inserts into variable queue on owner. 11 | -------------------------------------------------------------------------------- /moose-core/tests/python/Rallpacks/moose_vs_neuron/rallpack3/profile_neuron.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | echo "Profiling neuron simulator of rallpack3" 3 | ncomp=50 4 | while [ $ncomp -lt 50000 ]; do 5 | echo "Cable with compartment $ncomp" 6 | python ./neuron_sim.py --ncomp $ncomp --data data/L$ncomp.out 7 | ncomp=$(echo $ncomp+50 | bc) 8 | done 9 | -------------------------------------------------------------------------------- /macosx/port_moose.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # Test the port file. 3 | set -x 4 | export PATH=/opt/local/bin:$PATH 5 | rm -f ~/ports/science/moose/Portfile 6 | ln -s `pwd`/Portfile ~/ports/science/moose/Portfile 7 | ( cd ~/ports/ && portindex ) 8 | port lint --nitpick moose 9 | sudo port uninstall moose 10 | sudo port -vd install moose | tee _build_port.log 11 | -------------------------------------------------------------------------------- /moose-core/msg/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake) 3 | add_library(msg 4 | Msg.cpp 5 | DiagonalMsg.cpp 6 | OneToAllMsg.cpp 7 | OneToOneMsg.cpp 8 | SingleMsg.cpp 9 | SparseMsg.cpp 10 | OneToOneDataIndexMsg.cpp 11 | testMsg.cpp 12 | ) 13 | -------------------------------------------------------------------------------- /moose-examples/.travis/matplotlibrc: -------------------------------------------------------------------------------- 1 | # This is configuration file for matplotlib used in examples. 2 | # We use this configuration file to test the examples. Copy this configuration 3 | # file in the current working directory and run the snippet. 4 | 5 | # This configuration file does the followings: 6 | # This makes all plots non-blocking. 7 | interactive : True 8 | -------------------------------------------------------------------------------- /moose-gui/plugins/defines.py: -------------------------------------------------------------------------------- 1 | ELECTRICAL_SIMULATION_DT_CLOCKS = [1,2,3,4,5,6,7] 2 | ELECTRICAL_PLOT_UPDATE_INTERVAL_CLOCKS = [8] 3 | ELECTRICAL_DIFFUSION_INTERVAL_CLOCKS = [10] 4 | 5 | CHEMICAL_SIMULATION_DT_CLOCKS = [11, 12, 13, 14, 15, 16, 17] 6 | CHEMICAL_PLOT_UPDATE_INTERVAL_CLOCKS = [18] 7 | CHEMICAL_DIFFUSION_DT_CLOCKS = [10] 8 | -------------------------------------------------------------------------------- /moose-examples/cuda/check_error.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import sys 3 | 4 | f1 = sys.argv[1] 5 | f2 = sys.argv[2] 6 | 7 | val1 = np.loadtxt(f1) 8 | val2 = np.loadtxt(f2) 9 | 10 | e = abs(val1-val2) 11 | Totalerror = sum(e.flatten()) 12 | avgError = Totalerror/len(val1) 13 | 14 | filename = f1.split('/')[-1] 15 | 16 | print(filename, Totalerror, avgError) 17 | -------------------------------------------------------------------------------- /scripts/build-moogli: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | (cd ../moogli; make build) 4 | local_site_package_directory=`python -c "import site; print site.getusersitepackages()"` 5 | mkdir -p "$local_site_package_directory" 6 | echo $(echo `pwd` | sed "s/\/[^\/]*$//")'/moogli' > "$local_site_package_directory/moogli.pth" 7 | #echo "`pwd`/moogli" > "$local_site_package_directory/moogli.pth" 8 | -------------------------------------------------------------------------------- /moose-core/diffusion/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake) 3 | 4 | if(WITH_GSL) 5 | include_directories(${GSL_INCLUDE_DIRS}) 6 | endif(WITH_GSL) 7 | 8 | add_library(diffusion 9 | FastMatrixElim.cpp 10 | DiffPoolVec.cpp 11 | Dsolve.cpp 12 | testDiffusion.cpp 13 | ) 14 | -------------------------------------------------------------------------------- /moose-core/external/muparser/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | 3 | file(GLOB files_SRC "src/*.cpp") 4 | 5 | include_directories(../msg) 6 | include_directories(../basecode ./include) 7 | 8 | add_library(muparser ${files_SRC}) 9 | set_target_properties( muparser 10 | PROPERTIES COMPILE_FLAGS "-Wno-switch -Wno-unknown-pragmas" 11 | ) 12 | -------------------------------------------------------------------------------- /moose-examples/tutorials/Rdesigneur/ex2.0_currentPulse.py: -------------------------------------------------------------------------------- 1 | import moose 2 | import rdesigneur as rd 3 | rdes = rd.rdesigneur( 4 | stimList = [['soma', '1', '.', 'inject', '(t>0.1 && t<0.2) * 2e-8' ]], 5 | plotList = [['soma', '1', '.', 'Vm', 'Soma membrane potential']] 6 | ) 7 | rdes.buildModel() 8 | moose.reinit() 9 | moose.start( 0.3 ) 10 | 11 | rdes.display() -------------------------------------------------------------------------------- /moose-core/mpi/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake) 3 | IF(USE_MPI) 4 | find_package(MPI REQUIRED) 5 | include_directories(MPI_INCLUDE_PATH) 6 | ADD_DEFINITIONS(-DUSE_MPI) 7 | ENDIF(USE_MPI) 8 | 9 | add_library(moose_mpi 10 | PostMaster.cpp 11 | testMpi.cpp 12 | ) 13 | 14 | -------------------------------------------------------------------------------- /moose-core/tests/python/_neuroml/README: -------------------------------------------------------------------------------- 1 | This is a modified version of contents of directory 2 | ../../../Demos/neuroml/CA1PyramidalCell/ . This is here for purpose of testing 3 | only. 4 | 5 | File ./ca1_test.py adds two tests: injected current vs frequency and no of spike 6 | when a certain amount of current is inject. If these test fails, neuroml parser 7 | is not working properly. 8 | -------------------------------------------------------------------------------- /docs/source/user/py/rdesigneur/index_rd.rst: -------------------------------------------------------------------------------- 1 | .. MOOSE documentation master file, created by 2 | sphinx-quickstart on Tue Jul 31 19:05:47 2018. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Rdesignuer 7 | =========== 8 | 9 | .. toctree:: 10 | :maxdepth: 2 11 | 12 | rdes 13 | multi_rdes 14 | -------------------------------------------------------------------------------- /moose-core/external/boost-numeric-bindings/boost/numeric/bindings/blas/blas.hpp: -------------------------------------------------------------------------------- 1 | #ifndef boost_blasbindings_blasbindings_hpp 2 | #define boost_blasbindings_blasbindings_hpp 3 | 4 | #include 5 | #include 6 | #include 7 | 8 | 9 | #endif // boost_blasbindings_blasbindings_hpp 10 | -------------------------------------------------------------------------------- /moose-core/tests/python/test_all.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | test_scripts="./test_function.py 4 | test_function.py 5 | test_moose_paths.py 6 | test_mumbl.py 7 | test_pymoose.py 8 | test_synchan.py 9 | test_vec.py 10 | test_difshells.py" 11 | 12 | for testFile in $test_scripts; do 13 | echo "Executing $testFile" 14 | python $testFile | tee test_all.sh.log 15 | done 16 | -------------------------------------------------------------------------------- /macosx/brew_moose.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -x 3 | 4 | PATH=/usr/local/bin:$PATH 5 | rm -f /Library/Caches/Homebrew/moose*.tar.gz 6 | rm -f /Library/Caches/Homebrew/moose*.zip 7 | cp ./moose.rb /usr/local/Library/Formula/moose.rb 8 | 9 | brew -v install moose --with-gui | tee _build_moose.log 10 | 11 | echo "Checking brew script for submission" 12 | brew audit --strict moose 13 | brew -v test moose 14 | -------------------------------------------------------------------------------- /moose-core/tests/python/run_mumble.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | set -e 3 | echo "Running mumble script $1" 4 | if [ $# -lt 1 ]; then 5 | echo "Usage: $0 python_script" 6 | exit 7 | fi 8 | script_name="$1" 9 | export PYTHONPATH=$PYTHONPATH:../../python/ 10 | echo "PYTHONPATH $PYTHONPATH" 11 | python $script_name 12 | dot -Teps $script_name.dot > $script_name.eps 13 | #evince $script_name.eps & 14 | -------------------------------------------------------------------------------- /moose-core/tests/python/two_cells_nml_1.8/cellMechanisms/README: -------------------------------------------------------------------------------- 1 | This is the directory where Cell Mechanism (channel, synapse, etc) files are stored, either the native environment (e.g. *.mod) files, or ChannelML based files. 2 | Unlike the older cellProcesses dir, simply cutting and pasting these cell mech directories into another neuroConstruct project is sufficient for copying the cell mech to that project. 3 | -------------------------------------------------------------------------------- /scripts/build-moose-core: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | (cd ../moose-core; make clean; make) 4 | local_site_package_directory=`python -c "import site; print site.getusersitepackages()"` 5 | mkdir -p "$local_site_package_directory" 6 | echo $(echo `pwd` | sed "s/\/[^\/]*$//")'/moose-core/python' > "$local_site_package_directory/moose.pth" 7 | #echo "`pwd`/moose-core/python" > "$local_site_package_directory/moose.pth" 8 | 9 | -------------------------------------------------------------------------------- /moose-core/.pre-commit-config.yaml: -------------------------------------------------------------------------------- 1 | repos: 2 | - repo: https://github.com/pre-commit/pre-commit-hooks 3 | sha: v1.2.1 4 | hooks: 5 | - id: check-added-large-files 6 | - id: check-ast 7 | - id: check-merge-conflict 8 | - id: check-case-conflict 9 | - id: check-docstring-first 10 | - id: debug-statements 11 | - id: fix-encoding-pragma 12 | - id: trailing-whitespace 13 | -------------------------------------------------------------------------------- /macosx/brew_moogli.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -x 3 | 4 | PATH=/usr/local/bin:$PATH 5 | 6 | rm -f /Library/Caches/Homebrew/moogli*.tar.gz 7 | rm -f /Library/Caches/Homebrew/moogli*.zip 8 | cp ./moogli.rb /usr/local/Library/Formula/moogli.rb 9 | 10 | brew -v install moogli --debug | tee _build_moogli.log 11 | 12 | echo "Checking brew script for submission" 13 | brew audit --strict moogli 14 | brew -v test moogli 15 | -------------------------------------------------------------------------------- /moose-core/builtins/MooseParser.cpp: -------------------------------------------------------------------------------- 1 | /*** 2 | * Description: Class MooseParser. 3 | * 4 | * Created: 2019-05-30 5 | 6 | * Author: Dilawar Singh 7 | * Organization: NCBS Bangalore 8 | * License: MIT License 9 | */ 10 | 11 | #include "MooseParser.h" 12 | 13 | MooseParser::MooseParser() 14 | {} 15 | 16 | MooseParser::~MooseParser() 17 | {} 18 | 19 | -------------------------------------------------------------------------------- /docs/source/user/py/references/Enz.rst: -------------------------------------------------------------------------------- 1 | Enz 2 | --- 3 | 4 | .. py:class:: Enz 5 | 6 | 7 | .. py:method:: setKmK1 8 | 9 | (*destination message field*) Low-level function used when you wish to explicitly set Km and k1, without doing any of the volume calculations.Needed by ReadKkit and other situations where the numbers must be set before all the messaging is in place.Not relevant for zombie enzymes. 10 | -------------------------------------------------------------------------------- /moose-core/hsolve/CTestTestfile.cmake: -------------------------------------------------------------------------------- 1 | # CMake generated Testfile for 2 | # Source directory: /home/dilawar/Work/NCBS/moose_svn_1.8/moose/branches/async_multiscale_cmake/hsolve 3 | # Build directory: /home/dilawar/Work/NCBS/moose_svn_1.8/moose/branches/async_multiscale_cmake/hsolve 4 | # 5 | # This file includes the relevant testing commands required for 6 | # testing this directory and lists subdirectories to be tested as well. 7 | -------------------------------------------------------------------------------- /data/matplotlibrc: -------------------------------------------------------------------------------- 1 | # This is configuration file for matplotlib used in examples. 2 | # We use this configuration file to test the examples. Copy this configuration 3 | # file in the current working directory and run the snippet. 4 | 5 | # This configuration file does the followings: 6 | # - plt.show() function become non-blocking. 7 | 8 | backend = qt4agg 9 | 10 | # This makes all plots non-blocking. 11 | interactive = True 12 | -------------------------------------------------------------------------------- /docs/source/user/py/quickstart/index_qs.rst: -------------------------------------------------------------------------------- 1 | .. MOOSE documentation master file, created by 2 | sphinx-quickstart on Tue Jul 1 19:05:47 2014. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Quick Start 7 | =========== 8 | 9 | .. toctree:: 10 | :maxdepth: 2 11 | 12 | qs_inter 13 | qs_GUI 14 | moose_quickstart 15 | demos 16 | classes_demos 17 | -------------------------------------------------------------------------------- /moose-core/hsolve/README.txt: -------------------------------------------------------------------------------- 1 | A high-level overview for the HSolve code can be found at: 2 | Docs/developer/HSolve-developer-overview.cpp 3 | 4 | The 'doxygen' tool can be used to convert this file into an easy-to-read HTML 5 | document. Run 'doxygen' in the top-level directory of the MOOSE source tree to 6 | generate all the HTML docs. The HTML docs can also be found on the MOOSE 7 | website (http://moose.ncbs.res.in/) in the Developer Documentation section. 8 | -------------------------------------------------------------------------------- /moose-core/mesh/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake) 3 | add_library(mesh 4 | ChemCompt.cpp 5 | MeshCompt.cpp 6 | MeshEntry.cpp 7 | CubeMesh.cpp 8 | CylBase.cpp 9 | CylMesh.cpp 10 | NeuroNode.cpp 11 | NeuroMesh.cpp 12 | SpineEntry.cpp 13 | SpineMesh.cpp 14 | PsdMesh.cpp 15 | EndoMesh.cpp 16 | testMesh.cpp 17 | ) 18 | -------------------------------------------------------------------------------- /docs/source/known_issues/index.rst: -------------------------------------------------------------------------------- 1 | Known issues 2 | ============ 3 | 4 | Full report can be found at the following places 5 | 6 | - Related to `build, packages and documentation `_ 7 | - Related to `moose-core `_ 8 | - Related to `MOOSE-GUI `_ 9 | - Related to `moogli `_ 10 | -------------------------------------------------------------------------------- /moose-examples/tutorials/Rdesigneur/ex2.1_vclamp.py: -------------------------------------------------------------------------------- 1 | import moose 2 | import rdesigneur as rd 3 | rdes = rd.rdesigneur( 4 | stimList = [['soma', '1', '.', 'vclamp', '-0.065 + (t>0.1 && t<0.2) * 0.02' ]], 5 | plotList = [ 6 | ['soma', '1', '.', 'Vm', 'Soma membrane potential'], 7 | ['soma', '1', 'vclamp', 'current', 'Soma holding current'], 8 | ] 9 | ) 10 | rdes.buildModel() 11 | moose.reinit() 12 | moose.start( 0.3 ) 13 | 14 | rdes.display() 15 | -------------------------------------------------------------------------------- /moose-core/synapse/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake) 3 | 4 | set( SYNAPSE_SRCS 5 | GraupnerBrunel2012CaPlasticitySynHandler.cpp 6 | RollingMatrix.cpp 7 | SeqSynHandler.cpp 8 | SimpleSynHandler.cpp 9 | STDPSynapse.cpp 10 | STDPSynHandler.cpp 11 | Synapse.cpp 12 | SynHandlerBase.cpp 13 | testSynapse.cpp 14 | ) 15 | 16 | add_library(synapse ${SYNAPSE_SRCS} ) 17 | -------------------------------------------------------------------------------- /moose-gui/plugins/constants.py: -------------------------------------------------------------------------------- 1 | INVALID = 6 2 | 3 | INTERIOR = 7 4 | BOUNDARY = 8 5 | 6 | SAME_OBJECT = 9 7 | OTHER_OBJECT = 10 8 | NO_OBJECT = 11 9 | 10 | RUBBERBAND_SELECTION = 12 11 | VALID = 13 12 | 13 | ITEM = 0 14 | CONNECTOR = 1 15 | CONNECTION = 2 16 | EMPTY = 3 17 | 18 | COMPARTMENT = 14 19 | COMPARTMENT_BOUNDARY = 4 20 | COMPARTMENT_INTERIOR = 5 21 | 22 | GROUP = 15 23 | GROUP_BOUNDARY = 16 24 | GROUP_INTERIOR = 17 25 | -------------------------------------------------------------------------------- /moose-core/hsolve/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake) 3 | add_library(hsolve 4 | HSolveStruct.cpp 5 | HinesMatrix.cpp 6 | Cell.cpp 7 | HSolvePassive.cpp 8 | RateLookup.cpp 9 | HSolveActive.cpp 10 | HSolveActiveSetup.cpp 11 | HSolveInterface.cpp 12 | HSolve.cpp 13 | HSolveUtils.cpp 14 | testHSolve.cpp 15 | ZombieCompartment.cpp 16 | ZombieCaConc.cpp 17 | ZombieHHChannel.cpp 18 | ) 19 | 20 | -------------------------------------------------------------------------------- /docs/source/user/py/cookbook/index_ckbk.rst: -------------------------------------------------------------------------------- 1 | .. MOOSE documentation master file, created by 2 | sphinx-quickstart on Tue Jul 1 19:05:47 2014. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Cook Book 7 | ========= 8 | 9 | The MOOSE Cookbook contains recipes showing you, how to do specific tasks in MOOSE. 10 | 11 | .. toctree:: 12 | :maxdepth: 2 13 | 14 | elec 15 | chem 16 | network 17 | multiscale 18 | -------------------------------------------------------------------------------- /.travis_build_linux.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | set -o nounset # Treat unset variables as an error 3 | set -e -x 4 | PATH=/usr/bin:/usr/local/bin:$PATH 5 | gbp buildpackage --git-ignore-branch --git-ignore-new -uc -us -d | tee _gbp.log 6 | pwd 7 | ls ../*.deb 8 | 9 | if [ -n "$TRAVIS" ]; then 10 | echo "We are on travis" 11 | sudo dpkg -i ../*.deb 12 | sudo apt-get install -f 13 | python -c 'import moose; print(moose.__file__); print(moose.__version__)' 14 | fi 15 | -------------------------------------------------------------------------------- /moose-core/tests/python/Rallpacks/moose_vs_neuron/rallpack3/compare.hs: -------------------------------------------------------------------------------- 1 | -- This haskell script compares data generated by NEURON and MOOSE. This is not 2 | -- a generic script. 3 | import System.Environment 4 | import qualified Data.Text.IO as IO 5 | import qualified Data.Text as T 6 | 7 | txtToData text = map toFloat lines where 8 | lines = T.lines text 9 | 10 | main = do 11 | args <- getArgs 12 | a <- mapM IO.readFile args 13 | let r = map txtToData a 14 | print r 15 | putStrLn "Done" 16 | -------------------------------------------------------------------------------- /moose-examples/README.md: -------------------------------------------------------------------------------- 1 | [![Build Status](https://travis-ci.org/BhallaLab/moose-examples.svg?branch=master)](https://travis-ci.org/BhallaLab/moose-examples). 2 | 3 | Examples, tutorial and demo scripts. 4 | 5 | # How to run 6 | 7 | First install `pymoose` from PyPI using `pip`. 8 | 9 | $ pip install pymoose --pre --user # get the latest version 10 | 11 | Make sure that you have `matplotlib`, and `scipy` (optional) installed as well. 12 | 13 | Some scripts might require `PyQt4` or `PyQt5` as well. 14 | -------------------------------------------------------------------------------- /docs/source/user/py/references/OneToAllMsg.rst: -------------------------------------------------------------------------------- 1 | OneToAllMsg 2 | ----------- 3 | 4 | .. py:class:: OneToAllMsg 5 | 6 | 7 | .. py:method:: setI1 8 | 9 | (*destination message field*) Assigns field value. 10 | 11 | 12 | .. py:method:: getI1 13 | 14 | (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value. 15 | 16 | 17 | .. py:attribute:: i1 18 | 19 | unsigned int (*value field*) DataId of source Element. 20 | -------------------------------------------------------------------------------- /moose-core/kinetics/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake) 3 | add_library(kinetics 4 | PoolBase.cpp 5 | Pool.cpp 6 | BufPool.cpp 7 | ReacBase.cpp 8 | Reac.cpp 9 | EnzBase.cpp 10 | CplxEnzBase.cpp 11 | Enz.cpp 12 | MMenz.cpp 13 | Species.cpp 14 | ConcChan.cpp 15 | ReadKkit.cpp 16 | WriteKkit.cpp 17 | ReadCspace.cpp 18 | lookupVolumeFromMesh.cpp 19 | testKinetics.cpp 20 | ) 21 | -------------------------------------------------------------------------------- /moose-core/external/boost-numeric-bindings/boost/numeric/bindings/mumps/mumps_driver.hpp: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright Karl Meerbergen 2007 3 | // 4 | // Distributed under the Boost Software License, Version 1.0. 5 | // (See accompanying file LICENSE_1_0.txt or copy at 6 | // http://www.boost.org/LICENSE_1_0.txt) 7 | // 8 | 9 | #ifndef BOOST_NUMERIC_BINDINGS_MUMPS_MUMPS_DRIVER_HPP 10 | #define BOOST_NUMERIC_BINDINGS_MUMPS_MUMPS_DRIVER_HPP 11 | 12 | #include 13 | 14 | #endif 15 | -------------------------------------------------------------------------------- /docs/source/user/py/references/Pool.rst: -------------------------------------------------------------------------------- 1 | Pool 2 | ---- 3 | 4 | .. py:class:: Pool 5 | 6 | 7 | .. py:method:: increment 8 | 9 | (*destination message field*) Increments mol numbers by specified amount. Can be +ve or -ve 10 | 11 | 12 | .. py:method:: decrement 13 | 14 | (*destination message field*) Decrements mol numbers by specified amount. Can be +ve or -ve 15 | 16 | 17 | .. py:method:: nIn 18 | 19 | (*destination message field*) Set the number of molecules by specified amount 20 | -------------------------------------------------------------------------------- /moose-core/scheduling/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake) 3 | file(GLOB scheduling_SRC "*.cpp" ) 4 | if(NOTIFY_PROGRESS) 5 | add_definitions("-DNOTIFY_PROGRESS") 6 | endif(NOTIFY_PROGRESS) 7 | 8 | if(PARALLELIZED_CLOCK) 9 | message( STATUS "Enabling high-level parallelization of moose::Clock" ) 10 | add_definitions( -DPARALLELIZE_CLOCK_USING_CPP11_ASYNC ) 11 | endif(PARALLELIZED_CLOCK) 12 | 13 | add_library(scheduling ${scheduling_SRC}) 14 | -------------------------------------------------------------------------------- /moose-core/mpi/testMpi.cpp: -------------------------------------------------------------------------------- 1 | /********************************************************************** 2 | ** This program is part of 'MOOSE', the 3 | ** Messaging Object Oriented Simulation Environment. 4 | ** Copyright (C) 2003-2013 Upinder S. Bhalla. and NCBS 5 | ** It is made available under the terms of the 6 | ** GNU Lesser General Public License version 2.1 7 | ** See the file COPYING.LIB for the full notice. 8 | **********************************************************************/ 9 | 10 | void testMpi() 11 | { 12 | ; 13 | } 14 | -------------------------------------------------------------------------------- /moose-core/tests/issues/issue_47.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # Issue 47 on moose-core 3 | import moose 4 | import os 5 | sdir = os.path.dirname( __file__ ) 6 | print( '[INFO] Using moose from %s' % moose.__file__ ) 7 | print( '[WONTFIX] See https://github.com/BhallaLab/moose-core/issues/47') 8 | if False: 9 | moose.loadModel(os.path.join(sdir,'../data/acc94.g'),'/acc94','gsl') 10 | #moose.loadModel(os.path.join(sdir,'../data/acc94.g'),'/acc94','gssa') 11 | moose.reinit() 12 | moose.start( 10 ) 13 | else: 14 | quit(0) 15 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/NontuftedRS.levels: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 2 4 | 4 2 5 | 5 2 6 | 6 2 7 | 7 2 8 | 8 2 9 | 9 2 10 | 10 2 11 | 11 2 12 | 12 2 13 | 13 3 14 | 14 3 15 | 15 3 16 | 16 3 17 | 17 3 18 | 18 3 19 | 19 3 20 | 20 3 21 | 21 3 22 | 22 3 23 | 23 3 24 | 24 4 25 | 25 4 26 | 26 4 27 | 27 4 28 | 28 4 29 | 29 4 30 | 30 4 31 | 31 4 32 | 32 4 33 | 33 4 34 | 34 4 35 | 35 5 36 | 36 6 37 | 37 7 38 | 38 8 39 | 39 9 40 | 40 10 41 | 41 11 42 | 42 12 43 | 43 13 44 | 44 14 45 | 45 0 46 | 46 0 47 | 47 0 48 | 48 0 49 | 49 0 50 | 50 0 51 | 52 | 53 | -------------------------------------------------------------------------------- /packaging_scripts/build_using_xcode.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ( 3 | mkdir -p _build_macosx_ 4 | cd _build_macosx_ 5 | PROJECT=Moose.xcodeproj 6 | cmake -G "Xcode" .. 7 | xcodebuild -list 8 | xcodebuild clean -project $PROJECT -configuration Release -alltargets 9 | xcodebuild archive -project $PROJECT -configuration Release \ 10 | -scheme moose.bin \ 11 | -archivePath Moose.xcarhive 12 | xcodebuild -exportArchive -archivePath Moose.xcarhive -exportPath Moose \ 13 | -exportFormat pkg 14 | ) 15 | -------------------------------------------------------------------------------- /moose-core/utility/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake) 3 | 4 | IF(WITH_BOOST) 5 | include(CheckIncludeFiles) 6 | check_include_files( ${Boost_INCLUDE_DIRS}/boost/random/random_device.hpp 7 | BOOST_RANDOM_DEVICE_EXISTS 8 | ) 9 | endif(WITH_BOOST) 10 | 11 | add_library(utility 12 | strutil.cpp 13 | types.cpp 14 | setupenv.cpp 15 | numutil.cpp 16 | Annotator.cpp 17 | Vec.cpp 18 | cnpy.cpp 19 | fileutils.cpp 20 | #matrix_util.cpp 21 | ) 22 | -------------------------------------------------------------------------------- /moose-core/AUTHORS: -------------------------------------------------------------------------------- 1 | # Active developers 2 | 3 | Upinder S. Bhalla Primary Architect, rdesigneur 4 | HarshaRani. G.V MOOSE Website, SBML support, GUI 5 | Dilawar Singh Multithreading, GSoC, Packaging, Maintenance, BOOST solvers 6 | 7 | # Past developers 8 | 9 | Subhasis Ray Python interface, GUI 10 | Niraj Dudani Neuronal solver 11 | Aditya Gilra NeuroML support 12 | Aviral Goel Moogli 13 | 14 | # Contributors 15 | 16 | Padraid Gleeson NeuroML2 support 17 | Dharma Teja GPU parallelization using CUDA 18 | -------------------------------------------------------------------------------- /docs/source/user/py/references/PoissonRng.rst: -------------------------------------------------------------------------------- 1 | PoissonRng 2 | ---------- 3 | 4 | .. py:class:: PoissonRng 5 | 6 | Poisson distributed random number generator. 7 | 8 | .. py:method:: setMean 9 | 10 | (*destination message field*) Assigns field value. 11 | 12 | 13 | .. py:method:: getMean 14 | 15 | (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value. 16 | 17 | 18 | .. py:attribute:: mean 19 | 20 | double (*value field*) Mean of the Poisson distribution. 21 | -------------------------------------------------------------------------------- /moose-examples/tutorials/Rdesigneur/ex3.0_squid_currentPulse.py: -------------------------------------------------------------------------------- 1 | import moose 2 | import pylab 3 | import rdesigneur as rd 4 | rdes = rd.rdesigneur( 5 | chanProto = [['make_HH_Na()', 'Na'], ['make_HH_K()', 'K']], 6 | chanDistrib = [ 7 | ['Na', 'soma', 'Gbar', '1200' ], 8 | ['K', 'soma', 'Gbar', '360' ]], 9 | stimList = [['soma', '1', '.', 'inject', '(t>0.1 && t<0.2) * 1e-8' ]], 10 | plotList = [['soma', '1', '.', 'Vm', 'Membrane potential']] 11 | ) 12 | 13 | rdes.buildModel() 14 | moose.reinit() 15 | moose.start( 0.3 ) 16 | 17 | rdes.display() 18 | -------------------------------------------------------------------------------- /scripts/install-dependencies-on-debian: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | # AUTHOR : AVIRAL GOEL 4 | # EMAIL-ID : aviralg@ncbs.res.in 5 | # UPDATED BY: Harsha Rani 6 | # UPDATED ON: Aug 16 2016 7 | echo "Installing moose-core dependencies" 8 | sudo -E apt-get install g++ libgsl0-dev libhdf5-dev libpython-dev python-numpy 9 | 10 | 11 | #echo "Installing moose-gui and moogli dependencies" 12 | sudo -E apt-get install python-setuptools libqt4-dev python-qt4-dev libopenscenegraph-dev python-qt4-gl python-sip-dev python-matplotlib python-scipy python-suds python-networkx python-pygraphviz 13 | -------------------------------------------------------------------------------- /docs/doxygen/doxy_1.4.6/docgen: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | echo "###############################################################" 4 | echo "# Generating C++ Documentation #" 5 | echo "###############################################################" 6 | doxygen ./Doxyfile.full 7 | 8 | echo "##############################################################" 9 | echo "# Generating Python Documentation #" 10 | echo "##############################################################" 11 | 12 | ( cd Docs/user/py && make html || true ) 13 | 14 | -------------------------------------------------------------------------------- /moose-core/basecode/doubleEq.h: -------------------------------------------------------------------------------- 1 | /********************************************************************** 2 | ** This program is part of 'MOOSE', the 3 | ** Messaging Object Oriented Simulation Environment. 4 | ** Copyright (C) 2003-2010 Upinder S. Bhalla. and NCBS 5 | ** It is made available under the terms of the 6 | ** GNU Lesser General Public License version 2.1 7 | ** See the file COPYING.LIB for the full notice. 8 | **********************************************************************/ 9 | 10 | bool doubleEq( double x, double y ); 11 | bool doubleApprox( double x, double y ); 12 | -------------------------------------------------------------------------------- /docs/source/user/py/references/SimpleSynHandler.rst: -------------------------------------------------------------------------------- 1 | SimpleSynHandler 2 | ---------------- 3 | 4 | .. py:class:: SimpleSynHandler 5 | 6 | The SimpleSynHandler handles simple synapses without plasticity. It uses a priority queue to manage them. 7 | 8 | .. py:method:: setNumSynapse 9 | 10 | (*destination message field*) Assigns number of field entries in field array. 11 | 12 | 13 | .. py:method:: getNumSynapse 14 | 15 | (*destination message field*) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value. 16 | -------------------------------------------------------------------------------- /moose-core/tests/python/benchmark.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | from __future__ import print_function 3 | 4 | from datetime import datetime 5 | import moose 6 | 7 | def time_creation(n=1000): 8 | elist = [] 9 | start = datetime.now() 10 | for ii in range(n): 11 | elist.append(moose.Neutral('a_%d' % (ii))) 12 | end = datetime.now() 13 | delta = end - start 14 | print('total time to create %d Neutral elements: %g' % (n, delta.days * 86400 + delta.seconds + delta.microseconds * 1e-6)) 15 | return delta 16 | 17 | if __name__ == '__main__': 18 | time_creation() 19 | -------------------------------------------------------------------------------- /moose-examples/run_pylint.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | set -e 3 | PYLINT="python3 -m pylint -E --disable=no-member --disable=no-name-in-module \ 4 | --disable=invalid-unary-operand-type \ 5 | --disable=import-error \ 6 | " 7 | FILES=$(find . -type f -name "*.py" | shuf) 8 | i=0 9 | N=3 10 | for f in $FILES; do 11 | i=$((i+1)) 12 | if [ $i -eq $N ]; then 13 | wait 14 | i=0 15 | fi 16 | ( 17 | echo "Checking $f" 18 | DIR=$(dirname $f) 19 | SNAME=$(basename $f) 20 | cd $DIR 21 | $PYLINT $@ $SNAME 22 | ) & 23 | done 24 | -------------------------------------------------------------------------------- /moose-core/utility/fileutils.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * Description: Filesystem related utilities. 3 | * 4 | * Author: Dilawar Singh (), dilawars@ncbs.res.in 5 | * Organization: NCBS Bangalore 6 | */ 7 | 8 | #include 9 | #include 10 | #include 11 | #include 12 | #include 13 | 14 | using namespace std; 15 | 16 | #include "utility.h" 17 | 18 | namespace moose { 19 | 20 | bool filepath_exists( const string& path ) 21 | { 22 | struct stat buffer; 23 | return (stat (path.c_str(), &buffer) == 0); 24 | } 25 | 26 | } //namespace moose. 27 | -------------------------------------------------------------------------------- /docs/README.txt: -------------------------------------------------------------------------------- 1 | The source code of documentation is /source directory. 2 | 3 | This directory contains MOOSE user documentation in reST format that can be 4 | compiled into various formats by sphinx. To build the documentation in HTML, 5 | format enter the command: 6 | 7 | make html 8 | 9 | in this directory. Then you can open build/html/index.html in browser to 10 | browse the generated documentation. 11 | 12 | Other files in /source folder 13 | - conf.py: the Sphinx configuration file. 14 | - index.rst: This is the index file for use when building the Python 15 | docs using sphinx. 16 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/nRT.levels: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 3 4 | 4 3 5 | 5 4 6 | 6 4 7 | 7 4 8 | 8 5 9 | 9 5 10 | 10 5 11 | 11 6 12 | 12 7 13 | 13 8 14 | 14 9 15 | 15 2 16 | 16 3 17 | 17 3 18 | 18 4 19 | 19 4 20 | 20 4 21 | 21 5 22 | 22 5 23 | 23 5 24 | 24 6 25 | 25 7 26 | 26 8 27 | 27 9 28 | 28 2 29 | 29 3 30 | 30 3 31 | 31 4 32 | 32 4 33 | 33 4 34 | 34 5 35 | 35 5 36 | 36 5 37 | 37 6 38 | 38 7 39 | 39 8 40 | 40 9 41 | 41 2 42 | 42 3 43 | 43 3 44 | 44 4 45 | 45 4 46 | 46 4 47 | 47 5 48 | 48 5 49 | 49 5 50 | 50 6 51 | 51 7 52 | 52 8 53 | 53 9 54 | 54 0 55 | 55 0 56 | 56 0 57 | 57 0 58 | 58 0 59 | 59 0 60 | 61 | -------------------------------------------------------------------------------- /docs/user/tutorials/index.rst: -------------------------------------------------------------------------------- 1 | .. MOOSE documentation master file, created by 2 | sphinx-quickstart on Tue Feb 2 14:05:47 2016. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Tutorials for MOOSE 7 | ================================== 8 | A set of tutorials for teaching a range of topics, including integrate-and-fire networks, chemical bistables, and oscillators. Has stand-alone graphics and the Python scripts are meant to tinker with. 9 | 10 | .. toctree:: 11 | :maxdepth: 2 12 | :numbered: 13 | 14 | 15 | tutorial 16 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/DeepLTS.levels: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 3 4 | 4 3 5 | 5 4 6 | 6 4 7 | 7 4 8 | 8 5 9 | 9 5 10 | 10 5 11 | 11 6 12 | 12 7 13 | 13 8 14 | 14 9 15 | 15 2 16 | 16 3 17 | 17 3 18 | 18 4 19 | 19 4 20 | 20 4 21 | 21 5 22 | 22 5 23 | 23 5 24 | 24 6 25 | 25 7 26 | 26 8 27 | 27 9 28 | 28 2 29 | 29 3 30 | 30 3 31 | 31 4 32 | 32 4 33 | 33 4 34 | 34 5 35 | 35 5 36 | 36 5 37 | 37 6 38 | 38 7 39 | 39 8 40 | 40 9 41 | 41 2 42 | 42 3 43 | 43 3 44 | 44 4 45 | 45 4 46 | 46 4 47 | 47 5 48 | 48 5 49 | 49 5 50 | 50 6 51 | 51 7 52 | 52 8 53 | 53 9 54 | 54 0 55 | 55 0 56 | 56 0 57 | 57 0 58 | 58 0 59 | 59 0 60 | 61 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/SpinyStellate.levels: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 3 4 | 4 3 5 | 5 4 6 | 6 4 7 | 7 4 8 | 8 5 9 | 9 5 10 | 10 5 11 | 11 6 12 | 12 7 13 | 13 8 14 | 14 9 15 | 15 2 16 | 16 3 17 | 17 3 18 | 18 4 19 | 19 4 20 | 20 4 21 | 21 5 22 | 22 5 23 | 23 5 24 | 24 6 25 | 25 7 26 | 26 8 27 | 27 9 28 | 28 2 29 | 29 3 30 | 30 3 31 | 31 4 32 | 32 4 33 | 33 4 34 | 34 5 35 | 35 5 36 | 36 5 37 | 37 6 38 | 38 7 39 | 39 8 40 | 40 9 41 | 41 2 42 | 42 3 43 | 43 3 44 | 44 4 45 | 45 4 46 | 46 4 47 | 47 5 48 | 48 5 49 | 49 5 50 | 50 6 51 | 51 7 52 | 52 8 53 | 53 9 54 | 54 0 55 | 55 0 56 | 56 0 57 | 57 0 58 | 58 0 59 | 59 0 60 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/SupLTS.levels: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 3 4 | 4 3 5 | 5 4 6 | 6 4 7 | 7 4 8 | 8 5 9 | 9 5 10 | 10 5 11 | 11 6 12 | 12 7 13 | 13 8 14 | 14 9 15 | 15 2 16 | 16 3 17 | 17 3 18 | 18 4 19 | 19 4 20 | 20 4 21 | 21 5 22 | 22 5 23 | 23 5 24 | 24 6 25 | 25 7 26 | 26 8 27 | 27 9 28 | 28 2 29 | 29 3 30 | 30 3 31 | 31 4 32 | 32 4 33 | 33 4 34 | 34 5 35 | 35 5 36 | 36 5 37 | 37 6 38 | 38 7 39 | 39 8 40 | 40 9 41 | 41 2 42 | 42 3 43 | 43 3 44 | 44 4 45 | 45 4 46 | 46 4 47 | 47 5 48 | 48 5 49 | 49 5 50 | 50 6 51 | 51 7 52 | 52 8 53 | 53 9 54 | 54 0 55 | 55 0 56 | 56 0 57 | 57 0 58 | 58 0 59 | 59 0 60 | 61 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/DeepAxoaxonic.levels: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 3 4 | 4 3 5 | 5 4 6 | 6 4 7 | 7 4 8 | 8 5 9 | 9 5 10 | 10 5 11 | 11 6 12 | 12 7 13 | 13 8 14 | 14 9 15 | 15 2 16 | 16 3 17 | 17 3 18 | 18 4 19 | 19 4 20 | 20 4 21 | 21 5 22 | 22 5 23 | 23 5 24 | 24 6 25 | 25 7 26 | 26 8 27 | 27 9 28 | 28 2 29 | 29 3 30 | 30 3 31 | 31 4 32 | 32 4 33 | 33 4 34 | 34 5 35 | 35 5 36 | 36 5 37 | 37 6 38 | 38 7 39 | 39 8 40 | 40 9 41 | 41 2 42 | 42 3 43 | 43 3 44 | 44 4 45 | 45 4 46 | 46 4 47 | 47 5 48 | 48 5 49 | 49 5 50 | 50 6 51 | 51 7 52 | 52 8 53 | 53 9 54 | 54 0 55 | 55 0 56 | 56 0 57 | 57 0 58 | 58 0 59 | 59 0 60 | 61 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/DeepBasket.levels: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 3 4 | 4 3 5 | 5 4 6 | 6 4 7 | 7 4 8 | 8 5 9 | 9 5 10 | 10 5 11 | 11 6 12 | 12 7 13 | 13 8 14 | 14 9 15 | 15 2 16 | 16 3 17 | 17 3 18 | 18 4 19 | 19 4 20 | 20 4 21 | 21 5 22 | 22 5 23 | 23 5 24 | 24 6 25 | 25 7 26 | 26 8 27 | 27 9 28 | 28 2 29 | 29 3 30 | 30 3 31 | 31 4 32 | 32 4 33 | 33 4 34 | 34 5 35 | 35 5 36 | 36 5 37 | 37 6 38 | 38 7 39 | 39 8 40 | 40 9 41 | 41 2 42 | 42 3 43 | 43 3 44 | 44 4 45 | 45 4 46 | 46 4 47 | 47 5 48 | 48 5 49 | 49 5 50 | 50 6 51 | 51 7 52 | 52 8 53 | 53 9 54 | 54 0 55 | 55 0 56 | 56 0 57 | 57 0 58 | 58 0 59 | 59 0 60 | 61 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/SupBasket.levels: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 3 4 | 4 3 5 | 5 4 6 | 6 4 7 | 7 4 8 | 8 5 9 | 9 5 10 | 10 5 11 | 11 6 12 | 12 7 13 | 13 8 14 | 14 9 15 | 15 2 16 | 16 3 17 | 17 3 18 | 18 4 19 | 19 4 20 | 20 4 21 | 21 5 22 | 22 5 23 | 23 5 24 | 24 6 25 | 25 7 26 | 26 8 27 | 27 9 28 | 28 2 29 | 29 3 30 | 30 3 31 | 31 4 32 | 32 4 33 | 33 4 34 | 34 5 35 | 35 5 36 | 36 5 37 | 37 6 38 | 38 7 39 | 39 8 40 | 40 9 41 | 41 2 42 | 42 3 43 | 43 3 44 | 44 4 45 | 45 4 46 | 46 4 47 | 47 5 48 | 48 5 49 | 49 5 50 | 50 6 51 | 51 7 52 | 52 8 53 | 53 9 54 | 54 0 55 | 55 0 56 | 56 0 57 | 57 0 58 | 58 0 59 | 59 0 60 | 61 | -------------------------------------------------------------------------------- /_travis/prepare_linux.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | sudo apt-get update -qq 4 | sudo apt-get install libxml2-dev libbz2-dev wget 5 | sudo apt-get install libhdf5-serial-dev 6 | sudo apt-get install python-numpy python-setuptools python-networkx python-pip 7 | sudo apt-get install cmake cdbs 8 | sudo apt-get install python-suds python-matplotlib python-nose python-lxml 9 | sudo apt-get install python-qt4-dev python-qt4-gl python-sip-dev libqt4-dev libopenscenegraph-dev 10 | sudo apt-get install libgsl0-dev 11 | sudo apt-get install doxygen python-sphinx 12 | sudo apt-get install git-buildpackage 13 | sudo apt-get install -f 14 | -------------------------------------------------------------------------------- /docs/user/py/cookbook/README.txt: -------------------------------------------------------------------------------- 1 | This directory contains MOOSE user documentation in reST format that can be 2 | compiled into various formats by sphinx. To build the documentation in HTML, 3 | format enter the command: 4 | 5 | make html 6 | 7 | in this directory. Then you can open _build/html/index.html in browser to 8 | browse the generated documentation. 9 | 10 | files 11 | - conf.py: the Sphinx configuration file. 12 | - index.rst: This is the index file for use when building the Python 13 | docs using sphinx. 14 | - moose_cookbook.rst: Recipes for specific tasks in moose. 15 | 16 | 17 | -------------------------------------------------------------------------------- /moose-core/basecode/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake ) 3 | add_library(basecode 4 | consts.cpp 5 | Element.cpp 6 | DataElement.cpp 7 | GlobalDataElement.cpp 8 | LocalDataElement.cpp 9 | Eref.cpp 10 | Finfo.cpp 11 | DestFinfo.cpp 12 | Cinfo.cpp 13 | SrcFinfo.cpp 14 | ValueFinfo.cpp 15 | SharedFinfo.cpp 16 | FieldElementFinfo.cpp 17 | FieldElement.cpp 18 | Id.cpp 19 | ObjId.cpp 20 | global.cpp 21 | SetGet.cpp 22 | OpFuncBase.cpp 23 | EpFunc.cpp 24 | HopFunc.cpp 25 | SparseMatrix.cpp 26 | doubleEq.cpp 27 | testAsync.cpp 28 | ) 29 | -------------------------------------------------------------------------------- /moose-core/cmake_modules/FindSIP.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # FindSIP.py 3 | # 4 | # Copyright (c) 2007, Simon Edwards 5 | # Redistribution and use is allowed according to the terms of the BSD license. 6 | # For details see the accompanying COPYING-CMAKE-SCRIPTS file. 7 | 8 | import sys 9 | import sipconfig 10 | 11 | sipcfg = sipconfig.Configuration() 12 | print("sip_version:%06.0x" % sipcfg.sip_version) 13 | print("sip_version_str:%s" % sipcfg.sip_version_str) 14 | print("sip_bin:%s" % sipcfg.sip_bin) 15 | print("default_sip_dir:%s" % sipcfg.default_sip_dir) 16 | print("sip_inc_dir:%s" % sipcfg.sip_inc_dir) 17 | -------------------------------------------------------------------------------- /moose-examples/tutorials/Rdesigneur/ex6_chem_osc.py: -------------------------------------------------------------------------------- 1 | import moose 2 | import pylab 3 | import rdesigneur as rd 4 | rdes = rd.rdesigneur( 5 | turnOffElec = True, 6 | diffusionLength = 1e-3, # Default diffusion length is 2 microns 7 | chemProto = [['makeChemOscillator()', 'osc']], 8 | chemDistrib = [['osc', 'soma', 'install', '1' ]], 9 | plotList = [['soma', '1', 'dend/a', 'conc', 'a Conc'], 10 | ['soma', '1', 'dend/b', 'conc', 'b Conc']] 11 | ) 12 | 13 | rdes.buildModel() 14 | b = moose.element( '/model/chem/dend/b' ) 15 | b.concInit *= 5 16 | moose.reinit() 17 | moose.start( 200 ) 18 | 19 | rdes.display() 20 | -------------------------------------------------------------------------------- /docs/user/py/quickstart/README.txt: -------------------------------------------------------------------------------- 1 | This directory contains MOOSE user documentation in reST format that can be 2 | compiled into various formats by sphinx. To build the documentation in HTML, 3 | format enter the command: 4 | 5 | make html 6 | 7 | in this directory. Then you can open _build/html/index.html in browser to 8 | browse the generated documentation. 9 | 10 | files 11 | - conf.py: the Sphinx configuration file. 12 | - index.rst: This is the index file for use when building the Python 13 | docs using sphinx. 14 | - moose_quickstart.rst: Recipes for specific tasks in moose. 15 | 16 | 17 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_ka.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("ka", 1e-9) 17 | // (50 ms start positive current, 150 ms stop positive current, 200 18 | // ms start negative current, 300 ms stop negative current 350 ms stop 19 | // simulation) 20 | 21 | testcomp.setup_recording("ka", Dt) 22 | run() 23 | testcomp.save_data("KA", Dt) 24 | 25 | quit() 26 | 27 | 28 | -------------------------------------------------------------------------------- /moose-core/shell/LoadModels.h: -------------------------------------------------------------------------------- 1 | /********************************************************************** 2 | ** This program is part of 'MOOSE', the 3 | ** Messaging Object Oriented Simulation Environment. 4 | ** Copyright (C) 2003-2009 Upinder S. Bhalla. and NCBS 5 | ** It is made available under the terms of the 6 | ** GNU Lesser General Public License version 2.1 7 | ** See the file COPYING.LIB for the full notice. 8 | **********************************************************************/ 9 | enum ModelType { 10 | UNKNOWN, 11 | KKIT, 12 | DOTP, 13 | SBML, 14 | NEUROML, 15 | NINEML, 16 | SEDML, 17 | CSPACE, 18 | SWC 19 | }; 20 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_cal.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("cal", 1e-9) 17 | 18 | // (50 ms start positive current, 150 ms stop positive current, 200 19 | // ms start negative current, 300 ms stop negative current 350 ms stop 20 | // simulation) 21 | 22 | testcomp.setup_recording("cal", Dt) 23 | run() 24 | testcomp.save_data("CaL", Dt) 25 | 26 | quit() 27 | 28 | 29 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_cat.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("cat", 1e-9) 17 | 18 | // (50 ms start positive current, 150 ms stop positive current, 200 19 | // ms start negative current, 300 ms stop negative current 350 ms stop 20 | // simulation) 21 | 22 | testcomp.setup_recording("cat", Dt) 23 | run() 24 | testcomp.save_data("CaT", Dt) 25 | 26 | quit() 27 | 28 | 29 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_kdr.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("kdr", 1e-9) 17 | 18 | // (50 ms start positive current, 150 ms stop positive current, 200 19 | // ms start negative current, 300 ms stop negative current 350 ms stop 20 | // simulation) 21 | 22 | testcomp.setup_recording("kdr", Dt) 23 | run() 24 | testcomp.save_data("KDR", Dt) 25 | 26 | quit() 27 | 28 | 29 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_km.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("km", 1e-9) 17 | 18 | // (50 ms start positive current, 150 ms stop positive current, 200 19 | // ms start negative current, 300 ms stop negative current 350 ms stop 20 | // simulation) 21 | 22 | testcomp.setup_recording("km", Dt) 23 | run() 24 | testcomp.save_data("KM", Dt) 25 | 26 | quit() 27 | 28 | 29 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_nap.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("nap", 1e-9) 17 | 18 | // (50 ms start positive current, 150 ms stop positive current, 200 19 | // ms start negative current, 300 ms stop negative current 350 ms stop 20 | // simulation) 21 | 22 | testcomp.setup_recording("nap", Dt) 23 | run() 24 | testcomp.save_data("NaP", Dt) 25 | 26 | quit() 27 | 28 | 29 | -------------------------------------------------------------------------------- /docs/source/user/py/graphics/content_g.rst: -------------------------------------------------------------------------------- 1 | .. _graph-moogli: 2 | 3 | MOOGLI 4 | ====== 5 | 6 | Use Moogli for plotting 7 | ----------------------- 8 | 9 | .. automodule:: loadMorphology 10 | :members: 11 | :noindex: 12 | 13 | MatPlotLib 14 | ========== 15 | 16 | Displaying time-series plots 17 | ---------------------------- 18 | 19 | .. automodule:: crossComptNeuroMesh 20 | :members: 21 | :noindex: 22 | 23 | Animation of values along axis 24 | ------------------------------ 25 | 26 | .. automodule:: diffSpinyNeuron 27 | :members: 28 | :noindex: 29 | 30 | .. automodule:: reacDiffBranchingNeuron 31 | :members: 32 | :noindex: 33 | -------------------------------------------------------------------------------- /docs/source/user/py/references/DiagonalMsg.rst: -------------------------------------------------------------------------------- 1 | DiagonalMsg 2 | ----------- 3 | 4 | .. py:class:: DiagonalMsg 5 | 6 | 7 | .. py:method:: setStride 8 | 9 | (*destination message field*) Assigns field value. 10 | 11 | 12 | .. py:method:: getStride 13 | 14 | (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value. 15 | 16 | 17 | .. py:attribute:: stride 18 | 19 | int (*value field*) The stride is the increment to the src DataId that gives thedest DataId. It can be positive or negative, but bounds checkingtakes place and it does not wrap around. 20 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_napf.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("napf", 1e-9) 17 | 18 | // (50 ms start positive current, 150 ms stop positive current, 200 19 | // ms start negative current, 300 ms stop negative current 350 ms stop 20 | // simulation) 21 | 22 | testcomp.setup_recording("napf", Dt) 23 | run() 24 | testcomp.save_data("NaPF", Dt) 25 | 26 | quit() 27 | 28 | 29 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/TuftedIB.levels: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 2 4 | 4 2 5 | 5 2 6 | 6 2 7 | 7 2 8 | 8 2 9 | 9 2 10 | 10 2 11 | 11 2 12 | 12 2 13 | 13 3 14 | 14 3 15 | 15 3 16 | 16 3 17 | 17 3 18 | 18 3 19 | 19 3 20 | 20 3 21 | 21 3 22 | 22 3 23 | 23 3 24 | 24 4 25 | 25 4 26 | 26 4 27 | 27 4 28 | 28 4 29 | 29 4 30 | 30 4 31 | 31 4 32 | 32 4 33 | 33 4 34 | 34 4 35 | 35 5 36 | 36 6 37 | 37 7 38 | 38 8 39 | 39 9 40 | 40 10 41 | 41 11 42 | 42 12 43 | 43 13 44 | 44 14 45 | 45 15 46 | 46 16 47 | 47 17 48 | 48 18 49 | 49 18 50 | 50 18 51 | 51 18 52 | 52 18 53 | 53 18 54 | 54 18 55 | 55 18 56 | 56 0 57 | 57 0 58 | 58 0 59 | 59 0 60 | 60 0 61 | 61 0 62 | 63 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/TuftedRS.levels: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 2 4 | 4 2 5 | 5 2 6 | 6 2 7 | 7 2 8 | 8 2 9 | 9 2 10 | 10 2 11 | 11 2 12 | 12 2 13 | 13 3 14 | 14 3 15 | 15 3 16 | 16 3 17 | 17 3 18 | 18 3 19 | 19 3 20 | 20 3 21 | 21 3 22 | 22 3 23 | 23 3 24 | 24 4 25 | 25 4 26 | 26 4 27 | 27 4 28 | 28 4 29 | 29 4 30 | 30 4 31 | 31 4 32 | 32 4 33 | 33 4 34 | 34 4 35 | 35 5 36 | 36 6 37 | 37 7 38 | 38 8 39 | 39 9 40 | 40 10 41 | 41 11 42 | 42 12 43 | 43 13 44 | 44 14 45 | 45 15 46 | 46 16 47 | 47 17 48 | 48 18 49 | 49 18 50 | 50 18 51 | 51 18 52 | 52 18 53 | 53 18 54 | 54 18 55 | 55 18 56 | 56 0 57 | 57 0 58 | 58 0 59 | 59 0 60 | 60 0 61 | 61 0 62 | 63 | -------------------------------------------------------------------------------- /moose-examples/unsorted/test_function.py: -------------------------------------------------------------------------------- 1 | import moose 2 | 3 | a = moose.CubeMesh('/cube') 4 | a.volume = 1 5 | 6 | ca = moose.BufPool('/cube/ca') 7 | ca.concInit = 1.0 8 | 9 | f = moose.Function('/cube/ca/func') 10 | f.expr = 'sin(0.1*3.14*t) > 0.81 ? 25e-3 : 0' 11 | moose.connect(f, 'valueOut', ca, 'setConc') 12 | 13 | # create a table. 14 | tab = moose.Table2('/cube/ca/table') 15 | moose.connect( tab, 'requestOut', ca, 'getConc' ) 16 | 17 | # refine clock 18 | for i in range(10, 16): 19 | moose.setClock(i, 0.001) 20 | 21 | moose.reinit() 22 | moose.start(100) 23 | 24 | import pylab 25 | pylab.plot( tab.vector ) 26 | pylab.savefig('output.png') 27 | -------------------------------------------------------------------------------- /moose-examples/snippets/soma.p: -------------------------------------------------------------------------------- 1 | // genesis 2 | // cell parameter file for multiscale modeling snippet. 3 | *cartesian 4 | *relative 5 | 6 | *set_global RM 1.0 //ohm*m^2 7 | *set_global RA 1.0 //ohm*m 8 | *set_global CM 0.03 //F/m^2 9 | *set_global EREST_ACT -0.06 // volts 10 | 11 | // The format for each compartment parameter line is : 12 | // name parent x y z d ch dens ... 13 | // For channels, "dens" = maximum conductance per unit area of compartment 14 | 15 | // soma none 0 12 0 12 Ca_conc -17.402e12 Na 300 Ca 40 K_DR 250 K_A 50 K_C 250 16 | soma none 0 12 0 12 Ca_conc -1e13 Na 300 Ca 50 K_DR 250 K_A 200 17 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_cat_a.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("cat_a", 1e-9) 17 | 18 | // (50 ms start positive current, 150 ms stop positive current, 200 19 | // ms start negative current, 300 ms stop negative current 350 ms stop 20 | // simulation) 21 | 22 | testcomp.setup_recording("cat_a", Dt) 23 | run() 24 | testcomp.save_data("CaT_A", Dt) 25 | 26 | quit() 27 | 28 | 29 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_ka_ib.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("ka_ib", 1e-9) 17 | 18 | // (50 ms start positive current, 150 ms stop positive current, 200 19 | // ms start negative current, 300 ms stop negative current 350 ms stop 20 | // simulation) 21 | 22 | testcomp.setup_recording("ka_ib", Dt) 23 | run() 24 | testcomp.save_data("KA_IB", Dt) 25 | 26 | quit() 27 | 28 | 29 | -------------------------------------------------------------------------------- /moose-core/tests/issues/issue_69.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # Github issue #69, Also BhallaLab/moose-gui#3. 3 | 4 | import moose 5 | print( '[INFO] Importing moose from %s' % moose.__file__ ) 6 | print( '[INFO] Version : %s' % moose.__version__ ) 7 | moose.loadModel('../data/acc27.g','/acc27_1',"gsl") 8 | compts = moose.wildcardFind('/acc27_1/##[ISA=ChemCompt]') 9 | for compt in compts: 10 | if moose.exists(compt.path+'/stoich'): 11 | st = moose.element(compt.path+'/stoich') 12 | #print " stoich ksolve ",st.ksolve.path 13 | if moose.exists((st.ksolve).path): 14 | moose.delete(st.ksolve) 15 | moose.delete(st) 16 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_kdr_fs.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("kdr_fs", 1e-9) 17 | 18 | // (50 ms start positive current, 150 ms stop positive current, 200 19 | // ms start negative current, 300 ms stop negative current 350 ms stop 20 | // simulation) 21 | 22 | testcomp.setup_recording("kdr_fs", Dt) 23 | run() 24 | testcomp.save_data("KDR_FS", Dt) 25 | 26 | quit() 27 | 28 | 29 | -------------------------------------------------------------------------------- /moose-examples/symcomp/symcomp.p: -------------------------------------------------------------------------------- 1 | *cartesian 2 | *relative 3 | *symmetric 4 | *set_global EREST_ACT -0.06 5 | *set_compt_param ELEAK -0.06 6 | *set_compt_param RM 2.513274122871835 7 | *set_compt_param CM 0.003978873577297383 8 | *set_compt_param RA 7.853981633974484 9 | soma none 40 0 0 20 10 | *set_compt_param ELEAK -0.06 11 | *set_compt_param RM 0.15707963267948968 12 | *set_compt_param CM 0.06366197723675814 13 | *set_compt_param RA 15.707963267948967 14 | d1 soma 50 0 0 10 15 | *set_compt_param ELEAK -0.06 16 | *set_compt_param RM 0.025132741228718343 17 | *set_compt_param CM 0.3978873577297384 18 | *set_compt_param RA 12.56637061435917 19 | d2 soma 20 0 0 4 20 | 21 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_napf_tcr.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("napf_tcr", 1e-9) 17 | 18 | // (50 ms start positive current, 150 ms stop positive current, 200 19 | // ms start negative current, 300 ms stop negative current 350 ms stop 20 | // simulation) 21 | 22 | testcomp.setup_recording("napf_tcr", Dt) 23 | run() 24 | testcomp.save_data("NaPF_TCR", Dt) 25 | 26 | quit() 27 | 28 | 29 | -------------------------------------------------------------------------------- /moose-examples/tutorials/Rdesigneur/ex9.0_load_neuronal_morphology_file.py: -------------------------------------------------------------------------------- 1 | import sys 2 | import moose 3 | import rdesigneur as rd 4 | 5 | if len( sys.argv ) > 1: 6 | fname = sys.argv[1] 7 | else: 8 | fname = './cells/h10.CNG.swc' 9 | rdes = rd.rdesigneur( 10 | cellProto = [[fname, 'elec']], 11 | stimList = [['soma', '1', '.', 'inject', 't * 25e-9' ]], 12 | plotList = [['#', '1', '.', 'Vm', 'Membrane potential'], 13 | ['#', '1', 'Ca_conc', 'Ca', 'Ca conc (uM)']], 14 | moogList = [['#', '1', '.', 'Vm', 'Soma potential']] 15 | ) 16 | 17 | rdes.buildModel() 18 | 19 | moose.reinit() 20 | rdes.displayMoogli( 0.001, 0.1, rotation = 0.02 ) 21 | -------------------------------------------------------------------------------- /.travis_prepare_linux.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | sudo apt-get update -qq 3 | sudo apt-get -y install libxml2-dev libbz2-dev wget 4 | sudo apt-get -y install libhdf5-serial-dev 5 | sudo apt-get -y install python-numpy python-setuptools python-networkx python-pip 6 | sudo apt-get -y install cmake cdbs 7 | sudo apt-get -y install libgsl0-dev 8 | sudo apt-get -y install python-suds python-matplotlib 9 | sudo apt-get -y install python-qt4-dev python-qt4-gl python-sip-dev libqt4-dev libopenscenegraph-dev 10 | sudo apt-get -y install doxygen python-sphinx python-lxml 11 | sudo apt-get -y install git-buildpackage fakeroot 12 | sudo apt-get -y install -f 13 | sudo ldconfig /usr/lib64 14 | -------------------------------------------------------------------------------- /moose-core/external/boost-numeric-bindings/boost/numeric/bindings/traits/transpose.hpp: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright Kresimir Fresl, Toon Knapen, and Karl Meerbergen 2002, 2003 3 | // 4 | // Distributed under the Boost Software License, Version 1.0. 5 | // (See accompanying file LICENSE_1_0.txt or copy at 6 | // http://www.boost.org/LICENSE_1_0.txt) 7 | // 8 | 9 | #ifndef BOOST_BINDINGS_TRANSPOSE_HPP 10 | #define BOOST_BINDINGS_TRANSPOSE_HPP 11 | 12 | namespace boost { namespace numeric { namespace bindings { namespace traits { 13 | 14 | const char NO_TRANSPOSE = 'N' ; 15 | const char TRANSPOSE = 'T' ; 16 | const char CONJUGATE = 'C' ; 17 | 18 | }}}} 19 | 20 | #endif 21 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_k2.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | secondorder=0 5 | celsius=30 6 | dt = 1e-3 7 | v_init = -65.0 8 | Dt = 1e-2 9 | tstop = 350 // ms 10 | 11 | load_file("testutils.hoc") 12 | 13 | objref testcomp, vvec, gvec, tvec, vfile, gfile 14 | 15 | testcomp = new singlecomp() 16 | 17 | testcomp.setup_channel("k2", 1e-9) 18 | 19 | // (50 ms start positive current, 150 ms stop positive current, 200 20 | // ms start negative current, 300 ms stop negative current 350 ms stop 21 | // simulation) 22 | 23 | testcomp.setup_recording("k2", Dt) 24 | run() 25 | testcomp.save_data("K2", Dt) 26 | 27 | quit() 28 | 29 | 30 | -------------------------------------------------------------------------------- /moose-examples/squid/README.txt: -------------------------------------------------------------------------------- 1 | This is the port of Hodgkin-Huxley Squid Giant Axon demo from 2 | GENESIS. Run `python squid_demo.py` to start the GUI. Open help.org in 3 | a text editor or help.html in a web-browser (or click `Help` button in 4 | the GUI) to read the tutorial. 5 | 6 | The biophysical model is in `squid.py`. The electronics setup is in 7 | `electronics.py`. The combination of squid axon model and the 8 | electronics is in squid_setup.py. All these can be run without any GUI 9 | dependency. To run squid_demo.py you need PyQt and matplotlib with Qt 10 | backend installed. 11 | 12 | Author: Subhasis Ray 13 | Place: NCBS, Bangalore, INDIA 14 | Date: 21 September 2012 15 | -------------------------------------------------------------------------------- /moose-core/builtins/Group.h: -------------------------------------------------------------------------------- 1 | /********************************************************************** 2 | ** This program is part of 'MOOSE', the 3 | ** Messaging Object Oriented Simulation Environment. 4 | ** Copyright (C) 2003-2010 Upinder S. Bhalla. and NCBS 5 | ** It is made available under the terms of the 6 | ** GNU Lesser General Public License version 2.1 7 | ** See the file COPYING.LIB for the full notice. 8 | **********************************************************************/ 9 | #ifndef _GROUP_H 10 | #define _GROUP_H 11 | 12 | class Group 13 | { 14 | public: 15 | Group(); 16 | static const Cinfo* initCinfo(); 17 | private: 18 | }; 19 | 20 | #endif // _GROUP_H 21 | -------------------------------------------------------------------------------- /moose-core/tests/python/test_docs.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | """test_docs.py: 3 | 4 | Test if moose.doc is working. 5 | 6 | """ 7 | 8 | __author__ = "Dilawar Singh" 9 | __copyright__ = "Copyright 2017-, Dilawar Singh" 10 | __version__ = "1.0.0" 11 | __maintainer__ = "Dilawar Singh" 12 | __email__ = "dilawars@ncbs.res.in" 13 | __status__ = "Development" 14 | 15 | import sys 16 | import os 17 | import moose 18 | print( '[INFO] Using moose from %s' % moose.__file__ ) 19 | print( '[INFO] Version : %s' % moose.version( ) ) 20 | 21 | def main( ): 22 | moose.doc( 'Compartment' ) 23 | 24 | if __name__ == '__main__': 25 | main() 26 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = python -msphinx 7 | SPHINXPROJ = MOOSE 8 | SOURCEDIR = source 9 | BUILDDIR = build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) -------------------------------------------------------------------------------- /docs/source/user/py/references/Variable.rst: -------------------------------------------------------------------------------- 1 | Variable 2 | -------- 3 | 4 | .. py:class:: Variable 5 | 6 | Variable for storing double values. This is used in Function class. 7 | 8 | .. py:method:: setValue 9 | 10 | (*destination message field*) Assigns field value. 11 | 12 | 13 | .. py:method:: getValue 14 | 15 | (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value. 16 | 17 | 18 | .. py:method:: input 19 | 20 | (*destination message field*) Handles incoming variable value. 21 | 22 | 23 | .. py:attribute:: value 24 | 25 | double (*value field*) Variable value 26 | -------------------------------------------------------------------------------- /docs/source/user/py/quickstart/qs_inter.rst: -------------------------------------------------------------------------------- 1 | ********************* 2 | Interactive Tutorials 3 | ********************* 4 | 5 | Some of the pages in the documentation, such as the python scripting page and teaching tutorials are available in interactive form. 6 | 7 | These interactive tutorials serve as fully executable python environments that can run moose. Therefore, it is a great place to both learn about and play around with MOOSE. 8 | 9 | All the currently available interactive tutorials are available by clicking the link below: 10 | 11 | .. image:: https://mybinder.org/badge.svg 12 | :target: https://mybinder.org/v2/gh/BhallaLab/moose-binder/master?filepath=home%2Fmooser%2FIndex.ipynb 13 | -------------------------------------------------------------------------------- /moose-core/tests/python/Rallpacks/moose_vs_neuron/rallpack3/neuron.log: -------------------------------------------------------------------------------- 1 | 2 | 3 | 1000 4 | 5 | 6 | 4.0739159584 7 | 8 | 9 | 10 | 11 | 1000 12 | 13 | 14 | 0.0450360774994 15 | 16 | 17 | 18 | 19 | 1000 20 | 21 | 22 | 3.56457614899 23 | 24 | 25 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_naf2_nRT.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("naf2", 1e-9) 17 | // here no Na_shift is applied 18 | 19 | // (50 ms start positive current, 150 ms stop positive current, 200 20 | // ms start negative current, 300 ms stop negative current 350 ms stop 21 | // simulation) 22 | 23 | testcomp.setup_recording("naf2", Dt) 24 | run() 25 | testcomp.save_data("NaF2_nRT", Dt) 26 | 27 | quit() 28 | 29 | 30 | -------------------------------------------------------------------------------- /docs/source/user/py/references/Cinfo.rst: -------------------------------------------------------------------------------- 1 | Cinfo 2 | ----- 3 | 4 | 5 | 6 | .. py:class:: Cinfo 7 | 8 | Class information object. 9 | 10 | .. py:method:: getDocs 11 | 12 | (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value. 13 | 14 | 15 | .. py:method:: getBaseClass 16 | 17 | (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value. 18 | 19 | 20 | .. py:attribute:: docs 21 | 22 | string (*value field*) Documentation 23 | 24 | 25 | .. py:attribute:: baseClass 26 | 27 | string (*value field*) Name of base class 28 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_ar.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("ar", 1e-9) 17 | testcomp.soma { 18 | fastNa_shift_ar = -3.5 19 | } 20 | 21 | // (50 ms start positive current, 150 ms stop positive current, 200 22 | // ms start negative current, 300 ms stop negative current 350 ms stop 23 | // simulation) 24 | 25 | testcomp.setup_recording("ar", Dt) 26 | run() 27 | testcomp.save_data("AR", Dt) 28 | 29 | quit() 30 | 31 | 32 | -------------------------------------------------------------------------------- /moose-core/shell/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake) 3 | 4 | if(LIBSBML_FOUND) 5 | add_definitions(-DUSE_SBML) 6 | endif() 7 | 8 | add_library(shell 9 | Shell.cpp 10 | ShellCopy.cpp 11 | ShellThreads.cpp 12 | LoadModels.cpp 13 | SaveModels.cpp 14 | Neutral.cpp 15 | Wildcard.cpp 16 | testShell.cpp 17 | ) 18 | 19 | ## version is set by top-level script ../CMakeLists.txt . 20 | #if(NOT MOOSE_VERSION) 21 | # set(MOOSE_VERSION "undefined") 22 | #endif() 23 | # 24 | #set_target_properties(shell 25 | # PROPERTIES COMPILE_FLAGS ${COMPILE_FLAGS} -DMOOSE_VERSION=\"${MOOSE_VERSION}\" 26 | # ) 27 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_naf.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("naf", 1e-9) 17 | testcomp.soma { 18 | fastNa_shift_naf = -3.5 19 | } 20 | 21 | // (50 ms start positive current, 150 ms stop positive current, 200 22 | // ms start negative current, 300 ms stop negative current 350 ms stop 23 | // simulation) 24 | 25 | testcomp.setup_recording("naf", Dt) 26 | run() 27 | testcomp.save_data("NaF", Dt) 28 | 29 | quit() 30 | 31 | 32 | -------------------------------------------------------------------------------- /docs/source/user/py/quickstart/demos.rst: -------------------------------------------------------------------------------- 1 | ************************************** 2 | Demonstration of basic functionalities 3 | ************************************** 4 | 5 | .. _quickstart-load-run: 6 | 7 | Load and Run a Model 8 | -------------------- 9 | 10 | .. automodule:: helloMoose 11 | :members: 12 | 13 | .. _quickstart-timing: 14 | 15 | Start, Stop, and setting clocks 16 | ------------------------------- 17 | 18 | .. automodule:: startstop 19 | :members: 20 | 21 | .. automodule:: stimtable 22 | :members: 23 | 24 | Run Python from MOOSE 25 | --------------------- 26 | 27 | .. automodule:: pyrun 28 | :members: 29 | 30 | .. automodule: pyrun1 31 | .. :members: 32 | 33 | .. _quickstart-classes: 34 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_naf2.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("naf2", 1e-9) 17 | testcomp.soma { 18 | fastNa_shift_naf2 = -2.5 19 | } 20 | 21 | // (50 ms start positive current, 150 ms stop positive current, 200 22 | // ms start negative current, 300 ms stop negative current 350 ms stop 23 | // simulation) 24 | 25 | testcomp.setup_recording("naf2", Dt) 26 | run() 27 | testcomp.save_data("NaF2", Dt) 28 | 29 | quit() 30 | 31 | 32 | -------------------------------------------------------------------------------- /moose-core/external/boost-numeric-bindings/boost/numeric/bindings/traits/traits.hpp: -------------------------------------------------------------------------------- 1 | /* 2 | * 3 | * Copyright (c) 2002, 2003 Kresimir Fresl, Toon Knapen and Karl Meerbergen 4 | * 5 | * Distributed under the Boost Software License, Version 1.0. 6 | * (See accompanying file LICENSE_1_0.txt or copy at 7 | * http://www.boost.org/LICENSE_1_0.txt) 8 | * 9 | * KF acknowledges the support of the Faculty of Civil Engineering, 10 | * University of Zagreb, Croatia. 11 | * 12 | */ 13 | 14 | #ifndef BOOST_NUMERIC_BINDINGS_TRAITS_H 15 | #define BOOST_NUMERIC_BINDINGS_TRAITS_H 16 | 17 | #include 18 | #include 19 | 20 | #endif 21 | -------------------------------------------------------------------------------- /debian/changelog: -------------------------------------------------------------------------------- 1 | moose (3.2.0.3ubuntu1) experimental; urgency=medium 2 | 3 | * Version bumped. 4 | 5 | -- Dilawar Singh Tue, 11 Sep 2018 12:26:15 +0530 6 | 7 | moose (3.1.3ubuntu1) experimental; urgency=medium 8 | 9 | * Version bumped. 10 | 11 | -- Dilawar Singh Thu, 01 Feb 2018 12:26:15 +0530 12 | 13 | moose (3.1.2) unstable; urgency=medium 14 | 15 | * Chamcham release (3.1.x) series. 16 | 17 | -- Dilawar Singh Mon, 08 May 2017 13:43:42 +0530 18 | 19 | moose (3.1.2) unstable; urgency=low 20 | 21 | * Bugfixes over 3.1.1 22 | * Enhanced rdesigneur interface. 23 | 24 | -- Dilawar Sat, 22 Apr 2017 13:41:58 +0530 25 | -------------------------------------------------------------------------------- /docs/source/user/py/tutorials/index_tut.rst: -------------------------------------------------------------------------------- 1 | Teaching Tutorials 2 | ================== 3 | 4 | To see interactive and executable versions of ChemicalBistables and ChemicalOscillators, please click the following link: 5 | 6 | .. image:: https://mybinder.org/badge.svg 7 | :target: https://mybinder.org/v2/gh/BhallaLab/moose-binder/master?filepath=home%2Fmooser%2FIndex.ipynb 8 | 9 | These tutorials use the moose simulation environment to illustrate various scientific concepts, phenomena, and research. As such the materials in this section are useful for both teaching and learning about these topics. 10 | 11 | .. toctree:: 12 | :maxdepth: 2 13 | 14 | ChemicalBistables 15 | ChemicalOscillators 16 | Squid 17 | 18 | -------------------------------------------------------------------------------- /moose-core/external/boost-numeric-bindings/boost/numeric/bindings/atlas/cblas.hpp: -------------------------------------------------------------------------------- 1 | /* 2 | * 3 | * Copyright (c) Kresimir Fresl 2002 4 | * 5 | * Distributed under the Boost Software License, Version 1.0. 6 | * (See accompanying file LICENSE_1_0.txt or copy at 7 | * http://www.boost.org/LICENSE_1_0.txt) 8 | * 9 | * Author acknowledges the support of the Faculty of Civil Engineering, 10 | * University of Zagreb, Croatia. 11 | * 12 | */ 13 | 14 | #ifndef BOOST_NUMERIC_BINDINGS_CBLAS_HPP 15 | #define BOOST_NUMERIC_BINDINGS_CBLAS_HPP 16 | 17 | #include 18 | #include 19 | #include 20 | 21 | #endif 22 | -------------------------------------------------------------------------------- /moose-core/python/moose/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | from __future__ import absolute_import, division, print_function 3 | 4 | # Use this format in all logger inside logger. Define it before any moose 5 | # related module is imported. 6 | LOGGING_FORMAT = '%(asctime)s %(message)s' 7 | 8 | # Bring everything from c++ module to global namespace. Not everything is 9 | # imported by the pervios import statement. 10 | from moose._moose import * 11 | 12 | # Bring everything from moose.py to global namespace. 13 | # IMP: It will overwrite any c++ function with the same name. 14 | from moose.moose import * 15 | from moose.server import * 16 | 17 | # create a shorthand for version() call here. 18 | __version__ = version() 19 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_naf_tcr.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("naf_tcr", 1e-9) 17 | testcomp.soma { 18 | fastNa_shift_naf_tcr = 7 19 | } 20 | 21 | // (50 ms start positive current, 150 ms stop positive current, 200 22 | // ms start negative current, 300 ms stop negative current 350 ms stop 23 | // simulation) 24 | 25 | testcomp.setup_recording("naf_tcr", Dt) 26 | run() 27 | testcomp.save_data("NaF_TCR", Dt) 28 | 29 | quit() 30 | 31 | 32 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | sudo: required 2 | language: cpp 3 | 4 | os: 5 | - linux 6 | - osx 7 | 8 | branches: 9 | only: 10 | - master 11 | - chamcham 12 | - chhennapoda 13 | 14 | notifications: 15 | email: 16 | recipients: 17 | - dilawar.s.rajput@gmail.com 18 | - bhalla@ncbs.res.in 19 | - hrani@ncbs.res.in 20 | on_success: change 21 | on_failure: always 22 | 23 | before_script: 24 | - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.travis_prepare_linux.sh; fi 25 | 26 | script: 27 | - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then ./.travis_build_linux.sh; fi 28 | - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then ./.travis_build_osx.sh; fi 29 | -------------------------------------------------------------------------------- /docs/source/user/py/references/MarkovSolver.rst: -------------------------------------------------------------------------------- 1 | MarkovSolver 2 | ------------ 3 | 4 | .. py:class:: MarkovSolver 5 | 6 | 7 | .. py:attribute:: proc 8 | 9 | void (*shared message field*) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo. 10 | 11 | 12 | .. py:method:: process 13 | 14 | (*destination message field*) Handles process call 15 | 16 | 17 | .. py:method:: reinit 18 | 19 | (*destination message field*) Handles reinit call 20 | -------------------------------------------------------------------------------- /moose-core/examples/Ex.h: -------------------------------------------------------------------------------- 1 | #ifndef _EX_H 2 | #define _EX_H 3 | 4 | class Ex 5 | { 6 | public: 7 | Ex(); 8 | ~Ex(); 9 | static const Cinfo* initCinfo(); 10 | 11 | void process(const Eref& e, ProcPtr p); 12 | void reinit(const Eref& e, ProcPtr p); 13 | 14 | double getX() const; 15 | int getN() const; 16 | void setX(double x); 17 | void setN(int n); 18 | void setNX(int n, double x); 19 | double getVal(unsigned int index) const; 20 | void setVal(unsigned int index, double val); 21 | void getVal(unsigned int index, double val); 22 | 23 | void handleX(double x); 24 | void handleN(int n); 25 | 26 | private: 27 | double x_; 28 | int n_; 29 | vector< double > values_; 30 | }; 31 | 32 | #endif 33 | -------------------------------------------------------------------------------- /moose-examples/neuroml/PurkinjeCellPassivePulseInput/README: -------------------------------------------------------------------------------- 1 | This is the directory for the NeuroML files generated by neuroConstruct 1.5.3 (neuroConstruct.org) for Purkinje cell model. 2 | These files were exported from neuroConstruct as Level 3 NeuroML v 1.x files (not a single NeuroML Level 3 file). 3 | 4 | Fire up moose GUI. File->Load Model or Ctrl+L. Navigate to this directory. 5 | Open the PurkinjePassive.net.xml file. 6 | Presently this cell has only passive properties, no active channels, 7 | as all the channels exported by neuroConstruct were in old deprecated ChannelML format which current importer does not support. 8 | You can set the inject field in the soma or any other compartment and see how the voltage passive decays. 9 | 10 | -------------------------------------------------------------------------------- /moose-examples/parallelSolver/README: -------------------------------------------------------------------------------- 1 | Parallel solvers are implemented for Ksolve, Dsolve and Gsolve. 2 | 3 | Instructions to run the solvers in parallel. 4 | 5 | 1) Clone the repository from github/BhallaLab/moose-core/tree/multithreaded 6 | i.e., the multithreaded branch of the moose-core. 7 | 8 | 2) Build the code, compile and run it. 9 | 10 | 3) Set the environment variable NUM_THREADS to the number of threads with which you want to execute your script. 11 | 12 | 4) The environment variable has to be set to make use of the parallelization. It runs with 1 thread by default(sequential). 13 | 14 | 3) Run your python script regularly. The framwork will pick up the number of threads set by you and parallelize the solvers using them. 15 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/nrn/test_napf_ss.hoc: -------------------------------------------------------------------------------- 1 | load_file("nrngui.hoc") 2 | // PI=3.141592 3 | FARADAY=96485 4 | 5 | celsius=30 6 | v_init = -65.0 7 | Dt = 1e-2 8 | tstop = 350 // ms 9 | 10 | load_file("testutils.hoc") 11 | 12 | objref testcomp, vvec, gvec, tvec, vfile, gfile 13 | 14 | testcomp = new singlecomp() 15 | 16 | testcomp.setup_channel("napf_spinstell", 1e-9) 17 | testcomp.soma { 18 | fastNa_shift_napf_spinstell=-2.5 19 | } 20 | 21 | // (50 ms start positive current, 150 ms stop positive current, 200 22 | // ms start negative current, 300 ms stop negative current 350 ms stop 23 | // simulation) 24 | 25 | testcomp.setup_recording("napf_spinstell", Dt) 26 | run() 27 | testcomp.save_data("NaPF_SS", Dt) 28 | 29 | quit() 30 | 31 | 32 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/benchmark.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | if [[ $# < 3 ]]; then 3 | echo "Usage: $0 scriptpath loopcount outfile" 4 | echo "Run script specified by `scriptpath` for `loopcount` repeats and time it. The output is written in " 5 | exit 1 6 | fi 7 | scriptfile=$1 8 | loopcount=$2 9 | outfile=$3 10 | 11 | echo "Benchmarking Python script: $1 with $2 repeats" 12 | echo -e "Real\tUser\tSystem\tMem(K)" > "$outfile" 13 | for ((ii=1; ii <= loopcount; ++ii)); do 14 | /usr/bin/time -a -o "$outfile" -f "%E\t%U\t%S\t%K" python "$scriptfile" 15 | done 16 | # Command to extract the timings from the log files: 17 | # grep 'Simulation time with solver' /data/`date '%Y_%m_%d'`/*.log | sed 's/^.*Simulation time with solver [a-z:]+//' 18 | -------------------------------------------------------------------------------- /moose-gui/icons/clone.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 6 | 8 | 9 | -------------------------------------------------------------------------------- /packaging_scripts/HOWTO_MAC.md: -------------------------------------------------------------------------------- 1 | This document describes how to create DMG package on MAC OSX. 2 | 3 | 1. Run `./build_dmg_image_using_brew.sh` 4 | 5 | - This script create an empty dmg file. 6 | - Mount it on /Volume/Moose_3.0.2 7 | - Install brew in it with prefix /Volumes/Moose_3.0.2 and `brew install moose` 8 | with given prefix. 9 | - It also adds an `moosegui` script which launches gui and also setup PYTHONPATH 10 | in ~/.bash_profile. 11 | 12 | 2. Run `./release_dmg_file.sh` 13 | 14 | - Copy the dmg created in step 1 and mount it. 15 | - Remove unneccessay files `brew uninstall cmake gcc`. This saves us approx 400 16 | MB. 17 | - Create another dmg file from folder and compress it. 18 | - Compress this dmg file and test it on some MAC. 19 | -------------------------------------------------------------------------------- /docs/source/user/py/references/index_ref.rst: -------------------------------------------------------------------------------- 1 | References 2 | ========== 3 | 4 | How to use the documentation 5 | ---------------------------- 6 | 7 | MOOSE documentation is split into Python documentation and builtin 8 | documentation. The functions and classes that are only part of the 9 | Python interface can be viewed via Python's builtin ``help`` 10 | function:: 11 | 12 | >>> help(moose.connect) 13 | 14 | The documentation built into main C++ code of MOOSE can be accessed 15 | via the module function ``doc``:: 16 | 17 | >>> moose.doc('Neutral') 18 | 19 | To get documentation about a particular field:: 20 | 21 | >>> moose.doc('Neutral.childMsg') 22 | 23 | .. toctree:: 24 | :maxdepth: 2 25 | 26 | moose_functions 27 | moose_classes 28 | -------------------------------------------------------------------------------- /docs/user/py/builtins_classes/index.rst: -------------------------------------------------------------------------------- 1 | .. MOOSE documentation master file, created by 2 | sphinx-quickstart on Tue Jul 1 19:05:47 2014. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | the Multiscale Object-Oriented Simulation Environment 7 | ===================================================== 8 | Automatically generated documentation for MOOSE built-in functions and MOOSE classes, as accessed through Python. 9 | 10 | Contents: 11 | 12 | .. toctree:: 13 | :maxdepth: 2 14 | :numbered: 15 | 16 | moose_builtins 17 | moose_classes 18 | 19 | Indices and tables 20 | ================== 21 | 22 | * :ref:`genindex` 23 | * :ref:`modindex` 24 | * :ref:`search` 25 | 26 | -------------------------------------------------------------------------------- /moose-core/basecode/EpFunc.cpp: -------------------------------------------------------------------------------- 1 | /********************************************************************** 2 | ** This program is part of 'MOOSE', the 3 | ** Messaging Object Oriented Simulation Environment. 4 | ** Copyright (C) 2003-2013 Upinder S. Bhalla. and NCBS 5 | ** It is made available under the terms of the 6 | ** GNU Lesser General Public License version 2.1 7 | ** See the file COPYING.LIB for the full notice. 8 | **********************************************************************/ 9 | 10 | #include "header.h" 11 | #include "../shell/Shell.h" 12 | 13 | template<> Neutral* getEpFuncData< Neutral >( const Eref& e ) 14 | { 15 | static Neutral dummy; 16 | return &dummy; 17 | } 18 | ////////////////////////////////////////////////////////////////// 19 | -------------------------------------------------------------------------------- /moose-core/examples/Example.h: -------------------------------------------------------------------------------- 1 | #ifndef EXAMPLE_H 2 | #endif /* end of include guard: EXAMPLE_H */ 3 | class Example { 4 | 5 | private: 6 | double x_; 7 | double y_; 8 | double output_; 9 | 10 | public: 11 | 12 | Example(); 13 | 14 | double getX() const; 15 | void setX( double x ); 16 | double getY() const; 17 | void setY( double y ); 18 | 19 | void process( const Eref& e, ProcPtr p ); 20 | void reinit( const Eref& e, ProcPtr p ); 21 | 22 | void handleX(double arg); 23 | void handleY(double arg); 24 | 25 | vector< Id > getNeighbors( const Eref& e, string field ) const; 26 | 27 | static const Cinfo* initCinfo(); 28 | 29 | }; 30 | 31 | #define EXAMPLE_H 32 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/SupPyrFRB.levels: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 2 4 | 4 2 5 | 5 2 6 | 6 2 7 | 7 2 8 | 8 2 9 | 9 2 10 | 10 2 11 | 11 2 12 | 12 2 13 | 13 2 14 | 14 3 15 | 15 3 16 | 16 3 17 | 17 3 18 | 18 3 19 | 19 3 20 | 20 3 21 | 21 3 22 | 22 3 23 | 23 3 24 | 24 3 25 | 25 3 26 | 26 4 27 | 27 4 28 | 28 4 29 | 29 4 30 | 30 4 31 | 31 4 32 | 32 4 33 | 33 4 34 | 34 4 35 | 35 4 36 | 36 4 37 | 37 4 38 | 38 5 39 | 39 6 40 | 40 7 41 | 41 8 42 | 42 8 43 | 43 9 44 | 44 9 45 | 45 10 46 | 46 10 47 | 47 10 48 | 48 10 49 | 49 10 50 | 50 10 51 | 51 10 52 | 52 10 53 | 53 11 54 | 54 11 55 | 55 11 56 | 56 11 57 | 57 11 58 | 58 11 59 | 59 11 60 | 60 11 61 | 61 12 62 | 62 12 63 | 63 12 64 | 64 12 65 | 65 12 66 | 66 12 67 | 67 12 68 | 68 12 69 | 69 0 70 | 70 0 71 | 71 0 72 | 72 0 73 | 73 0 74 | 74 0 75 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/SupPyrRS.levels: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 2 4 | 4 2 5 | 5 2 6 | 6 2 7 | 7 2 8 | 8 2 9 | 9 2 10 | 10 2 11 | 11 2 12 | 12 2 13 | 13 2 14 | 14 3 15 | 15 3 16 | 16 3 17 | 17 3 18 | 18 3 19 | 19 3 20 | 20 3 21 | 21 3 22 | 22 3 23 | 23 3 24 | 24 3 25 | 25 3 26 | 26 4 27 | 27 4 28 | 28 4 29 | 29 4 30 | 30 4 31 | 31 4 32 | 32 4 33 | 33 4 34 | 34 4 35 | 35 4 36 | 36 4 37 | 37 4 38 | 38 5 39 | 39 6 40 | 40 7 41 | 41 8 42 | 42 8 43 | 43 9 44 | 44 9 45 | 45 10 46 | 46 10 47 | 47 10 48 | 48 10 49 | 49 10 50 | 50 10 51 | 51 10 52 | 52 10 53 | 53 11 54 | 54 11 55 | 55 11 56 | 56 11 57 | 57 11 58 | 58 11 59 | 59 11 60 | 60 11 61 | 61 12 62 | 62 12 63 | 63 12 64 | 64 12 65 | 65 12 66 | 66 12 67 | 67 12 68 | 68 12 69 | 69 0 70 | 70 0 71 | 71 0 72 | 72 0 73 | 73 0 74 | 74 0 75 | -------------------------------------------------------------------------------- /_travis/prepare_osx.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash - 2 | #=============================================================================== 3 | # 4 | # FILE: prepare_osx.sh 5 | # 6 | # USAGE: ./prepare_osx.sh 7 | # 8 | # DESCRIPTION: 9 | # 10 | # OPTIONS: --- 11 | # REQUIREMENTS: --- 12 | # BUGS: --- 13 | # NOTES: --- 14 | # AUTHOR: Dilawar Singh (), dilawars@ncbs.res.in 15 | # ORGANIZATION: NCBS Bangalore 16 | # CREATED: Wednesday 28 June 2017 10:23:28 IST 17 | # REVISION: --- 18 | #=============================================================================== 19 | 20 | set -o nounset # Treat unset variables as an error 21 | echo "Nothing to do here. The moose.rb formula will install all dependecnies" 22 | brew update 23 | -------------------------------------------------------------------------------- /cmake/build_moose-core.sh.in: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | set -x 4 | set -e 5 | 6 | # NOTICE: This file is parsed by cmake to create a shell script. Not all syntax 7 | # will play well with cmake. CMAKE replaces @FOO@ and ${FOO} with cmake variable 8 | # values. 9 | if [ -z $MAKEOPTS ]; then 10 | export MAKEOPTS="-j`nproc`" 11 | fi 12 | 13 | echo "Building pymoose and creating bdist." 14 | export GSL_ROOT_DIR=@GSL_ROOT_DIR@ 15 | export HDF5_ROOT=@HDF5_ROOT@ 16 | cd @PYMOOSE_BUILD_DIR@ 17 | cmake -DCMAKE_INSTALL_PREFIX=@PYMOOSE_INSTALL_DIR@ \ 18 | -DCMAKE_BUILD_TYPE=Release \ 19 | -DWITH_BOOST=@WITH_BOOST@ \ 20 | -DPYTHON_EXECUTABLE=@PYTHON_EXECUTABLE@ \ 21 | -DVERSION_MOOSE=@VERSION_MOOSE@ \ 22 | @CMAKE_PYMOOSE_ARGS@ \ 23 | @PYMOOSE_SOURCE_DIR@ 24 | make $MAKEOPTS 25 | make bdist 26 | -------------------------------------------------------------------------------- /moose-examples/neuroml/OlfactoryBulbPassive/README: -------------------------------------------------------------------------------- 1 | This is the directory for the NeuroML files used by Aditya Gilra in his rodent olfactory bulb model. 2 | 3 | Fire up moose GUI. File->Load Model or Ctrl+L. Navigate to this directory. Load any of these models: 4 | OBpassive_numgloms3_seed750.0.xml : 3 glomeruli (2 mitral cells in each) with lots of granule and PG cells. 5 | OBpassive_slice_numgloms2_seed100.0_fewcells.xml : 2 glomeruli with very few granule and PG cells (good for testing). 6 | OBpassive_slice_numgloms2_seed100.0.xml : 2 glomeruli with granules and PGs present only in a slice of 300 microns thickness. 7 | 8 | Presently all cells have only passive properties, no active channels, and no synapses and connections, 9 | as not all channels have been converted to ChannelML, and it saves loading time. 10 | -------------------------------------------------------------------------------- /moose-core/python/rdesigneur/chans/Glu.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 8 | 9 | Glutamate receptor synchan, 2 ms tau. 10 | 11 | 12 | 13 | Simple double exponential waveform glu synapse 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /moose-core/python/rdesigneur/chans/NMDA.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 8 | 9 | NMDA receptor synchan, 20 ms tau. 10 | 11 | 12 | 13 | Simple double exponential waveform NMDA synapse 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /moose-core/utility/simple_test.hpp: -------------------------------------------------------------------------------- 1 | /* 2 | * ============================================================================== 3 | * 4 | * Filename: simpletest.hpp 5 | * 6 | * Description: Main header file containing all definitions and macros. 7 | * 8 | * Version: 1.0 9 | * Created: 05/20/2014 09:22:42 PM 10 | * Revision: none 11 | * Compiler: gcc 12 | * 13 | * Author: Dilawar Singh (), dilawars@ncbs.res.in 14 | * Organization: 15 | * 16 | * ============================================================================== 17 | */ 18 | 19 | #ifndef SIMPLETEST_INC 20 | #define SIMPLETEST_INC 21 | 22 | #include "print_function.hpp" 23 | #include "testing_macros.hpp" 24 | #include "simple_assert.hpp" 25 | 26 | #endif /* ----- #ifndef SIMPLETEST_INC ----- */ 27 | -------------------------------------------------------------------------------- /docs/source/user/py/references/STDPSynapse.rst: -------------------------------------------------------------------------------- 1 | STDPSynapse 2 | ----------- 3 | 4 | .. py:class:: STDPSynapse 5 | 6 | Subclass of Synapse including variables for Spike Timing Dependent Plasticity (STDP). 7 | 8 | .. py:method:: setAPlus 9 | 10 | (*destination message field*) Assigns field value. 11 | 12 | 13 | .. py:method:: getAPlus 14 | 15 | (*destination message field*) Requests field value. The requesting Element must provide a handler for the returned value. 16 | 17 | 18 | .. py:attribute:: aPlus 19 | 20 | double (*value field*) aPlus is a pre-synaptic variable that keeps a decaying 'history' of previous pre-spike(s)and is used to update the synaptic weight when a post-synaptic spike appears.It determines the t\_pre < t\_post (pre before post) part of the STDP window. 21 | -------------------------------------------------------------------------------- /moose-examples/tutorials/Rdesigneur/chans/Glu.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 8 | 9 | Glutamate receptor synchan, 2 ms tau. 10 | 11 | 12 | 13 | Simple double exponential waveform glu synapse 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /moose-examples/tutorials/Rdesigneur/chans/NMDA.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 8 | 9 | NMDA receptor synchan, 20 ms tau. 10 | 11 | 12 | 13 | Simple double exponential waveform NMDA synapse 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /moose-examples/paper-2015/Fig2_elecModels/chans/Glu.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 8 | 9 | Glutamate receptor synchan, 2 ms tau. 10 | 11 | 12 | 13 | Simple double exponential waveform glu synapse 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /moose-examples/paper-2015/Fig2_elecModels/chans/NMDA.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 8 | 9 | NMDA receptor synchan, 20 ms tau. 10 | 11 | 12 | 13 | Simple double exponential waveform NMDA synapse 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /data/Makefile: -------------------------------------------------------------------------------- 1 | PWD:=$(shell dirname $(realpath $(lastword $(MAKEFILE_LIST)))) 2 | MOOSECORE_DIR=$(PWD)/moose-core 3 | MOOSEGUI_DIR=$(PWD)/moose-gui 4 | 5 | MOOSECORE_BUILD_DIR=_moose_core_build_dir_ 6 | 7 | MOOSEBIN:=$(MOOSECORE_BUILD_DIR)/moose.bin 8 | MOOSESDIST:=$(MOOSECORE_BUILD_DIR)/moose-3.0.2.tar.gz 9 | 10 | ## Prefix 11 | PREFIX:=/usr 12 | 13 | all: build_moose 14 | 15 | build_moose: build_moose_core build_moose_gui 16 | 17 | build_moose_core $(MOOSEBIN) $(MOOSESDIST): configure_moose_core 18 | cd $(MOOSECORE_BUILD_DIR) && make -j`proc` 19 | 20 | configure_moose_core: 21 | echo "Configuring moose-core" 22 | mkdir -p $(MOOSECORE_BUILD_DIR) 23 | cd $(MOOSECORE_BUILD_DIR) && cmake -DCMAKE_INSTALL_PREFIX=$(PREFIX) $(MOOSECORE_DIR) 24 | 25 | 26 | clean: 27 | git clean -fxd 28 | 29 | 30 | .PNONY: clean uninstall install 31 | -------------------------------------------------------------------------------- /moose-examples/paper-2015/Fig5_CellMultiscale/chans/Glu.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 8 | 9 | Glutamate receptor synchan, 2 ms tau. 10 | 11 | 12 | 13 | Simple double exponential waveform glu synapse 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /moose-examples/paper-2015/Fig5_CellMultiscale/chans/NMDA.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 8 | 9 | NMDA receptor synchan, 20 ms tau. 10 | 11 | 12 | 13 | Simple double exponential waveform NMDA synapse 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /moose-core/basecode/ProcInfo.h: -------------------------------------------------------------------------------- 1 | /********************************************************************** 2 | ** This program is part of 'MOOSE', the 3 | ** Messaging Object Oriented Simulation Environment. 4 | ** Copyright (C) 2003-2010 Upinder S. Bhalla. and NCBS 5 | ** It is made available under the terms of the 6 | ** GNU Lesser General Public License version 2.1 7 | ** See the file COPYING.LIB for the full notice. 8 | **********************************************************************/ 9 | 10 | #ifndef PROCINFO_INC 11 | #define PROCINFO_INC 12 | class ProcInfo 13 | { 14 | public: 15 | ProcInfo() 16 | : dt( 1.0 ), currTime( 0.0 ) 17 | {;} 18 | double dt; 19 | double currTime; 20 | }; 21 | 22 | typedef const ProcInfo* ProcPtr; 23 | #endif /* ----- #ifndef PROCINFO_INC ----- */ 24 | -------------------------------------------------------------------------------- /moose-core/tests/issues/hsolve/README: -------------------------------------------------------------------------------- 1 | This directory contains a test case comparing NEURON simulation of a 2 | neuron with results from MOOSE hsolve and ee solver. 3 | 4 | h10.CNG.swc: Cell morphology from NeuroMorpho.org. Taken from 5 | moose-examples/snippets. 6 | 7 | h10.CNG.moose.py: Loads the swc file in MOOSE and sets the passive 8 | properties. It records the Vm from the soma and the apical 9 | compartments and dumps them to the outout file. Simulates with hsolve 10 | if run with arguments, exponential Euler (EE) otherwise. 11 | 12 | h10.CNG.hoc : Passive model of this cell for NEURON. 13 | 14 | run_h10.CNG.hoc : Sets up current injection at the last apical section 15 | of the above cell, simulates it and dumps the time, soma Vm and 16 | stimulated compartment Vm. 17 | 18 | compare_moose_nrn.py : Plots the dumped Vm from the three cases. -------------------------------------------------------------------------------- /moose-examples/paper-2015/Fig6_NetMultiscale/cells_channels/Glu.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 8 | 9 | Glutamate receptor synchan, 2 ms tau. 10 | 11 | 12 | 13 | Simple double exponential waveform glu synapse 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /moose-examples/paper-2015/Fig6_NetMultiscale/cells_channels/NMDA.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 8 | 9 | NMDA receptor synchan, 20 ms tau. 10 | 11 | 12 | 13 | Simple double exponential waveform NMDA synapse 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /moose-examples/traub_2005/py/proto/SupAxoaxonic.levels: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2 3 | 3 3 4 | 4 3 5 | 5 4 6 | 6 4 7 | 7 4 8 | 8 5 9 | 9 5 10 | 10 5 11 | 11 6 12 | 12 7 13 | 13 8 14 | 14 9 15 | 15 2 16 | 16 3 17 | 17 3 18 | 18 4 19 | 19 4 20 | 20 4 21 | 21 5 22 | 22 5 23 | 23 5 24 | 24 6 25 | 25 7 26 | 26 8 27 | 27 9 28 | 28 2 29 | 29 3 30 | 30 3 31 | 31 4 32 | 32 4 33 | 33 4 34 | 34 5 35 | 35 5 36 | 36 5 37 | 37 6 38 | 38 7 39 | 39 8 40 | 40 9 41 | 41 2 42 | 42 3 43 | 43 3 44 | 44 4 45 | 45 4 46 | 46 4 47 | 47 5 48 | 48 5 49 | 49 5 50 | 50 6 51 | 51 7 52 | 52 8 53 | 53 9 54 | 54 0 55 | 55 0 56 | 56 0 57 | 57 0 58 | 58 0 59 | 59 0 60 | -------------------------------------------------------------------------------- /moose-examples/paper-2015/Fig6_NetMultiscale/cells_channels/GABA.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 8 | 9 | GABA receptor synchan, 2 ms tau. 10 | 11 | 12 | 13 | Simple double exponential waveform GABA synapse 14 | 15 | 16 | 17 | -------------------------------------------------------------------------------- /moose-examples/tutorials/Rdesigneur/ex7.0_spatial_chem_osc.py: -------------------------------------------------------------------------------- 1 | import moose 2 | import numpy as np 3 | import pylab 4 | import rdesigneur as rd 5 | rdes = rd.rdesigneur( 6 | turnOffElec = True, 7 | #This subdivides the length of the soma into 2 micron voxels 8 | diffusionLength = 2e-6, 9 | chemProto = [['makeChemOscillator()', 'osc']], 10 | chemDistrib = [['osc', 'soma', 'install', '1' ]], 11 | plotList = [['soma', '1', 'dend/a', 'conc', 'Concentration of a'], 12 | ['soma', '1', 'dend/b', 'conc', 'Concentration of b']], 13 | moogList = [['soma', '1', 'dend/a', 'conc', 'a Conc', 0, 360 ]] 14 | ) 15 | 16 | rdes.buildModel() 17 | bv = moose.vec( '/model/chem/dend/b' ) 18 | bv[0].concInit *= 2 19 | bv[-1].concInit *= 2 20 | moose.reinit() 21 | 22 | rdes.displayMoogli( 1, 400, rotation = 0, azim = np.pi/2, elev = 0.0 ) 23 | -------------------------------------------------------------------------------- /_travis/build_on_osx.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash - 2 | #=============================================================================== 3 | # 4 | # FILE: build_on_osx.sh 5 | # 6 | # USAGE: ./build_on_osx.sh 7 | # 8 | # DESCRIPTION: 9 | # 10 | # OPTIONS: --- 11 | # REQUIREMENTS: --- 12 | # BUGS: --- 13 | # NOTES: --- 14 | # AUTHOR: Dilawar Singh (), dilawars@ncbs.res.in 15 | # ORGANIZATION: NCBS Bangalore 16 | # CREATED: Tuesday 27 June 2017 01:55:11 IST 17 | # REVISION: --- 18 | #=============================================================================== 19 | 20 | set -o nounset # Treat unset variables as an error 21 | set -e 22 | ( 23 | cd _travis 24 | # brew audit --strict --online moose.rb # Failling with seg-fault. 25 | brew install -V --build-from-source moose.rb 26 | ) 27 | -------------------------------------------------------------------------------- /macosx/moogli.rb: -------------------------------------------------------------------------------- 1 | class Moogli < Formula 2 | desc "3d visualizer of neuronal simulation" 3 | homepage "http://moose.ncbs.res.in/moogli" 4 | url "https://github.com/BhallaLab/moogli/archive/macosx.tar.gz" 5 | version "0.5.0" 6 | 7 | depends_on "open-scene-graph" 8 | depends_on "python" if MacOS.version <= :snow_leopard 9 | depends_on "sip" 10 | depends_on "pyqt" 11 | 12 | def install 13 | ENV['CFLAGS'] = "" 14 | ENV['CXXFLAGS'] = "" 15 | # Copy QtCore.so etc to lib of our app. 16 | system "./build_on_macosx.sh" 17 | system "python", "setup.py", "install", "--prefix", prefix 18 | (prefix/"lib/python2.7/site-packages/moogli/core").install "moogli/core/_moogli.so" 19 | end 20 | 21 | test do 22 | system "#{HOMEBREW_PREFIX}/bin/python", "-c", "import moogli" 23 | system "python", "-c", "import moogli" 24 | end 25 | end 26 | -------------------------------------------------------------------------------- /moose-core/.travis/deploy_pypi.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash - 2 | #=============================================================================== 3 | # 4 | # FILE: deploy_pypi.sh 5 | # 6 | # USAGE: ./deploy_pypi.sh 7 | # 8 | # DESCRIPTION: Build docker image and deploy on PyPI. 9 | # 10 | # OPTIONS: --- 11 | # REQUIREMENTS: --- 12 | # BUGS: --- 13 | # NOTES: --- 14 | # AUTHOR: Dilawar Singh (), dilawars@ncbs.res.in 15 | # ORGANIZATION: NCBS Bangalore 16 | # CREATED: Sunday 04 February 2018 11:46:32 IST 17 | # REVISION: --- 18 | #=============================================================================== 19 | set -o nounset # Treat unset variables as an error 20 | 21 | git clone https://github.com/BhallaLab/pymoose-wheels 22 | cd pymoose-wheels && docker build -t bhallalab/wheels . 23 | --------------------------------------------------------------------------------