"""
TODO: redo 3507... there are actually 3 figures there... well, maybe, the models are the same
TODO: 146376: need to load morphometric file... not sure what it wants... need to manually curate
TODO: 139656 -- large network
TODO: 97917_*
TODO: 93326 -- maybe this should be more than 1... depending on VClamp/IClamp?
TODO: 147366 -- this is a lytton model... nonstandard setup
TODO: 140881 -- another lytton model... no fadvances, json_generator fails
TODO: 12631 -- another lytton model... no fadvances, json_generator fails
TODO: 19366_1 -- doesn't actually run... need to click the "Plot" buttons, but not clear where they come from
TODO: 22203 -- runs everything in a different process!
TODO: 124513 -- large model, complains about not running an fadvance, but seems like it must
TODO: 95960 -- can switch between many cells and many figures...
TODO: 51781 -- large network
TODO: 84612 -- push buttons... many many push buttons
TODO: 147460 -- buried code, no mosinit... shouldn't be that hard, looks like only two cases
TODO: 53437 -- possibly no sections?
TODO: 140038 -- push buttons, needs a manual setup
TODO: 144511 -- python... no mosinit.hoc (shouldn't be hard, but needs a manual setup)
TODO: 138379 -- no sections (lytton model)
TODO: 117207_* -- button pressing troubles (e.g. 'hoc.HocObject' object has no attribute 'RunBestFit')
TODO: 76879_* -- no sections (ermentrout)
TODO: 151404 -- runs with a script instead of mosinit... need to figure out what to do herer
TODO: 84589 -- no mosinit.hoc, but seems like it should have one (emailed Tom)
TODO: confirm 52034 sets up a structure (it says it doesn't run... figure out why not)
TODO: 21984 -- no sections
TODO: 140299_* -- should also have mixed diameter buttons but the files were missing when the run protocols were generated
TODO: 98017 -- useless mosinit, readme... no way of knowing how to run, lots of hoc files
TODO: 97985 -- shell scripts
TODO: 113435 -- modelview available, but only for 113435 which is an alternate of the xpp model 97747... database issues
TODO: 3658: lots of options, needs manual setup
TODO: 135902 -- can't figure out how to run
TODO: 114355 -- needs manual setup; many cell choices (see runme: main file is main.hoc)
TODO: 144549 -- no sections
TODO: 151282 -- extra_scatter_gather not allowed with multiple threads
TODO: 114359 -- methods paper. not sure what's going on here
TODO: 33728 -- pure artificial cells?
TODO: 139421 -- extra_scatter_gather not allowed with multiple threads
TODO: 144007 -- generates a large number of HOC files dynamically to run sweeps
TODO: 51196 -- two options selectable by a radio button somewhere, but too tired to find
TODO: 144570 -- mitral cell model from Shepherd lab... not sure how to create... modelview showed no sections
TODO: 144450 -- needs manual setup, not sure how to run
TODO: 33975 -- all but the outer two simulations crash
TODO: 151817 -- supports batch simulation, not quite sure what's going on, also radiobuttons
TODO: 144589 -- crashes NEURON's modelview
TODO: 150284 -- runs with scripts
TODO: 3808 -- MyFirstNEURON -- complicated NEURON demo, nearly infinite number of options
TODO: 97868 -- Sam model, weird errors from NQS
TODO: 136309 -- many cells to choose from, no GUI
TOFINISH: 83319_3 and 83319_4 -- no sections
TODO: 97874 -- NQS no demo
TODO: 3793 -- complicated model with many layers that needs to be done manually
TODO: 114665 -- not sure how to explain
TODO: 64229 -- multiple mosinits... it looks like the real one is in the root folder, but confused
TODO: 144579 -- looks like needs a PBS installation, runs with a script
TODO: 9888 -- choose parameters from two panels, needs manual setup
TODO: 141505 -- runs with scripts
TODO: 3817 -- no sections?
TODO: 83440 -- multiple versions
TODO: 149000 -- Loading morphology confusion
TODO: 105507 -- Lytton model
TODO: 116838 -- Lytton model
TODO: 144538 -- Sam, George, Cliff, Bill... seems to be missing files
TODO: 141063 -- multiple button sets to choose HCN type and graph
TODO: 18501 -- many many cells, and two figures for each
TODO: 3264_4,5 -- no sections (the other cases work)... protocol instructions commented out
TODO: 19746 -- broke h.allsec somehow. protocol instructions left in but commented out
TODO: 141272 -- couldn't find accept button somehow (also: uses xradiobuttons, but straightforwardish)
TODO: 152197 -- multiple threads breaks extra_scatter_gather
TODO: 143671 -- there is a button for pick a cell, but not visible... not sure how to run exactly
TODO: 137845 -- no sections? or are they all on different processors?
TODO: 125385 -- syntax errors with both branches
TODO: 5426 -- buttons, loading of idraw?
TODO: 144526 -- crashes NEURON's modelview
TODO: 149174 -- requires editing runall.py, also a script
TODO: 138273 -- MATLAB must be run before NEURON
TODO: 147461 -- extra_scatter_gather does not work with multiple threads
TODO: 150621 -- there are messages about changing parameters before running; should we add this?
TODO: 83523 -- no simulation; just mod files
TODO: 147141 -- runs via script
TODO: 144054 -- mitral cell model. requires selecting a cell
TODO: 53893 -- no sections?
TODO: 116838 -- repeated prompts
TODO: 53965 -- 3 choices of models, buttons for each
Some models need manual intervention:
53869 -- press enter after the h.restart
143114_* -- press enter after h.load_file
136715 -- contains additional instructions in the readme about changing parameters, which these instructions do not do
Skipped 39948 -- lots of buttons, not immediately clear how to use
Skipped for now: Traub et al 2005
123897_2 crashes with "NEURON: procedure too big", also have to rename lib/U_Dvdt.hoc to fix case sensitive filename issue
93321_* causes classic modelview to core dump
143635 -- Amanda Casale's model only presents one parameter set when run with mosinit.hoc, but two others are available; should these be viewable in modelview?
28316_1 -- classic modelview crashes due to point processes not being inserted in a section... still need to put in the rest of 28316_*, but seems no point for now
141273 -- no mosinit.hoc; not clear what's going on
127388 -- interesting model. no fadvance
144586 -- no sections. no modelview yet
71312 -- skipped for now, not sure if 1 modelview or 16
20212 -- to run, need to have . on path
Weird quirks:
19920 says it didn't fadvance, but it seems to
116862 says it didn't fadvance, but it seems to
"""
"""
added today:
(ran at work)
126640, 116491, 7988_*, 114394, 105385_*, 3660, 82849, 10360, 83319_*, 148644, 145672_*, 112359_*, 146565, 18742_*, 102288, 2730_*, 149415, 2487_*, 3342, 3648, 3665, 127995, 50210_*, 97263, 146030, 43039_*, 87454, 143100, 149100, 2488_*, 3677_*, 144482
3673, 135898, 150245_*, 140471, 128446, 3264_*, 29942, 64228_*, 150556, 9852_*, 87585, 120692_*, 62673, 110560_*, 53451_*, 62284, 8210_*, 143442, 3805_*, 3810, 3493, 18502_*, 116769, 39949, 50391, 144523, 108459_*, 64259, 64195_*, 150621_*, 121253_*, 150446_*, 139657_*, 136095, 19591_*, 124043, 3815_*, 19747, 129067_*, 19920, 9849, 116862, 9889, 3684, 3533, 3670_*, 17663_*, 3343_*, 37819, 122442_*
(ran at home)
74298, 64216, 139883_*, 84655, 151443, 3511, 127507_*, 83547, 97860, 147539_*, 118631, 3488, 3457, 3491, 3483, 3802, 144533_*, 50997_*, 95870
added from bottom up:
144566 3812 3682 93325 96444_* 20014_* 53569 62285 122442
***
NEXT TIME
***
From top down:
From bottom up: Tight junction model of CNS myelinated axons (Devaux and Gow 2008)
deal with 20212 (Poirazi?) -- only have one so far
remove 20212_2 since missing a variable definition? or make work?
'20212_2':
{
'variant': 'Disperse Equal Sized',
'compile': ['cd CA1_multi/experiment/cluster-dispersion', 'nrnivmodl ../../mechanism', 'chmod +x newshiftsyn', 'export PATH=.:$PATH'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Disperse_equal_sized.hoc")'],
'cleanup': ['cd ../../..', 'rm -fr CA1_multi']
},
"""
automatically_curated_protocols = {
'122442_1':
{
'variant': 'Double Cable Model (DCM)',
'compile': ['cd Gow_Devaux_2009'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("DCM_0.6um_axon.ses")'],
'cleanup': ['cd ../', 'rm -fr Gow_Devaux_2009']
},
'122442_2':
{
'variant': 'Tight Junction Model (TJM)',
'compile': ['cd Gow_Devaux_2009'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("TJM_0.6um_axon.ses")'],
'cleanup': ['cd ../', 'rm -fr Gow_Devaux_2009']
},
'37819':
{
'compile': ['cd thal_aug_resp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr thal_aug_resp']
},
'3343_1':
{
'variant': 'Spindle oscillations - short run',
'compile': ['cd DLGN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("Fspin")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr DLGN_NEW']
},
'3343_2':
{
'variant': 'Spindle oscillations - long run',
'compile': ['cd DLGN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("FspinL")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr DLGN_NEW']
},
'3343_3':
{
'variant': 'Bicuculline-induced oscillations - short run',
'compile': ['cd DLGN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("Fbic")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr DLGN_NEW']
},
'3343_4':
{
'variant': 'Bicuculline-induced oscillations - long run',
'compile': ['cd DLGN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("FbicL")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr DLGN_NEW']
},
'3343_5':
{
'variant': 'Delta oscillations - short run',
'compile': ['cd DLGN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("Fdelta")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr DLGN_NEW']
},
'3343_6':
{
'variant': 'Delta oscillations - long run',
'compile': ['cd DLGN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("FdeltaL")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr DLGN_NEW']
},
'17663_1':
{
'variant': 'Burst behavior in single-compartment model',
'compile': ['cd dendre', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("re1_cc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr dendre']
},
'17663_2':
{
'variant': 'Burst behavior in 3-compartment model',
'compile': ['cd dendre', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("re3_cc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr dendre']
},
'17663_3':
{
'variant': 'Voltage-clamp in 3-compartment cell model',
'compile': ['cd dendre', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("re3_vc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr dendre']
},
'17663_4':
{
'variant': 'Burst behavior in detailed cell model',
'compile': ['cd dendre', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("re80_cc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr dendre']
},
'17663_5':
{
'variant': 'Voltage-clamp in detailed cell model',
'compile': ['cd dendre', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("re80_vc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr dendre']
},
'17663_6':
{
'variant': 'Burst behavior in dissociated cell model',
'compile': ['cd dendre', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("reD_cc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr dendre']
},
'17663_7':
{
'variant': 'Voltage-clamp in dissociated cell model',
'compile': ['cd dendre', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("reD_vc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr dendre']
},
'3670_1':
{
'variant': 'Fig. 5a',
'compile': ['cd NTW_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("Fig5A")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr NTW_NEW']
},
'3670_2':
{
'variant': 'Fig. 5b',
'compile': ['cd NTW_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("Fig5B")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr NTW_NEW']
},
'3670_3':
{
'variant': 'Fig. 6a',
'compile': ['cd NTW_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("Fig6A")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr NTW_NEW']
},
'3670_4':
{
'variant': 'Fig. 6b',
'compile': ['cd NTW_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("Fig6B")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr NTW_NEW']
},
'3670_5':
{
'variant': 'Fig. 6c',
'compile': ['cd NTW_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("Fig6C")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr NTW_NEW']
},
'3670_6':
{
'variant': 'Fig. 6d',
'compile': ['cd NTW_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("Fig6D")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr NTW_NEW']
},
'3670_7':
{
'variant': 'Fig. 13a',
'compile': ['cd NTW_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("Fig13A")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr NTW_NEW']
},
'3670_8':
{
'variant': 'Fig. 13b',
'compile': ['cd NTW_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("Fig13B")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr NTW_NEW']
},
'3533':
{
'compile': ['cd IcaT', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr IcaT']
},
'3684':
{
'compile': ['cd h_tc', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr h_tc']
},
'9889':
{
'compile': ['cd lytton97', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr lytton97']
},
'116862':
{
'compile': ['cd b09jan13', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr b09jan13']
},
'9849':
{
'compile': ['cd westerfield78'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr westerfield78']
},
'19920':
{
'compile': ['cd CaT', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CaT']
},
'19747':
{
'compile': ['cd CoHCNS2000', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CoHCNS2000']
},
'3815_1':
{
'variant': 'Fig. 1A pyramid-->pyramid (depression)',
'compile': ['cd tsodyks', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_fig1a()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr tsodyks']
},
'3815_2':
{
'variant': 'Fig. 1B pyramid-->interneuron at 20 Hz (facilitation)',
'compile': ['cd tsodyks', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_fig1b()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr tsodyks']
},
'3815_3':
{
'variant': 'Fig. 1C pyramid-->interneuron at 70 Hz (facilitation-depression)',
'compile': ['cd tsodyks', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_fig1c()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr tsodyks']
},
'124043':
{
'compile': ['cd larkumEtAl2009_2', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr larkumEtAl2009_2']
},
'19591_1':
{
'variant': 'Figure 1A',
'compile': ['cd granule', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig1a")'],
'cleanup': ['cd ../', 'rm -fr granule']
},
'19591_2':
{
'variant': 'Figure 2A1',
'compile': ['cd granule', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig2a1")'],
'cleanup': ['cd ../', 'rm -fr granule']
},
'19591_3':
{
'variant': 'Figure 2A2',
'compile': ['cd granule', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig2a2")'],
'cleanup': ['cd ../', 'rm -fr granule']
},
'19591_4':
{
'variant': 'Figure 2A3',
'compile': ['cd granule', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig2a3")'],
'cleanup': ['cd ../', 'rm -fr granule']
},
'19591_5':
{
'variant': 'Figure 2B1',
'compile': ['cd granule', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig2b1")'],
'cleanup': ['cd ../', 'rm -fr granule']
},
'19591_6':
{
'variant': 'Figure 2B2',
'compile': ['cd granule', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig2b2")'],
'cleanup': ['cd ../', 'rm -fr granule']
},
'19591_7':
{
'variant': 'Figure 2B3',
'compile': ['cd granule', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig2b3")'],
'cleanup': ['cd ../', 'rm -fr granule']
},
'136095':
{
'variant': 'Run neocortical column simulation & display output',
'compile': ['cd ncdemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.dorun()'],
'cleanup': ['cd ../', 'rm -fr ncdemo']
},
'139657_1':
{
'variant': '50 hz',
'compile': ['cd Kopp-Scheinpflug2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.NetStim[0].interval=20', 'h.myrun(h.NetStim[0].interval)'],
'cleanup': ['cd ../', 'rm -fr Kopp-Scheinpflug2011']
},
'139657_2':
{
'variant': '100 hz',
'compile': ['cd Kopp-Scheinpflug2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.NetStim[0].interval=10', 'h.myrun(h.NetStim[0].interval)'],
'cleanup': ['cd ../', 'rm -fr Kopp-Scheinpflug2011']
},
'139657_3':
{
'variant': '200 hz',
'compile': ['cd Kopp-Scheinpflug2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.NetStim[0].interval=5', 'h.myrun(h.NetStim[0].interval)'],
'cleanup': ['cd ../', 'rm -fr Kopp-Scheinpflug2011']
},
'139657_4':
{
'variant': '300 hz',
'compile': ['cd Kopp-Scheinpflug2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.NetStim[0].interval=3.3', 'h.myrun(h.NetStim[0].interval)'],
'cleanup': ['cd ../', 'rm -fr Kopp-Scheinpflug2011']
},
'139657_5':
{
'variant': '400 hz',
'compile': ['cd Kopp-Scheinpflug2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.NetStim[0].interval=2.5', 'h.myrun(h.NetStim[0].interval)'],
'cleanup': ['cd ../', 'rm -fr Kopp-Scheinpflug2011']
},
'121253_1':
{
'variant': 'Short demo run',
'compile': ['cd stnAxonDbsModel', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.short_run()'],
'cleanup': ['cd ../', 'rm -fr stnAxonDbsModel']
},
'121253_2':
{
'variant': 'fig 2b (2 hour run)',
'compile': ['cd stnAxonDbsModel', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig2b()'],
'cleanup': ['cd ../', 'rm -fr stnAxonDbsModel']
},
'150621_1':
{
'variant': 'Figure 2A',
'compile': ['cd MahonEtAl2000', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig2a()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr MahonEtAl2000']
},
'150621_2':
{
'variant': 'Figure 3A',
'compile': ['cd MahonEtAl2000', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig3a()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr MahonEtAl2000']
},
'64195_1':
{
'variant': 'fig6B simulation',
'compile': ['cd Stochastic', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig6B")'],
'cleanup': ['cd ../', 'rm -fr Stochastic']
},
'64195_2':
{
'variant': 'Short run simulation',
'compile': ['cd Stochastic', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("shortRun")'],
'cleanup': ['cd ../', 'rm -fr Stochastic']
},
'64259':
{
'compile': ['cd NCnote', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr NCnote']
},
'144523':
{
'compile': ['cd LuthmanEtAl2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.DCNrun()'],
'cleanup': ['cd ../', 'rm -fr LuthmanEtAl2011']
},
'50391':
{
'compile': ['cd stochastichh'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr stochastichh']
},
'39949':
{
'compile': ['cd spinycell', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr spinycell']
},
'116769':
{
'compile': ['cd SpineCaModel', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr SpineCaModel']
},
'18502_1':
{
'variant': 'branch near shaft',
'compile': ['cd spinebranches', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("ltp_two")'],
'cleanup': ['cd ../', 'rm -fr spinebranches']
},
'18502_2':
{
'variant': 'regular sized necks',
'compile': ['cd spinebranches', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("ltp_spl")'],
'cleanup': ['cd ../', 'rm -fr spinebranches']
},
'18502_3':
{
'variant': '0.25 nS AMPA (control)',
'compile': ['cd spinebranches', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("ltp_ran")'],
'cleanup': ['cd ../', 'rm -fr spinebranches']
},
'18502_4':
{
'variant': '0.35 nS AMPA (control)',
'compile': ['cd spinebranches', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("ltp_ttt")'],
'cleanup': ['cd ../', 'rm -fr spinebranches']
},
'3493':
{
'compile': ['cd motoneuron', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr motoneuron']
},
'3810':
{
'compile': ['cd MRGaxon', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr MRGaxon']
},
'143442':
{
'compile': ['cd FoustEtAl2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.node_inj()'],
'cleanup': ['cd ../', 'rm -fr FoustEtAl2011']
},
'8210_1':
{
'variant': 'inject soma',
'compile': ['cd spikeinit', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.soma_inj()'],
'cleanup': ['cd ../', 'rm -fr spikeinit']
},
'8210_2':
{
'variant': 'inject dend',
'compile': ['cd spikeinit', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.dend_inj()'],
'cleanup': ['cd ../', 'rm -fr spikeinit']
},
'62284':
{
'compile': ['cd ba', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.steprun()'],
'cleanup': ['cd ../', 'rm -fr ba']
},
'110560_1':
{
'variant': 'Potassium 1. L5 Pyramidal Neuron',
'compile': ['cd SpaceClampDemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("potassium.hoc")', 'h.fig1a()'],
'cleanup': ['cd ../', 'rm -fr SpaceClampDemo']
},
'110560_2':
{
'variant': 'Potassium 2. L4 interneuron',
'compile': ['cd SpaceClampDemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("potassium.hoc")', 'h.fig1b()'],
'cleanup': ['cd ../', 'rm -fr SpaceClampDemo']
},
'110560_3':
{
'variant': 'Potassium 3. L2/3 bipolar interneuron',
'compile': ['cd SpaceClampDemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("potassium.hoc")', 'h.fig1c()'],
'cleanup': ['cd ../', 'rm -fr SpaceClampDemo']
},
'110560_4':
{
'variant': 'Potassium 4. L4 spiny stellate',
'compile': ['cd SpaceClampDemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("potassium.hoc")', 'h.fig1d()'],
'cleanup': ['cd ../', 'rm -fr SpaceClampDemo']
},
'110560_5':
{
'variant': 'Calcium 1. L5 Pyramidal Neuron',
'compile': ['cd SpaceClampDemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("calcium.hoc")', 'h.fig1a()'],
'cleanup': ['cd ../', 'rm -fr SpaceClampDemo']
},
'110560_6':
{
'variant': 'Calcium 2. L4 interneuron',
'compile': ['cd SpaceClampDemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("calcium.hoc")', 'h.fig1b()'],
'cleanup': ['cd ../', 'rm -fr SpaceClampDemo']
},
'110560_7':
{
'variant': 'Calcium 3. L2/3 bipolar interneuron',
'compile': ['cd SpaceClampDemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("calcium.hoc")', 'h.fig1c()'],
'cleanup': ['cd ../', 'rm -fr SpaceClampDemo']
},
'110560_8':
{
'variant': 'Calcium 4. L4 spiny stellate',
'compile': ['cd SpaceClampDemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("calcium.hoc")', 'h.fig1d()'],
'cleanup': ['cd ../', 'rm -fr SpaceClampDemo']
},
'62673':
{
'compile': ['cd na2006', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr na2006']
},
'120692_1':
{
'variant': 'Figure 2-3',
'compile': ['cd kootsey83', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load("fig2-3.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr kootsey83']
},
'120692_2':
{
'variant': 'Figure 4-6',
'compile': ['cd kootsey83', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load("fig4-6.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr kootsey83']
},
'120692_3':
{
'variant': 'Figure 7',
'compile': ['cd kootsey83', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load("fig7.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr kootsey83']
},
'120692_4':
{
'variant': 'Figure 8-10',
'compile': ['cd kootsey83', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load("fig8-10.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr kootsey83']
},
'120692_5':
{
'variant': 'Figure 11-12',
'compile': ['cd kootsey83', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load("fig11-12.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr kootsey83']
},
'87585':
{
'compile': ['cd R859C', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr R859C']
},
'121259_1':
{
'variant': 'homogenous network run',
'compile': ['cd bogaard2009', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("homrun.hoc")'],
'cleanup': ['cd ../', 'rm -fr bogaard2009']
},
'121259_2':
{
'variant': 'heterogenous network run',
'compile': ['cd bogaard2009', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("hetrun.hoc")'],
'cleanup': ['cd ../', 'rm -fr bogaard2009']
},
'9852_1':
{
'variant': 'Figure 1A',
'compile': ['cd moore83'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig1a()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_2':
{
'variant': 'Figure 1B',
'compile': ['cd moore83'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig1b()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_3':
{
'variant': 'Figure 1C',
'compile': ['cd moore83'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig1c()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_4':
{
'variant': 'Figure 1D',
'compile': ['cd moore83'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig1d()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_5':
{
'variant': 'Figure 2A',
'compile': ['cd moore83'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig2a()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_6':
{
'variant': 'Figure 2B',
'compile': ['cd moore83'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig2b()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_7':
{
'variant': 'Figure 3A',
'compile': ['cd moore83'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig3a()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_8':
{
'variant': 'Figure 3B',
'compile': ['cd moore83'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig3b()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_9':
{
'variant': 'Figure 3C',
'compile': ['cd moore83', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig3c()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_10':
{
'variant': 'Figure 4A',
'compile': ['cd moore83'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig4a()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_11':
{
'variant': 'Figure 4B',
'compile': ['cd moore83'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig4b()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_12':
{
'variant': 'Figure 4C',
'compile': ['cd moore83'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig4c()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_13':
{
'variant': 'Figure 5A',
'compile': ['cd moore83'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig5a()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_14':
{
'variant': 'Figure 5B',
'compile': ['cd moore83'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig5b()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_15':
{
'variant': 'Figure 5C',
'compile': ['cd moore83'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig5c()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'9852_16':
{
'variant': 'Figure 5D',
'compile': ['cd moore83', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig5d()'],
'cleanup': ['cd ../', 'rm -fr moore83']
},
'150556':
{
'compile': ['cd BiddellJohnson2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr BiddellJohnson2013']
},
'29942':
{
'compile': ['cd lgnsigint', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr lgnsigint']
},
# '19746':
# {
# 'compile': ['cd SNRCA1', 'nrnivmodl'],
# 'launch': ['nrngui -python'],
# 'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.steprun()'],
# 'cleanup': ['cd ../', 'rm -fr SNRCA1']
# },
'3264_1':
{
'variant': 'Fig. 3A using slow epsp',
'compile': ['cd varela', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_fig3a()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr varela']
},
'3264_2':
{
'variant': 'Fig. 3C using slow epsp',
'compile': ['cd varela', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_fig3c()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr varela']
},
'3264_3':
{
'variant': 'Fig. 3D using fast epsp',
'compile': ['cd varela', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_fig3d()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr varela']
},
# '3264_4':
# {
# 'variant': 'Fig. 3E',
# 'compile': ['cd varela', 'nrnivmodl'],
# 'launch': ['nrngui -python'],
# 'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_fig3e()', 'h.run()'],
# 'cleanup': ['cd ../', 'rm -fr varela']
# },
# '3264_5':
# {
# 'variant': 'Artificial (integrate and fire) cell',
# 'compile': ['cd varela', 'nrnivmodl'],
# 'launch': ['nrngui -python'],
# 'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_art()', 'h.run()'],
# 'cleanup': ['cd ../', 'rm -fr varela']
# },
'3264_6':
{
'variant': '\'Biophysical\' cell with fast epsp',
'compile': ['cd varela', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_cel()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr varela']
},
'3264_7':
{
'variant': '\'Biophysical\' cell with slow epsp',
'compile': ['cd varela', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_cel2()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr varela']
},
'3264_8':
{
'variant': '\'Biophysical\' cell with multiple input streams',
'compile': ['cd varela', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_test()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr varela']
},
'128446':
{
'variant': 'Init & Run',
'compile': ['cd ShortTermPlasticityMFGRC_Nieus2006', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr ShortTermPlasticityMFGRC_Nieus2006']
},
'140471':
{
'compile': ['cd Figure5', 'nrnivmodl mods'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr Figure5']
},
'150245_1':
{
'variant': 'trained network',
'compile': ['cd a2dmodeldb', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.trainedrun()'],
'cleanup': ['cd ../', 'rm -fr a2dmodeldb']
},
'150245_2':
{
'variant': 'naive network',
'compile': ['cd a2dmodeldb', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.naiverun()'],
'cleanup': ['cd ../', 'rm -fr a2dmodeldb']
},
'135898':
{
'compile': ['cd YuEtAlPNAS2007', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.soma_inj()'],
'cleanup': ['cd ../', 'rm -fr YuEtAlPNAS2007']
},
'3673':
{
'compile': ['cd 5chan', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr 5chan']
},
'95870':
{
'compile': ['cd ROD', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr ROD']
},
'144553_1':
{
'variant': 'Figure 9C-D ( dlPFC )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.xopen("main_fig9_pfcElec.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_2':
{
'variant': 'Figure 9C-D ( V1 )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.xopen("main_fig9_v1Elec.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_3':
{
'variant': 'Figure 10 ( dlPFC )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.xopen("main_fig10_pfc.hoc")'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_4':
{
'variant': 'Figure 10 ( baseline V1 )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.xopen("main_fig10_v1baseline.hoc")'],#, 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_5':
{
'variant': 'Figure 10 ( tuned V1 )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.xopen("main_fig10_v1tuned.hoc")'],#, 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_6':
{
'variant': 'Figure 11 ( PFC apical )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doApic = 1")', 'h.xopen("main_PFC-ApBas_fig11epsc.hoc")'],#, 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_7':
{
'variant': 'Figure 11 ( PFC basal )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doApic = 0")', 'h.xopen("main_PFC-ApBas_fig11epsc.hoc")'],#, 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_8':
{
'variant': 'Figure 11 V1, same gAMPA, apical )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doSynType = 0")', 'h.xopen("main_V1-ApBas_fig11epsc.hoc")'],#, 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_9':
{
'variant': 'Figure 11 ( V1, same gAMPA, basal )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doSynType = 1")', 'h.xopen("main_V1-ApBas_fig11epsc.hoc")'],#, 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_10':
{
'variant': 'Figure 11 ( V1, low gAMPA, apical )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doSynType = 2")', 'h.xopen("main_V1-ApBas_fig11epsc.hoc")'],#, 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_11':
{
'variant': 'Figure 11 ( V1, low gAMPA, basal )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doSynType = 3")', 'h.xopen("main_V1-ApBas_fig11epsc.hoc")'],#, 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_12':
{
'variant': 'Figure 12 ( PFC apical )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doApic = 1")', 'h.xopen("main_PFC-ApBas_fig12ipsc.hoc")'],#, 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_13':
{
'variant': 'Figure 12 ( PFC basal )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doApic = 0")', 'h.xopen("main_PFC-ApBas_fig12ipsc.hoc")'],#, 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_14':
{
'variant': 'Figure 12 ( V1, same gAMPA, apical )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doSynType = 0")', 'h.xopen("main_V1-ApBas_fig12ipsc.hoc")'],#, 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_15':
{
'variant': 'Figure 12 ( V1, same gAMPA, basal )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doSynType = 1")', 'h.xopen("main_V1-ApBas_fig12ipsc.hoc")'],#, 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_16':
{
'variant': 'Figure 12 ( V1, low gAMPA, apical )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doSynType = 2")', 'h.xopen("main_V1-ApBas_fig12ipsc.hoc")'],#, 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'144553_17':
{
'variant': 'Figure 12 ( V1, low gAMPA, basal )',
'compile': ['cd V1_PFC_ModelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doSynType = 3")', 'h.xopen("main_V1-ApBas_fig12ipsc.hoc")'],#, 'h.run()'],
'cleanup': ['cd ../', 'rm -fr V1_PFC_ModelDB']
},
'3802':
{
'compile': ['cd kx_photo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr kx_photo']
},
'3483':
{
'compile': ['cd na_rgc', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr na_rgc']
},
'3491':
{
'compile': ['cd kdr_rgc', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr kdr_rgc']
},
'3457':
{
'compile': ['cd ca_rgc', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr ca_rgc']
},
'3488':
{
'compile': ['cd ka_rgc', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr ka_rgc']
},
'118631':
{
'compile': ['cd KoendgenEtAl2008', 'nrnivmodl mechanisms'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.graph_and_run()'],
'cleanup': ['cd ../', 'rm -fr KoendgenEtAl2008']
},
'147539_1':
{
'variant': 'Membrane voltage sensitivity',
'compile': ['cd Chirp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Chirp_Ih_V()'],
'cleanup': ['cd ../', 'rm -fr Chirp']
},
'147539_2':
{
'variant': 'Rm sensitivity',
'compile': ['cd Chirp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Chirp_Ih_Rm()'],
'cleanup': ['cd ../', 'rm -fr Chirp']
},
'147539_3':
{
'variant': 'Cm sensitivity',
'compile': ['cd Chirp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Chirp_Ih_Cm()'],
'cleanup': ['cd ../', 'rm -fr Chirp']
},
'147539_4':
{
'variant': 'h conductance sensitivity',
'compile': ['cd Chirp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Chirp_Gh()'],
'cleanup': ['cd ../', 'rm -fr Chirp']
},
'147539_5':
{
'variant': 'h activation vhalf sensitivity',
'compile': ['cd Chirp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Chirp_Ih_vhalf()'],
'cleanup': ['cd ../', 'rm -fr Chirp']
},
'147539_6':
{
'variant': 'h activation time constant sensitivity',
'compile': ['cd Chirp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Chirp_Ih_tau()'],
'cleanup': ['cd ../', 'rm -fr Chirp']
},
'97860':
{
'compile': ['cd rejuvenation', 'nrnivmodl mod'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr rejuvenation']
},
'83547':
{
'compile': ['cd damodel', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr damodel']
},
'127507_1':
{
'variant': 'Fig. 2a2',
'compile': ['cd KuznetsovaEtAl2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig2a2()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr KuznetsovaEtAl2010']
},
'127507_2':
{
'variant': 'Fig. 2b2',
'compile': ['cd KuznetsovaEtAl2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig2b2()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr KuznetsovaEtAl2010']
},
'127507_3':
{
'variant': 'Fig. 2f2',
'compile': ['cd KuznetsovaEtAl2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig2f2()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr KuznetsovaEtAl2010']
},
'127507_4':
{
'variant': 'Fig. 6a solid',
'compile': ['cd KuznetsovaEtAl2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig6asolid()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr KuznetsovaEtAl2010']
},
'127507_5':
{
'variant': 'Fig. 6a dashed',
'compile': ['cd KuznetsovaEtAl2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig6adashed()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr KuznetsovaEtAl2010']
},
'3511':
{
'compile': ['cd mcn1', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr mcn1']
},
'151443':
{
'compile': ['cd BalbiEtAl2013', 'nrnivmodl channels'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr BalbiEtAl2013']
},
'84655':
{
'compile': ['cd oltedal', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.xopen("fig10a.hoc")'],
'cleanup': ['cd ../', 'rm -fr oltedal']
},
'139883_1':
{
'variant': 'In vitro',
'compile': ['cd ReConv', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Invitro()'],
'cleanup': ['cd ../', 'rm -fr ReConv']
},
'139883_2':
{
'variant': 'In vivo',
'compile': ['cd ReConv', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Invivo()'],
'cleanup': ['cd ../', 'rm -fr ReConv']
},
'64216':
{
'variant': 'Init & Run',
'compile': ['cd Kourennyi-etal2004', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.myrun()'],
'cleanup': ['cd ../', 'rm -fr Kourennyi-etal2004']
},
'74298':
{
'compile': ['cd sth-model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file(1,"sample.hoc")'],
'cleanup': ['cd ../', 'rm -fr sth-model']
},
'122442_1':
{
'variant': 'Double Cable Model (DCM)',
'compile': ['cd Gow_Devaux_2009', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("DCM_0.6um_axon.ses")'],
'cleanup': ['cd ../', 'rm -fr Gow_Devaux_2009']
},
'122442_2':
{
'variant': 'Tight Junction Model (TJM)',
'compile': ['cd Gow_Devaux_2009', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("TJM_0.6um_axon.ses")'],
'cleanup': ['cd ../', 'rm -fr Gow_Devaux_2009']
},
'62285':
{
'compile': ['cd b', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr b']
},
'53569':
{
'compile': ['cd lamina1', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr lamina1']
},
'20014_1':
{
'variant': 'Fig.2. A-D',
'compile': ['cd kkt98', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(1)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr kkt98']
},
'20014_2':
{
'variant': 'Fig.2. E-H',
'compile': ['cd kkt98', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(2)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr kkt98']
},
'20014_3':
{
'variant': 'Fig.3. A',
'compile': ['cd kkt98', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(3)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr kkt98']
},
'20014_4':
{
'variant': 'Fig.3.',
'compile': ['cd kkt98', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(4)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr kkt98']
},
'20014_5':
{
'variant': 'Fig.3. C',
'compile': ['cd kkt98', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(5)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr kkt98']
},
'96444_1':
{
'variant': 'Ring (Serial)',
'compile': ['cd HinesCarnevaleJNM2007', 'nrnivmodl random'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.launch("ring", "ringser.hoc")'],
'cleanup': ['cd ../', 'rm -fr HinesCarnevaleJNM2007']
},
'96444_2':
{
'variant': 'Ring (Parallel)',
'compile': ['cd HinesCarnevaleJNM2007', 'nrnivmodl random'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.launch("ring", "ringpar.hoc")'],
'cleanup': ['cd ../', 'rm -fr HinesCarnevaleJNM2007']
},
'96444_3':
{
'variant': 'Random (Serial)',
'compile': ['cd HinesCarnevaleJNM2007', 'nrnivmodl random'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.launch("random", "ran3ser.hoc")'],
'cleanup': ['cd ../', 'rm -fr HinesCarnevaleJNM2007']
},
'96444_4':
{
'variant': 'Random (Parallel)',
'compile': ['cd HinesCarnevaleJNM2007', 'nrnivmodl random'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.launch("random", "ran3par.hoc")'],
'cleanup': ['cd ../', 'rm -fr HinesCarnevaleJNM2007']
},
'93325':
{
'compile': ['cd nfrost', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr nfrost']
},
'3682':
{
'compile': ['cd synmap', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr synmap']
},
'3812':
{
'compile': ['cd anderson', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr anderson']
},
'144482':
{
'variant': 'Run',
'compile': ['cd Pyramidal_STDP_Gomez_Delgado_2010', 'nrnivmodl mechanism/mechanism_cell1/'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Pyramidal_STDP_Gomez_Delgado_2010']
},
'3289':
{
'compile': ['cd db', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr db']
},
'149100':
{
'compile': ['cd HayEtAl2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr HayEtAl2013']
},
'143100':
{
'compile': ['cd GPeNeuronKitano', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr GPeNeuronKitano']
},
'87454':
{
'compile': ['cd BahmerLangner2007/NEURON_Chopper_Network_Simulation', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runhere()'],
'cleanup': ['cd ../../', 'rm -fr BahmerLangner2007']
},
'43039_1':
{
'variant': 'control - no GJ (fig.6A)',
'compile': ['cd gap-modeldb', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runc()'],
'cleanup': ['cd ../', 'rm -fr gap-modeldb']
},
'43039_2':
{
'variant': 'with GJ (fig.6B)',
'compile': ['cd gap-modeldb', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.rung()'],
'cleanup': ['cd ../', 'rm -fr gap-modeldb']
},
'43039_3':
{
'variant': 'with GJ & Na+ block (fig.6C)',
'compile': ['cd gap-modeldb', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.rungb()'],
'cleanup': ['cd ../', 'rm -fr gap-modeldb']
},
'146030':
{
'compile': ['cd oconnoretal2012', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr oconnoretal2012']
},
'97263':
{
'compile': ['cd MT-GC', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr MT-GC']
},
'50210_1':
{
'variant': 'control',
'compile': ['cd saghatelyan', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.control()'],
'cleanup': ['cd ../', 'rm -fr saghatelyan']
},
'50210_2':
{
'variant': 'short dend',
'compile': ['cd saghatelyan', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.rundend()'],
'cleanup': ['cd ../', 'rm -fr saghatelyan']
},
'50210_3':
{
'variant': 'Na shift',
'compile': ['cd saghatelyan', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runshift()'],
'cleanup': ['cd ../', 'rm -fr saghatelyan']
},
'127995':
{
'compile': ['cd migliore2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr migliore2010']
},
'3665':
{
'compile': ['cd h_pg', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr h_pg']
},
'3648':
{
'compile': ['cd ka_kdr_mt', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr ka_kdr_mt']
},
'3342':
{
'compile': ['cd mitral_1999', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr mitral_1999']
},
'2487_1':
{
'variant': 'Stimulate soma with 0.2 uA/cm2',
'compile': ['cd mit4', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_fig6(0)'],
'cleanup': ['cd ../', 'rm -fr mit4']
},
'2487_2':
{
'variant': 'Stimulate soma with 1.6 uA/cm2',
'compile': ['cd mit4', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_fig6(1)'],
'cleanup': ['cd ../', 'rm -fr mit4']
},
'2487_3':
{
'variant': 'Stimulate glomerulus with 0.2 uA/cm2',
'compile': ['cd mit4', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_fig6(2)'],
'cleanup': ['cd ../', 'rm -fr mit4']
},
'2487_4':
{
'variant': 'Stimulate glomerulus with 1.6 uA/cm2',
'compile': ['cd mit4', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_fig6(3)'],
'cleanup': ['cd ../', 'rm -fr mit4']
},
'2733':
{
'compile': ['cd bbmit', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr bbmit']
},
'149415':
{
'compile': ['cd MiglioreMcTavish2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runm()'],
'cleanup': ['cd ../', 'rm -fr MiglioreMcTavish2013']
},
'102288_1':
{
'variant': 'Create Fig 9 A1',
'compile': ['cd RichyandStarfish', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig9A1()'],
'cleanup': ['cd ../', 'rm -fr RichyandStarfish']
},
'102288_2':
{
'variant': 'Create Fig 9 B1',
'compile': ['cd RichyandStarfish', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig9B1()'],
'cleanup': ['cd ../', 'rm -fr RichyandStarfish']
},
'102288_3':
{
'variant': 'Create Fig 9 C1',
'compile': ['cd RichyandStarfish', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig9C1()'],
'cleanup': ['cd ../', 'rm -fr RichyandStarfish']
},
'102288_4':
{
'variant': 'Create Fig 9 A2',
'compile': ['cd RichyandStarfish', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig9A2()'],
'cleanup': ['cd ../', 'rm -fr RichyandStarfish']
},
'102288_5':
{
'variant': 'Create Fig 9 B2',
'compile': ['cd RichyandStarfish', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig9B2()'],
'cleanup': ['cd ../', 'rm -fr RichyandStarfish']
},
'102288_6':
{
'variant': 'Create Fig 9 C2',
'compile': ['cd RichyandStarfish', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig9C2()'],
'cleanup': ['cd ../', 'rm -fr RichyandStarfish']
},
'102288_7':
{
'variant': 'Create Fig 9 A3',
'compile': ['cd RichyandStarfish', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig9A3()'],
'cleanup': ['cd ../', 'rm -fr RichyandStarfish']
},
'102288_8':
{
'variant': 'Create Fig 9 B3',
'compile': ['cd RichyandStarfish', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig9B3()'],
'cleanup': ['cd ../', 'rm -fr RichyandStarfish']
},
'102288_9':
{
'variant': 'Create Fig 9 C3',
'compile': ['cd RichyandStarfish', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig9C3()'],
'cleanup': ['cd ../', 'rm -fr RichyandStarfish']
},
'102288_10':
{
'variant': 'Create all of Fig 9',
'compile': ['cd RichyandStarfish', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig9()'],
'cleanup': ['cd ../', 'rm -fr RichyandStarfish']
},
'146565':
{
'compile': ['cd LavzinEtAl2012', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr LavzinEtAl2012']
},
'112359_1':
{
'variant': 'Control',
'compile': ['cd modeldb-etoh', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.control()'],
'cleanup': ['cd ../', 'rm -fr modeldb-etoh']
},
'112359_2':
{
'variant': '50mM',
'compile': ['cd modeldb-etoh', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.etohh()'],
'cleanup': ['cd ../', 'rm -fr modeldb-etoh']
},
'112359_3':
{
'variant': '100mM',
'compile': ['cd modeldb-etoh', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.etoh()'],
'cleanup': ['cd ../', 'rm -fr modeldb-etoh']
},
'145672_1':
{
'variant': 'Figure11C CSI',
'compile': ['cd Fineberg_et_al_2012', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("Figure11C CSI.hoc")', 'h.runu()'],
'cleanup': ['cd ../', 'rm -fr Fineberg_et_al_2012']
},
'145672_2':
{
'variant': 'Figure11D',
'compile': ['cd Fineberg_et_al_2012', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Fineberg_et_al_2012']
},
'145672_3':
{
'variant': 'Figure11E',
'compile': ['cd Fineberg_et_al_2012', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Fineberg_et_al_2012']
},
'145672_4':
{
'variant': 'Figure11C CSI+OSI',
'compile': ['cd Fineberg_et_al_2012', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("Figure11C CSIOSI.hoc")', 'h.runu()'],
'cleanup': ['cd ../', 'rm -fr Fineberg_et_al_2012']
},
'148644':
{
'compile': ['cd ParekhAscoli2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runm()'],
'cleanup': ['cd ../', 'rm -fr ParekhAscoli2013']
},
'83319_1':
{
'variant': 'CobaHH',
'compile': ['cd destexhe_benchmarks/NEURON', 'nrnivmodl coba cuba cubadv'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.mosinvl = 10', 'h.launch("cobahh", h.intrin)'],
'cleanup': ['cd ../../', 'rm -fr destexhe_benchmarks']
},
'83319_2':
{
'variant': 'Coba',
'compile': ['cd destexhe_benchmarks/NEURON', 'nrnivmodl coba cuba cubadv'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.mosinvl = 10', 'h.launch("coba", h.intrin)'],
'cleanup': ['cd ../../', 'rm -fr destexhe_benchmarks']
},
# '83319_3':
# {
# 'variant': 'Cuba',
# 'compile': ['cd destexhe_benchmarks/NEURON', 'nrnivmodl coba cuba cubadv'],
# 'launch': ['nrngui -python'],
# 'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.launch("cuba", h.intrin)'],
# 'cleanup': ['cd ../../', 'rm -fr destexhe_benchmarks']
# },
# '83319_4':
# {
# 'variant': 'CubaDV',
# 'compile': ['cd destexhe_benchmarks/NEURON', 'nrnivmodl coba cuba cubadv'],
# 'launch': ['nrngui -python'],
# 'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.launch("cubadv", h.intrin)'],
# 'cleanup': ['cd ../../', 'rm -fr destexhe_benchmarks']
# },
'10360':
{
'variant': 'Init & Run',
'compile': ['cd lindgren89', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr lindgren89']
},
'82849':
{
'compile': ['cd pcell', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("fig2A.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr pcell']
},
'3660':
{
'compile': ['cd ka_kdr_neoLI', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr ka_kdr_neoLI']
},
'114394':
{
'compile': ['cd NN_kole', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr NN_kole']
},
'7988_1':
{
'variant': 'NR2A',
'compile': ['cd murphy01', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.nrn2a_model()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr murphy01']
},
'7988_2':
{
'variant': 'NR2B',
'compile': ['cd murphy01', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.nrn2b_model()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr murphy01']
},
'126640':
{
'compile': ['cd withdrawal', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr withdrawal']
},
'116835':
{
'compile': ['cd GrC', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr GrC']
},
'7659_1':
{
'variant': 'S1 and S2 prox (black)',
'compile': ['cd window', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runp()'],
'cleanup': ['cd ../', 'rm -fr window']
},
'7659_2':
{
'variant': 'S1 prox, S2 dist (red)',
'compile': ['cd window', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runm()'],
'cleanup': ['cd ../', 'rm -fr window']
},
'7659_3':
{
'variant': 'S1 and S2 dist (blue)',
'compile': ['cd window', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.rund()'],
'cleanup': ['cd ../', 'rm -fr window']
},
'7659_4':
{
'variant': 'S1 prox, S2 dist, + Ih (green)',
'compile': ['cd window', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.rundh()'],
'cleanup': ['cd ../', 'rm -fr window']
},
# '144589':
# {
# 'compile': ['cd BerzThetaGamm2013', 'nrnivmodl'],
# 'launch': ['nrngui -python'],
# 'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file(1,"netwOPb.hoc")', 'h.xfield()', 'h.run()'],
# 'cleanup': ['cd ../', 'rm -fr BerzThetaGamm2013']
# },
'85112':
{
'compile': ['cd baker05', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.xopen("fig8.hoc")'],
'cleanup': ['cd ../', 'rm -fr baker05']
},
'119266':
{
'compile': ['cd CA1_Aged', 'nrnivmodl mechanism'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CA1_Aged']
},
'136310':
{
'variant': '=> 1. Calculate impedances',
'compile': ['cd LFP', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.calc_filter()', 'h.draw_filter()', 'h.runfft()', 'h.draw_fft()', 'h.calc_extracellular()', 'h.draw_extracellular()'],
'cleanup': ['cd ../', 'rm -fr LFP']
},
'122329_1':
{
'variant': 'with SK soma',
'compile': ['cd GPSingleCompartment', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("withSKsoma.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr GPSingleCompartment']
},
'122329_2':
{
'variant': 'no SK soma',
'compile': ['cd GPSingleCompartment', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("noSKsoma.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr GPSingleCompartment']
},
'6763':
{
'variant': 'Init & Run',
'compile': ['cd canavier1999', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr canavier1999']
},
'120798_1':
{
'variant': 'Fig. 5B',
'compile': ['cd PalmerStuart2009', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig5b()'],
'cleanup': ['cd ../', 'rm -fr PalmerStuart2009']
},
'120798_2':
{
'variant': 'Fig. 5',
'compile': ['cd PalmerStuart2009', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig5cd()'],
'cleanup': ['cd ../', 'rm -fr PalmerStuart2009']
},
'120798_3':
{
'variant': 'Suppl. Fig. 2 c',
'compile': ['cd PalmerStuart2009', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.suppl_fig2c()'],
'cleanup': ['cd ../', 'rm -fr PalmerStuart2009']
},
'138321':
{
'compile': ['cd pashut2011', 'nrnivmodl OneDimension/Neuron'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr pashut2011']
},
'20756_1':
{
'variant': 'Figure 2 ( left )',
'compile': ['cd Traub2003', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.pyr3_ = h.pyr3( 21 )', 'h.setFig2()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Traub2003']
},
'20756_2':
{
'variant': 'Figure 2 ( right )',
'compile': ['cd Traub2003', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.pyr3_ = h.pyr3( 22 )', 'h.setFig2()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Traub2003']
},
'20756_3':
{
'variant': 'Figure 4 Injection 2.5 nA',
'compile': ['cd Traub2003', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.pyr3_ = h.pyr3( 41 )', 'h.setFig4()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Traub2003']
},
'20756_4':
{
'variant': 'Figure 4 Injection 1.5 nA',
'compile': ['cd Traub2003', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.pyr3_ = h.pyr3( 42 )', 'h.setFig4()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Traub2003']
},
'20756_5':
{
'variant': 'Figure 4 Injection 1.1 nA',
'compile': ['cd Traub2003', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.pyr3_ = h.pyr3( 43 )', 'h.setFig4()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Traub2003']
},
'20756_6':
{
'variant': 'Figure 4 Injection 0.6 nA',
'compile': ['cd Traub2003', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.pyr3_ = h.pyr3( 44 )', 'h.setFig4()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Traub2003']
},
'20756_7':
{
'variant': 'Figure 5 B1',
'compile': ['cd Traub2003', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.pyr3_ = h.pyr3( 51 )', 'h.setFig5()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Traub2003']
},
'20756_8':
{
'variant': 'Figure 5 B2',
'compile': ['cd Traub2003', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.pyr3_ = h.pyr3( 52 )', 'h.setFig5()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Traub2003']
},
'20756_9':
{
'variant': 'Figure 6 B1',
'compile': ['cd Traub2003', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.pyr3_ = h.pyr3( 61 )', 'h.setFig6()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Traub2003']
},
'20756_10':
{
'variant': 'Figure 6 B2',
'compile': ['cd Traub2003', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.pyr3_ = h.pyr3( 62 )', 'h.setFig6()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Traub2003']
},
'20756_11':
{
'variant': 'Figure 7 g_NaP x 0.0',
'compile': ['cd Traub2003', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.pyr3_ = h.pyr3( 71 )', 'h.setFig7()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Traub2003']
},
'20756_12':
{
'variant': 'Figure 7 g_NaP x 0.7',
'compile': ['cd Traub2003', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.pyr3_ = h.pyr3( 72 )', 'h.setFig7()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Traub2003']
},
'20756_13':
{
'variant': 'Figure 7 g_NaP x 1.0',
'compile': ['cd Traub2003', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.pyr3_ = h.pyr3( 73 )', 'h.setFig7()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Traub2003']
},
'128559':
{
'compile': ['cd WDR-Model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr WDR-Model']
},
'93398_1':
{
'variant': 'Original GA settings',
'compile': ['cd StiefelSejnowskiCode', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("GA")'],
'cleanup': ['cd ../', 'rm -fr StiefelSejnowskiCode']
},
'93398_2':
{
'variant': 'Short run test',
'compile': ['cd StiefelSejnowskiCode', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("shortRun")'],
'cleanup': ['cd ../', 'rm -fr StiefelSejnowskiCode']
},
'97863':
{
'compile': ['cd beelerReuter', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr beelerReuter']
},
'3454_1':
{
'variant': '100 hz',
'compile': ['cd kv31model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.NetStim[0].interval=10', 'h.run(10)'],
'cleanup': ['cd ../', 'rm -fr kv31model']
},
'3454_2':
{
'variant': '200 hz',
'compile': ['cd kv31model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.NetStim[0].interval=5', 'h.run(5)'],
'cleanup': ['cd ../', 'rm -fr kv31model']
},
'3454_3':
{
'variant': '300 hz',
'compile': ['cd kv31model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.NetStim[0].interval=3.3', 'h.run(3.3)'],
'cleanup': ['cd ../', 'rm -fr kv31model']
},
'3454_4':
{
'variant': '400 hz',
'compile': ['cd kv31model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.NetStim[0].interval=2.5', 'h.run(2.5)'],
'cleanup': ['cd ../', 'rm -fr kv31model']
},
'113732_1':
{
'variant': 'Wiring configuration for the supra-threshold evoked response',
'compile': ['cd SS-cortex', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.suprathresh()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr SS-cortex']
},
'113732_2':
{
'variant': 'Wiring configuration for the non-perceived evoked response',
'compile': ['cd SS-cortex', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.nonperceived()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr SS-cortex']
},
'113732_3':
{
'variant': 'Wiring configuration for the perceived evoked response',
'compile': ['cd SS-cortex', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.perceived()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr SS-cortex']
},
'150239':
{
'compile': ['cd grid', 'nrnivmodl nrn/mod'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr grid']
},
'279_1':
{
'variant': 'Burst behavior in single-compartment model',
'compile': ['cd dendtc', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("tc1_cc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr dendtc']
},
'279_2':
{
'variant': 'Burst behavior in 3-compartment model',
'compile': ['cd dendtc', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("tc3_cc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr dendtc']
},
'279_3':
{
'variant': 'Burst behavior in detailed cell model',
'compile': ['cd dendtc', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("tc200_cc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr dendtc']
},
'279_4':
{
'variant': 'Voltage-clamp in detailed cell model',
'compile': ['cd dendtc', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("tc200_vc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr dendtc']
},
'279_5':
{
'variant': 'Voltage-clamp in dissociated cell model',
'compile': ['cd dendtc', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("tcD_vc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr dendtc']
},
'3807':
{
'compile': ['cd baccus98', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig6()'],
'cleanup': ['cd ../', 'rm -fr baccus98']
},
'64261':
{
'compile': ['cd bfstdp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr bfstdp']
},
'144089':
{
'compile': ['cd PFCcell', 'nrnivmodl mechanism'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_sim()'],
'cleanup': ['cd ../', 'rm -fr PFCcell']
},
'139653_1':
{
'variant': 'Fig 4A. (BAC_firing.hoc)',
'compile': ['cd L5bPCmodelsEH', 'nrnivmodl mod'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("BAC_firing")'],
'cleanup': ['cd ../', 'rm -fr L5bPCmodelsEH']
},
'139653_2':
{
'variant': 'Fig 4B. Upper trace. (Step_current_firing.hoc)',
'compile': ['cd L5bPCmodelsEH', 'nrnivmodl mod'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("Step_current_firing")'],
'cleanup': ['cd ../', 'rm -fr L5bPCmodelsEH']
},
'139653_3':
{
'variant': 'Fig 5A. (critical_frequency.hoc)',
'compile': ['cd L5bPCmodelsEH', 'nrnivmodl mod'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("critical_frequency")'],
'cleanup': ['cd ../', 'rm -fr L5bPCmodelsEH']
},
'150538':
{
'compile': ['cd XiEtal2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.circ_run()'],
'cleanup': ['cd ../', 'rm -fr XiEtal2013']
},
'50207':
{
'compile': ['cd NMDA_Mg', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr NMDA_Mg']
},
'106891':
{
'compile': ['cd b07dec27_20091025', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runeg()'],
'cleanup': ['cd ../', 'rm -fr b07dec27_20091025']
},
'82784':
{
'compile': ['cd DynBasIrregSpNMDA', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("runThis.hoc")'],
'cleanup': ['cd ../', 'rm -fr DynBasIrregSpNMDA']
},
'151825':
{
'compile': ['cd Demo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Demo']
},
'97756':
{
'compile': ['cd Ga_demo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.xopen("ga_run.hoc")'],
'cleanup': ['cd ../', 'rm -fr Ga_demo']
},
'135787_1':
{
'variant': 'spike initialization',
'compile': ['cd ShuEtAl20062007', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("best_full_axon_spike_init.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr ShuEtAl20062007']
},
'135787_2':
{
'variant': 'axon potential decay',
'compile': ['cd ShuEtAl20062007', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("best_full_axon_decay.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr ShuEtAl20062007']
},
'83590':
{
'compile': ['cd Arsiero_et_al2007', 'nrnivmodl mechanisms'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr Arsiero_et_al2007']
},
'139150':
{
'compile': ['cd Poleg-PolskyDiamond2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.visrun()'],
'cleanup': ['cd ../', 'rm -fr Poleg-PolskyDiamond2011']
},
'94321':
{
'compile': ['cd chain_1d', 'nrnivmodl mechanisms'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.execute_simulation()'],
'cleanup': ['cd ../', 'rm -fr chain_1d']
},
'147867_1':
{
'variant': '0% Atrophy',
'compile': ['cd CA3Atrophy', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.proc_load(1)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CA3Atrophy']
},
'147867_2':
{
'variant': '25% Atrophy',
'compile': ['cd CA3Atrophy', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.proc_load(2)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CA3Atrophy']
},
'147867_3':
{
'variant': '35% Atrophy',
'compile': ['cd CA3Atrophy', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.proc_load(3)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CA3Atrophy']
},
'147867_4':
{
'variant': '75% Atrophy',
'compile': ['cd CA3Atrophy', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.proc_load(4)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CA3Atrophy']
},
'82364_1':
{
'variant': 'regular - 20 Hz',
'compile': ['cd Welie-Wadman-JPhysiol-subiculum', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.reg_20()'],
'cleanup': ['cd ../', 'rm -fr Welie-Wadman-JPhysiol-subiculum']
},
'82364_2':
{
'variant': 'regular - 50 Hz',
'compile': ['cd Welie-Wadman-JPhysiol-subiculum', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.reg_50()'],
'cleanup': ['cd ../', 'rm -fr Welie-Wadman-JPhysiol-subiculum']
},
'82364_3':
{
'variant': 'burster - 20 Hz',
'compile': ['cd Welie-Wadman-JPhysiol-subiculum', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.burst_20()'],
'cleanup': ['cd ../', 'rm -fr Welie-Wadman-JPhysiol-subiculum']
},
'82364_4':
{
'variant': 'burster - 50 Hz',
'compile': ['cd Welie-Wadman-JPhysiol-subiculum', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.burst_50()'],
'cleanup': ['cd ../', 'rm -fr Welie-Wadman-JPhysiol-subiculum']
},
'2798_1':
{
'variant': 'before training',
'compile': ['cd HB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_u()'],
'cleanup': ['cd ../', 'rm -fr HB']
},
'2798_2':
{
'variant': 'after training',
'compile': ['cd HB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_c()'],
'cleanup': ['cd ../', 'rm -fr HB']
},
'2798_3':
{
'variant': 'random activation',
'compile': ['cd HB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_r()'],
'cleanup': ['cd ../', 'rm -fr HB']
},
'114735':
{
'compile': ['cd HFO', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr HFO']
},
'115357_1':
{
'variant': '++',
'compile': ['cd GeneralizedCarnevaleHinesScheme', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.makeplusplus()'],
'cleanup': ['cd ../', 'rm -fr GeneralizedCarnevaleHinesScheme']
},
'115357_2':
{
'variant': '+-',
'compile': ['cd GeneralizedCarnevaleHinesScheme', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.makeplusminus()'],
'cleanup': ['cd ../', 'rm -fr GeneralizedCarnevaleHinesScheme']
},
'115357_3':
{
'variant': '-+',
'compile': ['cd GeneralizedCarnevaleHinesScheme', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.makeminusplus()'],
'cleanup': ['cd ../', 'rm -fr GeneralizedCarnevaleHinesScheme']
},
'115357_4':
{
'variant': '--',
'compile': ['cd GeneralizedCarnevaleHinesScheme', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.makeminusminus()'],
'cleanup': ['cd ../', 'rm -fr GeneralizedCarnevaleHinesScheme']
},
'26997_1':
{
'variant': 'Fig 1A',
'compile': ['cd wang1996', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig1a()'],
'cleanup': ['cd ../', 'rm -fr wang1996']
},
'26997_2':
{
'variant': 'Fig 3A',
'compile': ['cd wang1996', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig3a()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr wang1996']
},
'21329':
{
'compile': ['cd inhibnet', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr inhibnet']
},
'114685_1':
{
'variant': 'Short test run of the GPi neuron similar to Fig 1A',
'compile': ['cd JohnsonMcIntyre2008', 'nrnivmodl GPi_model'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.short_run()'],
'cleanup': ['cd ../', 'rm -fr JohnsonMcIntyre2008']
},
'114685_2':
{
'variant': 'Sample run for the current injections that created Fig 2C',
'compile': ['cd JohnsonMcIntyre2008', 'nrnivmodl GPi_model'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig2c_point()'],
'cleanup': ['cd ../', 'rm -fr JohnsonMcIntyre2008']
},
'146509':
{
'compile': ['cd Branch_Point_Tapering', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_simulation()'],
'cleanup': ['cd ../', 'rm -fr Branch_Point_Tapering']
},
'139654_1':
{
'variant': 'Phasic model T8 step',
'compile': ['cd 2VN', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("stim_type = 1")', 'h("amp = 1")', 'h("cell_type = 1")', 'h("cell_nr = 8")', 'h.restart()', 'h.load_file(1, "control.hoc")'],
'cleanup': ['cd ../', 'rm -fr 2VN']
},
'139654_2':
{
'variant': 'Phasic model T8 ZAP',
'compile': ['cd 2VN', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("stim_type = 2")', 'h("amp = 1")', 'h("cell_type = 1")', 'h("cell_nr = 8")', 'h.restart()', 'h.load_file(1, "control.hoc")'],
'cleanup': ['cd ../', 'rm -fr 2VN']
},
'139654_3':
{
'variant': 'Tonic model T1 step',
'compile': ['cd 2VN', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("stim_type = 1")', 'h("amp = 0.6")', 'h("cell_type = 2")', 'h("cell_nr = 1")', 'h.restart()', 'h.load_file(1, "control.hoc")'],
'cleanup': ['cd ../', 'rm -fr 2VN']
},
'139654_4':
{
'variant': 'Tonic model T1 ZAP',
'compile': ['cd 2VN', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("stim_type = 2")', 'h("amp = 0.5")', 'h("cell_type = 2")', 'h("cell_nr = 1")', 'h.restart()', 'h.load_file(1, "control.hoc")'],
'cleanup': ['cd ../', 'rm -fr 2VN']
},
'139654_5':
{
'variant': 'Synaptic train stimulation, with inhibition',
'compile': ['cd 2VN', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("ton_inhib = 1")', 'h("cell_nr = 7")', 'h.restart()', 'h.load_file(1, "traincontrol.hoc")'],
'cleanup': ['cd ../', 'rm -fr 2VN']
},
'139654_6':
{
'variant': 'Synaptic train stimulation, no inhibition',
'compile': ['cd 2VN', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("ton_inhib = 0")', 'h("cell_nr = 7")', 'h.restart()', 'h.load_file(1, "traincontrol.hoc")'],
'cleanup': ['cd ../', 'rm -fr 2VN']
},
'140299_1':
{
'variant': 'BE17BNoActive',
'compile': ['cd KubotaEtAl2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.loadModel("BE17B_length_adjusted_NoActive.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr KubotaEtAl2011']
},
'140299_2':
{
'variant': 'BE59DNoActive',
'compile': ['cd KubotaEtAl2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.loadModel("BE59D_length_adjusted_NoActive.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr KubotaEtAl2011']
},
'140299_3':
{
'variant': 'BE77CNoActive',
'compile': ['cd KubotaEtAl2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.loadModel("BE77C_length_adjusted_NoActive.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr KubotaEtAl2011']
},
'140299_4':
{
'variant': 'LV38ENoActive',
'compile': ['cd KubotaEtAl2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.loadModel("LV38E_length_adjusted_NoActive.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr KubotaEtAl2011']
},
'116956':
{
'compile': ['cd vs4_modelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig10e()'],
'cleanup': ['cd ../', 'rm -fr vs4_modelDB']
},
'8115':
{
'compile': ['cd fluct', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr fluct']
},
'113435':
{
'compile': ['cd fs_internrn_neuron', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr fs_internrn_neuron']
},
'8284_1':
{
'variant': 'HT',
'compile': ['cd ihmodel', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.HT()'],
'cleanup': ['cd ../', 'rm -fr ihmodel']
},
'8284_2':
{
'variant': 'Control',
'compile': ['cd ihmodel', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Control()'],
'cleanup': ['cd ../', 'rm -fr ihmodel']
},
'19022':
{
'compile': ['cd geigerEtAl1997', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("fig8d.hoc")'],
'cleanup': ['cd ../', 'rm -fr geigerEtAl1997']
},
'3167':
{
'compile': ['cd timing', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runu()'],
'cleanup': ['cd ../', 'rm -fr timing']
},
'3676_1':
{
'variant': 'Fig 2',
'compile': ['cd ephaptic', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.xopen("fig2.hoc")'],
'cleanup': ['cd ../', 'rm -fr ephaptic']
},
'3676_2':
{
'variant': 'Fig 3B',
'compile': ['cd ephaptic', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.xopen("fig3.hoc")'],
'cleanup': ['cd ../', 'rm -fr ephaptic']
},
'123815':
{
'compile': ['cd Hipp_paper_code', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Hipp_paper_code']
},
'120910':
{
'compile': ['cd ElectricallycoupledRetziusneurons', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr ElectricallycoupledRetziusneurons']
},
'116981_1':
{
'variant': 'Fig. 5--exc central vs. peripheral tree',
'compile': ['cd rall1964', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig5()'],
'cleanup': ['cd ../', 'rm -fr rall1964']
},
'116981_2':
{
'variant': 'Fig. 5 inset--brief excitation',
'compile': ['cd rall1964', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig5inset()'],
'cleanup': ['cd ../', 'rm -fr rall1964']
},
'116981_3':
{
'variant': 'Fig. 6--effect of location of excitatory input',
'compile': ['cd rall1964', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig6()'],
'cleanup': ['cd ../', 'rm -fr rall1964']
},
'116981_4':
{
'variant': 'Fig. 7--effect of activation sequence',
'compile': ['cd rall1964', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig7()'],
'cleanup': ['cd ../', 'rm -fr rall1964']
},
'116981_5':
{
'variant': 'Fig. 8--effect of inh location',
'compile': ['cd rall1964', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig8()'],
'cleanup': ['cd ../', 'rm -fr rall1964']
},
'151126':
{
'compile': ['cd BianchiEtAl2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr BianchiEtAl2013']
},
'121060':
{
'compile': ['cd MSN2009', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Exec()'],
'cleanup': ['cd ../', 'rm -fr MSN2009']
},
'148253':
{
'compile': ['cd Chloride_Model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Chloride_Model']
},
'123453':
{
'compile': ['cd AkemannEtAl2009', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run_model( prot )")'],
'cleanup': ['cd ../', 'rm -fr AkemannEtAl2009']
},
'64296_1':
{
'variant': 'Figure 2A Top Trace',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig2Atop()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_2':
{
'variant': 'Figure 2A Middle Trace',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig2Amiddle()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_3':
{
'variant': 'Figure 2A Bottom Trace',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig2Abottom()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_4':
{
'variant': 'Figure 2B Top Trace',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig2Btop()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_5':
{
'variant': 'Figure 2B Second Trace',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig2Bsecond()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_6':
{
'variant': 'Figure 2B Third Trace',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig2Bthird()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_7':
{
'variant': 'Figure 2B Bottom Trace',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig2Bbottom()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_8':
{
'variant': 'Figure 3A',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig3A()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_9':
{
'variant': 'Figure 3B',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig3B()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_10':
{
'variant': 'Figure 3C Top',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig3Ctop()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_11':
{
'variant': 'Figure 3C Bottom',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig3Cbottom()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_12':
{
'variant': 'Figure 4A',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig4A()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_13':
{
'variant': 'Figure 5B',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig5B()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_14':
{
'variant': 'Figure 6A',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig6A()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_15':
{
'variant': 'Figure 6B',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig6B()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_16':
{
'variant': 'Figure 6C',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig6C()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_17':
{
'variant': 'Figure 6D',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig6D()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_18':
{
'variant': 'Figure 6E',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig6E()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_19':
{
'variant': 'Figure 7A',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig7A()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_20':
{
'variant': 'Figure 7B',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig7B()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_21':
{
'variant': 'Figure 8A',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig8A()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_22':
{
'variant': 'Figure 8B',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig8B()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'64296_23':
{
'variant': 'Figure 8C',
'compile': ['cd mitral', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig8C()")'],
'cleanup': ['cd ../', 'rm -fr mitral']
},
'118662_1':
{
'variant': 'Figure 4a cell 1',
'compile': ['cd dm1_pn_model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("restart_(\\"figure_4a_cell1\\")")'],
'cleanup': ['cd ../', 'rm -fr dm1_pn_model']
},
'118662_2':
{
'variant': 'Figure 4a cell 2',
'compile': ['cd dm1_pn_model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("restart_(\\"figure_4a_cell2\\")")'],
'cleanup': ['cd ../', 'rm -fr dm1_pn_model']
},
'118662_3':
{
'variant': 'Figure 4a cell 3',
'compile': ['cd dm1_pn_model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("restart_(\\"figure_4a_cell3\\")")'],
'cleanup': ['cd ../', 'rm -fr dm1_pn_model']
},
'118662_4':
{
'variant': 'Figure 4b dendrite 1',
'compile': ['cd dm1_pn_model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("restart_(\\"figure_4b_dendrite1\\")")'],
'cleanup': ['cd ../', 'rm -fr dm1_pn_model']
},
'118662_5':
{
'variant': 'Figure 4b dendrite 2',
'compile': ['cd dm1_pn_model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("restart_(\\"figure_4b_dendrite2\\")")'],
'cleanup': ['cd ../', 'rm -fr dm1_pn_model']
},
'118662_6':
{
'variant': 'Figure 4b dendrite 3',
'compile': ['cd dm1_pn_model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("restart_(\\"figure_4b_dendrite3\\")")'],
'cleanup': ['cd ../', 'rm -fr dm1_pn_model']
},
'51022':
{
'compile': ['cd amirdevor03', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr amirdevor03']
},
'140789':
{
'compile': ['cd DG_BC/Figure_2', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../../', 'rm -fr DG_BC']
},
'116740_1':
{
'variant': 'T-Ca',
'compile': ['cd aradi1999', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("control()")'],
'cleanup': ['cd ../', 'rm -fr aradi1999']
},
'116740_2':
{
'variant': 'T-Ca and BK',
'compile': ['cd aradi1999', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("bk()")'],
'cleanup': ['cd ../', 'rm -fr aradi1999']
},
'116740_3':
{
'variant': 'T-Ca and SK',
'compile': ['cd aradi1999', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("sk()")'],
'cleanup': ['cd ../', 'rm -fr aradi1999']
},
'124291':
{
'compile': ['cd FFI/MOPP_Fig_1B_left', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runa()")'],
'cleanup': ['cd ../../', 'rm -fr FFI']
},
'3801_1':
{
'variant': 'All three synaptic terminals are active',
'compile': ['cd dgbc', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doit(3)")'],
'cleanup': ['cd ../', 'rm -fr dgbc']
},
'3801_2':
{
'variant': 'synapse 0 only',
'compile': ['cd dgbc', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doit(0)")'],
'cleanup': ['cd ../', 'rm -fr dgbc']
},
'3801_3':
{
'variant': 'synapse 1 only',
'compile': ['cd dgbc', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doit(1)")'],
'cleanup': ['cd ../', 'rm -fr dgbc']
},
'3801_4':
{
'variant': 'synapse 2 only',
'compile': ['cd dgbc', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("doit(2)")'],
'cleanup': ['cd ../', 'rm -fr dgbc']
},
'144385':
{
'compile': ['cd ShepherdBrayton1979', 'nrnivmodl mod'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr ShepherdBrayton1979']
},
'18738':
{
'compile': ['cd dendgeom', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr dendgeom']
},
'147218':
{
'compile': ['cd genet_PC', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr genet_PC']
},
'124394':
{
'compile': ['cd nevian', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr nevian']
},
'140828':
{
'compile': ['cd Branco_2010', 'nrnivmodl mod.files'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr Branco_2010']
},
'151949':
{
'compile': ['cd SousaEtAl2014', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr SousaEtAl2014']
},
'3344':
{
'compile': ['cd ka_dg', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr ka_dg']
},
'98005':
{
'compile': ['cd D2modulation', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr D2modulation']
},
'9853':
{
'compile': ['cd joyner80', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr joyner80']
},
'52034':
{
'compile': ['cd ctxnet', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run_fig6()")'],
'cleanup': ['cd ../', 'rm -fr ctxnet']
},
'138382_1':
{
'variant': 'Detailed Calcium dynamics model',
'compile': ['cd AnwarEtAl2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("restart(\\"runDM\\")")'],
'cleanup': ['cd ../', 'rm -fr AnwarEtAl2010']
},
'138382_2':
{
'variant': 'Calcium transients using different buffering models',
'compile': ['cd AnwarEtAl2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("restart(\\"runCaTransients\\")")'],
'cleanup': ['cd ../', 'rm -fr AnwarEtAl2010']
},
'138382_3':
{
'variant': 'Calcium spikes using single pool model',
'compile': ['cd AnwarEtAl2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("restart(\\"runCaSpikesSP\\")")'],
'cleanup': ['cd ../', 'rm -fr AnwarEtAl2010']
},
'138382_4':
{
'variant': 'Calcium spikes using double pool model',
'compile': ['cd AnwarEtAl2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("restart(\\"runCaSpikesDP\\")")'],
'cleanup': ['cd ../', 'rm -fr AnwarEtAl2010']
},
'138382_5':
{
'variant': 'Calcium spikes using detailed model',
'compile': ['cd AnwarEtAl2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("restart(\\"runCaSpikesDM\\")")'],
'cleanup': ['cd ../', 'rm -fr AnwarEtAl2010']
},
'138382_6':
{
'variant': 'Calcium spikes using DCM',
'compile': ['cd AnwarEtAl2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("restart(\\"runCaSpikesDCM\\")")'],
'cleanup': ['cd ../', 'rm -fr AnwarEtAl2010']
},
'114637':
{
'compile': ['cd SSC_model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr SSC_model']
},
'9851':
{
'compile': ['cd moore78', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr moore78']
},
'19366_1':
{
'variant': 'Fig.1. A-C',
'compile': ['cd korogod', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Main(1)")'],
'cleanup': ['cd ../', 'rm -fr korogod']
},
'19366_2':
{
'variant': 'Fig.2. A',
'compile': ['cd korogod', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Main(2)")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr korogod']
},
'19366_3':
{
'variant': 'Fig.2. B',
'compile': ['cd korogod', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Main(3)")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr korogod']
},
'19366_4':
{
'variant': 'Fig.3. A-D',
'compile': ['cd korogod', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Main(4)")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr korogod']
},
'19366_5':
{
'variant': 'Fig.3. E-H',
'compile': ['cd korogod', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Main(5)")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr korogod']
},
'119283_1':
{
'variant': '(1-4) Gray - Control',
'compile': ['cd FerranteEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runi()")'],
'cleanup': ['cd ../', 'rm -fr FerranteEtAl2008']
},
'119283_2':
{
'variant': '(1) Black - Lamotrigine',
'compile': ['cd FerranteEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runii()")'],
'cleanup': ['cd ../', 'rm -fr FerranteEtAl2008']
},
'119283_3':
{
'variant': '(2) Black - Diazepam',
'compile': ['cd FerranteEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runiii()")'],
'cleanup': ['cd ../', 'rm -fr FerranteEtAl2008']
},
'119283_4':
{
'variant': '(3) Black - Flindokalner',
'compile': ['cd FerranteEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runiv()")'],
'cleanup': ['cd ../', 'rm -fr FerranteEtAl2008']
},
'119283_5':
{
'variant': '(4) Black - Lamotrigine+Flindokalner',
'compile': ['cd FerranteEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runv()")'],
'cleanup': ['cd ../', 'rm -fr FerranteEtAl2008']
},
'123927':
{
'compile': ['cd Wimmer-et-al2009', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run_sim_graph_coarse()")'],
'cleanup': ['cd ../', 'rm -fr Wimmer-et-al2009']
},
'143604_1':
{
'variant': 'spine inhibiton with bAP (compartmentalized inhibition)',
'compile': ['cd singleDendrite', 'nrnivmodl mod'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("spineinhib_bAP_demo()")'],
'cleanup': ['cd ../', 'rm -fr singleDendrite']
},
'143604_2':
{
'variant': '10x dend inhib with bAP (widespread inhib with smaller change in amplitude)',
'compile': ['cd singleDendrite', 'nrnivmodl mod'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("dend10x_bAP_demo()")'],
'cleanup': ['cd ../', 'rm -fr singleDendrite']
},
'93326':
{
'compile': ['cd ngetting', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr ngetting']
},
'3434':
{
'compile': ['cd cdlab', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr cdlab']
},
'64212':
{
'compile': ['cd VNO', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr VNO']
},
'147578_1':
{
'variant': 'Compute Input Resistances Along Trunk',
'compile': ['cd MultiChirp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("RN_Trunk()")'],
'cleanup': ['cd ../', 'rm -fr MultiChirp']
},
'147578_2':
{
'variant': 'Save Local Chirp Responses for Locations Along Trunk',
'compile': ['cd MultiChirp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Chirp_Trunk()")'],
'cleanup': ['cd ../', 'rm -fr MultiChirp']
},
'80769_1':
{
'variant': 'Off On Off original protocol',
'compile': ['cd AkemannKnopfelPurkinje_cell_model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("restart(\\"OFF_ON_OFF_protocol\\")")'],
'cleanup': ['cd ../', 'rm -fr AkemannKnopfelPurkinje_cell_model']
},
'80769_2':
{
'variant': 'Short demo run simulation',
'compile': ['cd AkemannKnopfelPurkinje_cell_model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("restart(\\"shortRun\\")")'],
'cleanup': ['cd ../', 'rm -fr AkemannKnopfelPurkinje_cell_model']
},
'17664':
{
'compile': ['cd prknj', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr prknj']
},
'48332':
{
'compile': ['cd purkinje', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr purkinje']
},
'112685':
{
'compile': ['cd Golgi_cell', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Golgi_cell']
},
'126467':
{
'compile': ['cd NegroniLascano', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr NegroniLascano']
},
'144520':
{
'compile': ['cd DiFrancescoNoble1985', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr DiFrancescoNoble1985']
},
'3800':
{
'compile': ['cd cardiac1998', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr cardiac1998']
},
'125745':
{
'compile': ['cd fink2000', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr fink2000']
},
'150551_1':
{
'variant': 'Figure 4F-G',
'compile': ['cd AshhadNarayanan2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("{ load_file(\\"Fig4F-G.hoc\\") }")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr AshhadNarayanan2013']
},
'150551_2':
{
'variant': 'Figure 6C-F',
'compile': ['cd AshhadNarayanan2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("{ load_file(\\"Fig6C-F.hoc\\") }")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr AshhadNarayanan2013']
},
'108458':
{
'compile': ['cd KampaStuart2006', 'nrnivmodl mod'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr KampaStuart2006']
},
'151458':
{
'compile': ['cd Nakano_FICN_model', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr Nakano_FICN_model']
},
'140462':
{
'compile': ['cd MasurkarChen2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig7c()'],
'cleanup': ['cd ../', 'rm -fr MasurkarChen2011']
},
'118098':
{
'compile': ['cd ca3-summ', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runl()")'],
'cleanup': ['cd ../', 'rm -fr ca3-summ']
},
'76879_1':
{
'variant': 'No drive (slow)',
'compile': ['cd WC', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run1(1)")'],
'cleanup': ['cd ../', 'rm -fr WC']
},
'76879_2':
{
'variant': 'Driven (slow)',
'compile': ['cd WC', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run1(2)")'],
'cleanup': ['cd ../', 'rm -fr WC']
},
'76879_3':
{
'variant': 'As set (slow)',
'compile': ['cd WC', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run1(3)")'],
'cleanup': ['cd ../', 'rm -fr WC']
},
'76879_4':
{
'variant': 'No drive (fast)',
'compile': ['cd WC', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run1(4)")'],
'cleanup': ['cd ../', 'rm -fr WC']
},
'76879_5':
{
'variant': 'Driven (fast)',
'compile': ['cd WC', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run1(5)")'],
'cleanup': ['cd ../', 'rm -fr WC']
},
'76879_6':
{
'variant': 'As set (fast)',
'compile': ['cd WC', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run1(6)")'],
'cleanup': ['cd ../', 'rm -fr WC']
},
'3509_1':
{
'variant': 'rate',
'compile': ['cd kca', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("prate()")'],
'cleanup': ['cd ../', 'rm -fr kca']
},
'3509_2':
{
'variant': 'steady state current',
'compile': ['cd kca', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("pcur2()")'],
'cleanup': ['cd ../', 'rm -fr kca']
},
'3509_3':
{
'variant': 'voltage clamp',
'compile': ['cd kca', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("pvc()")'],
'cleanup': ['cd ../', 'rm -fr kca']
},
'3332':
{
'compile': ['cd h_cno', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr h_cno']
},
'101629_1':
{
'variant': 'Fig.9B',
'compile': ['cd ca3b', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig9b()")'],
'cleanup': ['cd ../', 'rm -fr ca3b']
},
'101629_2':
{
'variant': 'Fig.9C',
'compile': ['cd ca3b', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig9c()")'],
'cleanup': ['cd ../', 'rm -fr ca3b']
},
'101629_3':
{
'variant': 'Fig.9D',
'compile': ['cd ca3b', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig9d()")'],
'cleanup': ['cd ../', 'rm -fr ca3b']
},
'101629_4':
{
'variant': 'Fig.9E',
'compile': ['cd ca3b', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("fig9e()")'],
'cleanup': ['cd ../', 'rm -fr ca3b']
},
'126814':
{
'compile': ['cd develop', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr develop']
},
'20007':
{
'compile': ['cd ca3_2002', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr ca3_2002']
},
'3263_1':
{
'variant': 'burst',
'compile': ['cd ca3_db', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runb()")'],
'cleanup': ['cd ../', 'rm -fr ca3_db']
},
'3263_2':
{
'variant': 'no-burst short',
'compile': ['cd ca3_db', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runnbs()")'],
'cleanup': ['cd ../', 'rm -fr ca3_db']
},
'3263_3':
{
'variant': 'no-burst long',
'compile': ['cd ca3_db', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runnbl()")'],
'cleanup': ['cd ../', 'rm -fr ca3_db']
},
'118986':
{
'compile': ['cd mutant', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr mutant']
},
'144392_1':
{
'variant': 'soma=0',
'compile': ['cd modeldb', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runs()")'],
'cleanup': ['cd ../', 'rm -fr modeldb']
},
'144392_2':
{
'variant': 'km in both',
'compile': ['cd modeldb', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runii()")'],
'cleanup': ['cd ../', 'rm -fr modeldb']
},
'144392_3':
{
'variant': 'axon=0',
'compile': ['cd modeldb', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runa()")'],
'cleanup': ['cd ../', 'rm -fr modeldb']
},
'144976_1':
{
'variant': 'control',
'compile': ['cd alzheimer', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("control()")'],
'cleanup': ['cd ../', 'rm -fr alzheimer']
},
'144976_2':
{
'variant': 'alzheimer',
'compile': ['cd alzheimer', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("AD()")'],
'cleanup': ['cd ../', 'rm -fr alzheimer']
},
'144976_3':
{
'variant': 'KA-treatment',
'compile': ['cd alzheimer', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("AD_KA()")'],
'cleanup': ['cd ../', 'rm -fr alzheimer']
},
'87535':
{
'compile': ['cd magical7', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runm()'],
'cleanup': ['cd ../', 'rm -fr magical7']
},
'55035':
{
'compile': ['cd obliques', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runm()")'],
'cleanup': ['cd ../', 'rm -fr obliques']
},
'126776_1':
{
'variant': 'control',
'compile': ['cd rebound', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runc()")'],
'cleanup': ['cd ../', 'rm -fr rebound']
},
'126776_2':
{
'variant': '4-AP',
'compile': ['cd rebound', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run4ap()")'],
'cleanup': ['cd ../', 'rm -fr rebound']
},
'126776_3':
{
'variant': '4-AP+ZD',
'compile': ['cd rebound', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run4apzd()")'],
'cleanup': ['cd ../', 'rm -fr rebound']
},
'19696_1':
{
'variant': 'full model (black)',
'compile': ['cd sc-pp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runf()")'],
'cleanup': ['cd ../', 'rm -fr sc-pp']
},
'19696_2':
{
'variant': 'uniform KA (red)',
'compile': ['cd sc-pp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runa()")'],
'cleanup': ['cd ../', 'rm -fr sc-pp']
},
'19696_3':
{
'variant': 'uniform KA and I-h (blue)',
'compile': ['cd sc-pp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runh()")'],
'cleanup': ['cd ../', 'rm -fr sc-pp']
},
'112546_1':
{
'variant': 'fig.4(i)',
'compile': ['cd km', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runi()")'],
'cleanup': ['cd ../', 'rm -fr km']
},
'112546_2':
{
'variant': 'fig.4(ii)',
'compile': ['cd km', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runii()")'],
'cleanup': ['cd ../', 'rm -fr km']
},
'112546_3':
{
'variant': 'fig.4(iii)',
'compile': ['cd km', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runiii()")'],
'cleanup': ['cd ../', 'rm -fr km']
},
'112546_4':
{
'variant': 'fig.4(iv)',
'compile': ['cd km', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runiv()")'],
'cleanup': ['cd ../', 'rm -fr km']
},
'116983':
{
'compile': ['cd theta', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runm()")'],
'cleanup': ['cd ../', 'rm -fr theta']
},
'148094':
{
'compile': ['cd kv72-R213QW-mutations', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("run()")'],
'cleanup': ['cd ../', 'rm -fr kv72-R213QW-mutations']
},
'9769_distal':
{
'variant': 'distal',
'compile': ['cd lamotrigine', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("rund()")'],
'cleanup': ['cd ../', 'rm -fr lamotrigine']
},
'9769_proximal':
{
'variant': 'proximal',
'compile': ['cd lamotrigine', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runp()")'],
'cleanup': ['cd ../', 'rm -fr lamotrigine']
}
}
manually_curated_protocols = {
'129067_1':
{
'variant': 'Fig 9A',
'compile': ['cd Welday_et_al/Welday_et_al_Fig9AB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("RUNSIM_FIG9A.hoc")', 'h.run()'],
'cleanup': ['cd ../..', 'rm -fr Welday_et_al']
},
'129067_2':
{
'variant': 'Fig 9B',
'compile': ['cd Welday_et_al/Welday_et_al_Fig9AB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("RUNSIM_FIG9B.hoc")', 'h.run()'],
'cleanup': ['cd ../..', 'rm -fr Welday_et_al']
},
'150446_1':
{
'variant': '16PC 1IN',
'compile': ['cd VladimirovTuTraub2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit_16PC_1IN.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr VladimirovTuTraub2013']
},
'150446_2':
{
'variant': '1PC 1IN',
'compile': ['cd VladimirovTuTraub2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit_1PC_1IN.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr VladimirovTuTraub2013']
},
'150446_3':
{
'variant': '1PC 1IN myelinated Ax',
'compile': ['cd VladimirovTuTraub2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit_1PC_1INmyelinatedAx.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr VladimirovTuTraub2013']
},
'150446_4':
{
'variant': '1PC 1IN silent2firing',
'compile': ['cd VladimirovTuTraub2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit_1PC_1INsilent2firing.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr VladimirovTuTraub2013']
},
'150446_5':
{
'variant': '81PC 9IN forward',
'compile': ['cd VladimirovTuTraub2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit_81PC_9INforward.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr VladimirovTuTraub2013']
},
'108459_1':
{
'variant': '3 AP burst',
'compile': ['cd LetzkusEtAl2006', 'nrnivmodl mod'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.three_AP()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr LetzkusEtAl2006']
},
'108459_2':
{
'variant': 'no APs',
'compile': ['cd LetzkusEtAl2006', 'nrnivmodl mod'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.no_AP()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr LetzkusEtAl2006']
},
'3805_1':
{
'variant': 'Fig 3 Soma voltage clamp',
'compile': ['cd dodge73', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart(0)', 'h.load_file(1, "fig3.hoc")'],
'cleanup': ['cd ../', 'rm -fr dodge73']
},
'3805_2':
{
'variant': 'Fig 5 IS conductance',
'compile': ['cd dodge73', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart(1)', 'h.load_file(1, "fig5.hoc")'],
'cleanup': ['cd ../', 'rm -fr dodge73']
},
'3805_3':
{
'variant': 'Fig 6 Threshold difference',
'compile': ['cd dodge73', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart(1)', 'h.load_file(1, "fig6.hoc")'],
'cleanup': ['cd ../', 'rm -fr dodge73']
},
'3805_4':
{
'variant': 'Fig 7 Soma hyperpolarization',
'compile': ['cd dodge73', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart(1)', 'h.load_file(1, "fig7.hoc")'],
'cleanup': ['cd ../', 'rm -fr dodge73']
},
'3805_5':
{
'variant': 'Fig 8 Antidromic spatial pattern',
'compile': ['cd dodge73', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart(1)', 'h.load_file(1, "fig8.hoc")'],
'cleanup': ['cd ../', 'rm -fr dodge73']
},
'53451_1':
{
'variant': 'Fig 1',
'compile': ['cd hines2001', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig1")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr hines2001']
},
'53451_2':
{
'variant': 'Fig 3,4',
'compile': ['cd hines2001', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig34")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr hines2001']
},
'53451_3':
{
'variant': 'Fig 5',
'compile': ['cd hines2001', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig5")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr hines2001']
},
'53451_4':
{
'variant': 'Fig 7',
'compile': ['cd hines2001', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig7")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr hines2001']
},
'53451_5':
{
'variant': 'Fig 8',
'compile': ['cd hines2001', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig8")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr hines2001']
},
'53451_6':
{
'variant': 'Fig 9',
'compile': ['cd hines2001', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig9")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr hines2001']
},
'64228_1':
{
'variant': 'Fig5_IVCompare',
'compile': ['cd Liu-Kourennyi_2004', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("Fig5_IVCompare.ses")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Liu-Kourennyi_2004']
},
'64228_2':
{
'variant': 'fig 8B. AP_BR',
'compile': ['cd Liu-Kourennyi_2004', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("0222AP_BR.ses")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Liu-Kourennyi_2004']
},
'64228_3':
{
'variant': 'fig 8D. AP_DIM',
'compile': ['cd Liu-Kourennyi_2004', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("0222AP_DIM.ses")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Liu-Kourennyi_2004']
},
'64228_4':
{
'variant': 'Kx_BR',
'compile': ['cd Liu-Kourennyi_2004', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("0222Kx_BR.ses")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Liu-Kourennyi_2004']
},
'64228_5':
{
'variant': 'Kx_DIM',
'compile': ['cd Liu-Kourennyi_2004', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("0222Kx_DIM.ses")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Liu-Kourennyi_2004']
},
'64228_6':
{
'variant': 'Fig9_AP_Patterns',
'compile': ['cd Liu-Kourennyi_2004', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("Fig9_AP_Patterns.ses")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Liu-Kourennyi_2004']
},
# '152197':
# {
# 'compile': ['cd colorModelDemo', 'nrnivmodl'],
# 'launch': ['nrngui -python'],
# 'run': ['from neuron import h, gui', 'execfile("runMe.py")'],
# 'cleanup': ['cd ../', 'rm -fr colorModelDemo']
# },
'50997_1':
{
'variant': 'Fig 7',
'compile': ['cd Ribbon', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("makefig7")'],
'cleanup': ['cd ../', 'rm -fr Ribbon']
},
'50997_2':
{
'variant': 'Fig 8a',
'compile': ['cd Ribbon', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("makefig8a")'],
'cleanup': ['cd ../', 'rm -fr Ribbon']
},
'50997_3':
{
'variant': 'Fig 8b',
'compile': ['cd Ribbon', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("makefig8b")'],
'cleanup': ['cd ../', 'rm -fr Ribbon']
},
'50997_4':
{
'variant': 'Fig 8c',
'compile': ['cd Ribbon', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("makefig8c")'],
'cleanup': ['cd ../', 'rm -fr Ribbon']
},
'50997_5':
{
'variant': 'Fig 8c_250',
'compile': ['cd Ribbon', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("makefig8c_250ms")'],
'cleanup': ['cd ../', 'rm -fr Ribbon']
},
'50997_6':
{
'variant': 'Fig 9',
'compile': ['cd Ribbon', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig9-11")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Ribbon']
},
'144566':
{
'compile': ['cd modeldb_package', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'execfile("claudia_pairing.py")'],
'cleanup': ['cd ../', 'rm -fr modeldb_package']
},
'3677_1':
{
'variant': 'Ri18',
'compile': ['cd spru1998/Ri18', 'nrnivmodl ..'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("ri18run.hoc")'],
'cleanup': ['cd ../..', 'rm -fr spru1998']
},
'3677_2':
{
'variant': 'Ri21',
'compile': ['cd spru1998/Ri21', 'nrnivmodl ..'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("ri21run.hoc")'],
'cleanup': ['cd ../..', 'rm -fr spru1998']
},
'3677_3':
{
'variant': 'Ri22',
'compile': ['cd spru1998/Ri22', 'nrnivmodl ..'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("ri22run.hoc")'],
'cleanup': ['cd ../..', 'rm -fr spru1998']
},
'2488_1':
{
'variant': '1a. L3 Aspiny',
'compile': ['cd patdemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig_1()', 'h.fig1a()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr patdemo']
},
'2488_2':
{
'variant': '1b. L4 Stellate',
'compile': ['cd patdemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig_1()', 'h.fig1b()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr patdemo']
},
'2488_3':
{
'variant': '1c. L3 Pyramid',
'compile': ['cd patdemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig_1()', 'h.fig1c()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr patdemo']
},
'2488_4':
{
'variant': '1d. L5 Pyramid',
'compile': ['cd patdemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig_1()', 'h.fig1d()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr patdemo']
},
'2488_5':
{
'variant': '2',
'compile': ['cd patdemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig_2()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr patdemo']
},
'2730_1':
{
'variant': 'Fig 2 (Olfactory nerve shock)',
'compile': ['cd bulbNet', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_experiment("ddi_baseline")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr bulbNet']
},
'2730_2':
{
'variant': 'Fig 8 (Odor stimulus)',
'compile': ['cd bulbNet', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_experiment("odour_baseline")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr bulbNet']
},
'18742_1':
{
'variant': '6A',
'compile': ['cd nainact', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig6A")'],
'cleanup': ['cd ../', 'rm -fr nainact']
},
'18742_2':
{
'variant': '6B',
'compile': ['cd nainact', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig6B")'],
'cleanup': ['cd ../', 'rm -fr nainact']
},
'18742_3':
{
'variant': '7A',
'compile': ['cd nainact', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig7A")'],
'cleanup': ['cd ../', 'rm -fr nainact'],
'stopmidsim': False
},
'105385_1':
{
'variant': 'Figure 9',
'compile': ['cd gp', 'nrnivmodl mod'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.loadfig9()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr gp']
},
'105385_2':
{
'variant': 'Figure 10',
'compile': ['cd gp', 'nrnivmodl mod'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.loadfig10()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr gp']
},
'116491':
{
'compile': ['cd nrnpython', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['execfile("ch6_model.py")'],
'cleanup': ['cd ../', 'rm -fr nrnpython']
},
'9848_1':
{
'variant': 'Figure 1',
'compile': ['cd brill77', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig1")'],
'cleanup': ['cd ../', 'rm -fr brill77']
},
'9848_2':
{
'variant': 'Figure 2A',
'compile': ['cd brill77', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig2a")'],
'cleanup': ['cd ../', 'rm -fr brill77']
},
'9848_3':
{
'variant': 'Figure 2B',
'compile': ['cd brill77', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig2b")'],
'cleanup': ['cd ../', 'rm -fr brill77']
},
# '151282':
# {
# 'compile': ['cd ca3ihdemo', 'nrnivmodl'],
# 'launch': ['nrngui -python'],
# 'run': ['from neuron import h, gui', 'import sys', 'sys.argv = ["python", "sim.py", "8000"]', 'execfile("sim.py")'],
# 'cleanup': ['cd ../', 'rm -fr ca3ihdemo']
# },
'53876_1':
{
'variant': '2 A1 B1',
'compile': ['cd mvns', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig2a1b1")'],
'cleanup': ['cd ../', 'rm -fr mvns']
},
'53876_2':
{
'variant': '2 A2 B2',
'compile': ['cd mvns', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig2a2b2")'],
'cleanup': ['cd ../', 'rm -fr mvns']
},
'53876_3':
{
'variant': '2 C',
'compile': ['cd mvns', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig2c")'],
'cleanup': ['cd ../', 'rm -fr mvns']
},
'53876_4':
{
'variant': '2 D',
'compile': ['cd mvns', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig2d")'],
'cleanup': ['cd ../', 'rm -fr mvns']
},
'53876_5':
{
'variant': '3',
'compile': ['cd mvns', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig3")'],
'cleanup': ['cd ../', 'rm -fr mvns']
},
'53876_6':
{
'variant': '4 A',
'compile': ['cd mvns', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("fig4a")'],
'cleanup': ['cd ../', 'rm -fr mvns']
},
'33975_1':
{
'variant': 'Fig 1',
'compile': ['cd locstepperf', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig1()'],
'cleanup': ['cd ../', 'rm -fr locstepperf']
},
'33975_2':
{
'variant': 'Fig 5 Ring Performance',
'compile': ['cd locstepperf', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.ringperf()'],
'cleanup': ['cd ../', 'rm -fr locstepperf']
},
'116094_1':
{
'variant': 'Long Dendrite - Fig1bde',
'compile': ['cd DendroDendriticInhibition/LongDendrite', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("init.hoc")', 'h.run_experiment("fig1")', 'h.run_fig1bde()'],
'cleanup': ['cd ../../', 'rm -fr DendroDendriticInhibition']
},
'116094_2':
{
'variant': 'Long Dendrite - Fig1fg',
'compile': ['cd DendroDendriticInhibition/LongDendrite', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("init.hoc")', 'h.run_experiment("fig1")', 'h.run_fig1fg()'],
'cleanup': ['cd ../../', 'rm -fr DendroDendriticInhibition']
},
'116094_3':
{
'variant': 'Long Dendrite - Fig2ace',
'compile': ['cd DendroDendriticInhibition/LongDendrite', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("init.hoc")', 'h.run_experiment("fig2ace")', 'h.run_fig2()'],
'cleanup': ['cd ../../', 'rm -fr DendroDendriticInhibition']
},
'116094_4':
{
'variant': 'Short Dendrite - Fig1cde',
'compile': ['cd DendroDendriticInhibition/ShortDendrite', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("init.hoc")', 'h.run_experiment("fig1cde")', 'h.run_fig1cde()'],
'cleanup': ['cd ../../', 'rm -fr DendroDendriticInhibition']
},
'116094_5':
{
'variant': 'Short Dendrite - Fig1fg',
'compile': ['cd DendroDendriticInhibition/ShortDendrite', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("init.hoc")', 'h.run_experiment("fig1fg")', 'h.run_fig1fg()'],
'cleanup': ['cd ../../', 'rm -fr DendroDendriticInhibition']
},
'116094_6':
{
'variant': 'Short Dendrite - Fig2bf',
'compile': ['cd DendroDendriticInhibition/ShortDendrite', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("init.hoc")', 'h.run_experiment("fig2bdf")', 'h.run_fig2bdf()'],
'cleanup': ['cd ../../', 'rm -fr DendroDendriticInhibition']
},
'116094_7':
{
'variant': 'Short Dendrite - Fig3',
'compile': ['cd DendroDendriticInhibition/ShortDendrite', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("init.hoc")', 'h.run_experiment("fig3")', 'h.run_fig3()'],
'cleanup': ['cd ../../', 'rm -fr DendroDendriticInhibition']
},
'116094_8':
{
'variant': 'Short Dendrite - Fig4abcd',
'compile': ['cd DendroDendriticInhibition/ShortDendrite', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("init.hoc")', 'h.run_experiment("fig4")', 'h.run_fig4abcd()'],
'cleanup': ['cd ../../', 'rm -fr DendroDendriticInhibition']
},
'116094_9':
{
'variant': 'Short Dendrite - Fig4ef',
'compile': ['cd DendroDendriticInhibition/ShortDendrite', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("init.hoc")', 'h.run_experiment("fig4")', 'h.run_fig4ef()'],
'cleanup': ['cd ../../', 'rm -fr DendroDendriticInhibition']
},
'116094_10':
{
'variant': 'Short Dendrite - Fig5',
'compile': ['cd DendroDendriticInhibition/ShortDendrite', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("init.hoc")', 'h.run_experiment("fig5")', 'h.run_fig5()'],
'cleanup': ['cd ../../', 'rm -fr DendroDendriticInhibition']
},
'116094_11':
{
'variant': 'Short Dendrite - Fig6',
'compile': ['cd DendroDendriticInhibition/ShortDendrite', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("init.hoc")', 'h.run_experiment("fig6")', 'h.run_fig6()'],
'cleanup': ['cd ../../', 'rm -fr DendroDendriticInhibition']
},
'18500_1':
{
'variant': 'AMPA/Kainate glutamatergic receptors',
'compile': ['cd Channels_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("demo_ampa.oc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Channels_NEW']
},
'18500_2':
{
'variant': 'NMDA glutamatergic receptors',
'compile': ['cd Channels_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("demo_nmda.oc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Channels_NEW']
},
'18500_3':
{
'variant': 'GABA-A receptors',
'compile': ['cd Channels_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("demo_gabaa.oc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Channels_NEW']
},
'18500_4':
{
'variant': 'GABA-B receptors',
'compile': ['cd Channels_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("demo_gabab.oc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Channels_NEW']
},
'150024_1':
{
'variant': 'Fig 9A,B',
'compile': ['cd CNModel_May2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("DCN_spontact_loop_main.hoc")'],
'cleanup': ['cd ../', 'rm -fr CNModel_May2013']
},
'150024_2':
{
'variant': 'Fig 9C,D',
'compile': ['cd CNModel_May2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("DCN_rebound_main.hoc")'],
'cleanup': ['cd ../', 'rm -fr CNModel_May2013']
},
'150024_3':
{
'variant': 'Fig 9E',
'compile': ['cd CNModel_May2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("DCN_cip_fi_main.hoc")'],
'cleanup': ['cd ../', 'rm -fr CNModel_May2013']
},
'150024_4':
{
'variant': 'Fig 9F',
'compile': ['cd CNModel_May2013', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("DCN_cip_axis_main.hoc")'],
'cleanup': ['cd ../', 'rm -fr CNModel_May2013']
},
'144502':
{
'compile': ['cd package', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'execfile("cluster_hyp.py")'],
'cleanup': ['cd ../', 'rm -fr package']
},
'123623_1':
{
'variant': 'Regular-spiking pyramidal cell',
'compile': ['cd PospischilEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr PospischilEtAl2008']
},
'123623_2':
{
'variant': 'Bursting pyramidal cell',
'compile': ['cd PospischilEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("demo_PY_IB")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr PospischilEtAl2008']
},
'123623_3':
{
'variant': 'Repetitive bursting pyramidal cell',
'compile': ['cd PospischilEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("demo_PY_IBR")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr PospischilEtAl2008']
},
'123623_4':
{
'variant': 'LTS pyramidal cell',
'compile': ['cd PospischilEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("demo_PY_LTS")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr PospischilEtAl2008']
},
'123623_5':
{
'variant': 'Fast-spiking interneuron',
'compile': ['cd PospischilEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("demo_IN_FS")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr PospischilEtAl2008']
},
'7400':
{
'compile': ['cd lytton99', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr lytton99']
},
'114047':
{
'compile': ['cd Basketcell', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.tstop=1e4', 'h.xopen("fig6.hoc")'],
'cleanup': ['cd ../', 'rm -fr Basketcell']
},
'19214_1':
{
'variant': 'Fig.1. A,C',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(1)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_2':
{
'variant': 'Fig.1. B,D',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(2)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_3':
{
'variant': 'Fig.2. A,C',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(3)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_4':
{
'variant': 'Fig.2. B,D',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(4)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_5':
{
'variant': 'Fig.3. A-C Symmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(5)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_6':
{
'variant': 'Fig.3. A-C Asymmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(6)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_7':
{
'variant': 'Fig.3. D Symmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(7)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_8':
{
'variant': 'Fig.3. D Asymmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(8)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_9':
{
'variant': 'Fig.3. E-G Symmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(9)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_10':
{
'variant': 'Fig.3. E-G Asymmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(10)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_11':
{
'variant': 'Fig.4. A-C Symmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(11)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_12':
{
'variant': 'Fig.4. A-C Asymmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(12)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_13':
{
'variant': 'Fig.4. D Symmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(13)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_14':
{
'variant': 'Fig.4. D Asymmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(14)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_15':
{
'variant': 'Fig.4. E-G Symmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(15)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_16':
{
'variant': 'Fig.4. E-G Asymmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(16)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_17':
{
'variant': 'Fig.5. A-C Symmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(17)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_18':
{
'variant': 'Fig.5. A-C Asymmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(18)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_19':
{
'variant': 'Fig.5. D Symmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(19)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_20':
{
'variant': 'Fig.5. D Asymmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(20)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_21':
{
'variant': 'Fig.5. E-G Symmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(21)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'19214_22':
{
'variant': 'Fig.5. E-G Asymmetric',
'compile': ['cd geomindu', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Main(22)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr geomindu']
},
'136026_1':
{
'variant': 'Passive tuft, control',
'compile': ['cd djurisic2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("init_spiketuft.hoc")', 'h.setparams(h.BOTHCONTROL)', 'h.doit()'],
'cleanup': ['cd ../', 'rm -fr djurisic2008']
},
'136026_2':
{
'variant': 'Passive tuft, cm = 2*control',
'compile': ['cd djurisic2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("init_spiketuft.hoc")', 'h.setparams(h.CMx2)', 'h.doit()'],
'cleanup': ['cd ../', 'rm -fr djurisic2008']
},
'136026_3':
{
'variant': 'Passive tuft, Ra = 2*control',
'compile': ['cd djurisic2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("init_spiketuft.hoc")', 'h.setparams(h.RAx2)', 'h.doit()'],
'cleanup': ['cd ../', 'rm -fr djurisic2008']
},
'136026_4':
{
'variant': 'Passive tuft, both 2*control',
'compile': ['cd djurisic2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("init_spiketuft.hoc")', 'h.setparams(h.BOTHx2)', 'h.doit()'],
'cleanup': ['cd ../', 'rm -fr djurisic2008']
},
'136026_5':
{
'variant': 'Active tuft',
'compile': ['cd djurisic2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("init_active.hoc")', 'h.doit()'],
'cleanup': ['cd ../', 'rm -fr djurisic2008']
},
'7399':
{
'compile': ['cd lytton98', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.sim_panel()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr na8st']
},
'128079':
{
'compile': ['cd na8st', 'nrnivmodl mod/'],
'launch': ['nrngui -python'],
'run': ['execfile("ap.py")'],
'cleanup': ['cd ../', 'rm -fr na8st']
},
'113997_1':
{
'variant': 'HPGA non-saturating',
'compile': ['cd HAGPA', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("demo_HPGA_non-saturating.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr HAGPA']
},
'113997_2':
{
'variant': 'HPGA non-saturating (no Ih)',
'compile': ['cd HAGPA', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("demo_HPGA_non-saturating_noIh.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr HAGPA']
},
'113997_3':
{
'variant': 'HPGA saturating',
'compile': ['cd HAGPA', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("demo_HPGA_saturating.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr HAGPA']
},
'144376_1':
{
'variant': 'HPGA non-saturating',
'compile': ['cd Skolnik_python_WinogradEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['execfile("demo_HPGA_non_saturating.py")'],
'cleanup': ['cd ../', 'rm -fr Skolnik_python_WinogradEtAl2008']
},
'144376_2':
{
'variant': 'HPGA non-saturating (no Ih)',
'compile': ['cd Skolnik_python_WinogradEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['execfile("demo_HPGA_non_saturating_noIh.py")'],
'cleanup': ['cd ../', 'rm -fr Skolnik_python_WinogradEtAl2008']
},
'144376_3':
{
'variant': 'HPGA saturating',
'compile': ['cd Skolnik_python_WinogradEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['execfile("demo_HPGA_saturating.py")'],
'cleanup': ['cd ../', 'rm -fr Skolnik_python_WinogradEtAl2008']
},
'62266':
{
'compile': ['cd b1', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr b1']
},
'138379':
{
'compile': ['cd fdemo', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.mytstop=20e3', 'h.finish_run()'],
'cleanup': ['cd ../', 'rm -fr fdemo']
},
'18197_1':
{
'variant': 'fig 1A (Glutamate)',
'compile': ['cd Neural_Computation', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("demo_glutamate_neuralcomputation")'],
'cleanup': ['cd ../', 'rm -fr Neural_Computation']
},
'18197_2':
{
'variant': 'fig 1D (GABA)',
'compile': ['cd Neural_Computation', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("demo_gaba_neuralcomputation")'],
'cleanup': ['cd ../', 'rm -fr Neural_Computation']
},
'143114_1':
{
'variant': 'Synaptic Input',
'compile': ['cd ZhouColburn2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("LSO_synaptic_input.hoc")', 'h.rerun()'],
'cleanup': ['cd ../', 'rm -fr ZhouColburn2010']
},
'143114_2':
{
'variant': 'Current Input',
'compile': ['cd ZhouColburn2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("LSO_current_input.hoc")', 'h.rerun()'],
'cleanup': ['cd ../', 'rm -fr ZhouColburn2010']
},
'3798_1':
{
'variant': 'A',
'compile': ['cd shrager91', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.inter_fhdens(0.4e-3)', 'h.unmyl()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr shrager91']
},
'3798_2':
{
'variant': 'B',
'compile': ['cd shrager91', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.inter_fhdens(0.5e-3)', 'h.unmyl()', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr shrager91']
},
'3798_3':
{
'variant': 'C',
'compile': ['cd shrager91', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.inter_fhdens(0.4e-3)', 'h.demyl1(1, 3)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr shrager91']
},
'3798_4':
{
'variant': 'D',
'compile': ['cd shrager91', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.inter_fhdens(0.4e-3)', 'h.demyl1(1, 19)', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr shrager91']
},
'19491':
{
'compile': ['cd EurJNeurosci2000', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr EurJNeurosci2000']
},
'113446':
{
'compile': ['cd NEURON-2008b', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr NEURON-2008b']
},
'117459':
{
'compile': ['cd CruzEtAlS_cellModel', 'nrnivmodl plus5HT/3cell'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CruzEtAlS_cellModel']
},
'53435_1':
{
'variant': 'Real EPSP',
'compile': ['cd anyas2005/model_bf_real_EPSP', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../../', 'rm -fr anyas2005']
},
'53435_2':
{
'variant': 'HPP',
'compile': ['cd anyas2005/model_bf_HPP', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../../', 'rm -fr anyas2005']
},
'112086_1':
{
'variant': 'Metal electrode',
'compile': ['cd giuglianoEtAl2007', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("metal()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr giuglianoEtAl2007']
},
'112086_2':
{
'variant': 'Metal electrode',
'compile': ['cd giuglianoEtAl2007', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("cntel()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr giuglianoEtAl2007']
},
'112086_3':
{
'variant': 'Metal electrode',
'compile': ['cd giuglianoEtAl2007', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("cntel2()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr giuglianoEtAl2007']
},
'37856_1':
{
'variant': 'Fig 2',
'compile': ['cd CN_Pyr', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runiv()")'],
'cleanup': ['cd ../', 'rm -fr CN_Pyr']
},
'37856_2':
{
'variant': 'Fig 3A',
'compile': ['cd CN_Pyr', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runhyp(1,0,0,0)")'],
'cleanup': ['cd ../', 'rm -fr CN_Pyr']
},
'37856_3':
{
'variant': 'Fig 3B',
'compile': ['cd CN_Pyr', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runhyp(1,0,1,0)")'],
'cleanup': ['cd ../', 'rm -fr CN_Pyr']
},
'37856_4':
{
'variant': 'Fig 4A',
'compile': ['cd CN_Pyr', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runhyp(1,1,0,0)")'],
'cleanup': ['cd ../', 'rm -fr CN_Pyr']
},
'37856_5':
{
'variant': 'Fig 4B',
'compile': ['cd CN_Pyr', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runhyp(1,1,1,0)")'],
'cleanup': ['cd ../', 'rm -fr CN_Pyr']
},
'37856_6':
{
'variant': 'Fig 10A',
'compile': ['cd CN_Pyr', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runhyp(1,0,0,1)")'],
'cleanup': ['cd ../', 'rm -fr CN_Pyr']
},
'37856_7':
{
'variant': 'Fig 10B',
'compile': ['cd CN_Pyr', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("runhyp(1,1,0,1)")'],
'cleanup': ['cd ../', 'rm -fr CN_Pyr']
},
'37857_1':
{
'variant': 'Figure2A',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Fig2A()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_2':
{
'variant': 'Figure2B',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Fig2B()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_3':
{
'variant': 'Figure2C',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Fig2C()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_4':
{
'variant': 'Figure2D',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Fig2D()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_5':
{
'variant': 'Panel A',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Fig3A()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_6':
{
'variant': 'Panel B',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Fig3B()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_7':
{
'variant': 'Panel C',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Fig3C()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_8':
{
'variant': 'Panel D',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Fig3D()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_9':
{
'variant': 'Type I',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Fig4A()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_10':
{
'variant': 'Type I-II',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Fig4B()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_11':
{
'variant': 'Type II-I',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Fig4C()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_12':
{
'variant': 'Type II',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Fig4D()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_13':
{
'variant': 'Type I-c',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Type1c()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_14':
{
'variant': 'Type I-t',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Type1t()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_15':
{
'variant': 'Type I-II',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Type12()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_16':
{
'variant': 'Type II-I',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Type21()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_17':
{
'variant': 'Type II',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Type2()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'37857_18':
{
'variant': 'Type IIo (Octopus)',
'compile': ['cd CN_Bushy_Stellate', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("Type2o()")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr CN_Bushy_Stellate']
},
'35358':
{
'compile': ['cd b04feb12', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../', 'rm -fr b04feb12']
},
'136176':
{
'compile': ['cd Katona_et_al', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ../', 'rm -fr Katona_et_al']
},
'138205':
{
'compile': ['cd Schizophr', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h("display_cell()")'],
'cleanup': ['cd ../', 'rm -fr Schizophr']
},
'144490':
{
'compile': ['cd bpap', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.gui_run_bpap()'],
'cleanup': ['cd ../', 'rm -fr bpap']
},
'143719':
{
'compile': ['cd Ca1_Bianchi/experiment', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../../', 'rm -fr Ca1_Bianchi']
},
'20212_1':
{
'variant': 'Disperse 6_2',
'compile': ['cd CA1_multi/experiment/cluster-dispersion', 'nrnivmodl ../../mechanism', 'chmod +x newshiftsyn', 'export PATH=.:$PATH'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Disperse_6_2.hoc")'],
'cleanup': ['cd ../../..', 'rm -fr CA1_multi']
},
'44050_1':
{
'variant': 'Control',
'compile': ['cd gaspiriniEtAl2004', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runc()'],
'cleanup': ['cd ..', 'rm -fr gaspiriniEtAl2004']
},
'44050_2':
{
'variant': 'AMPA',
'compile': ['cd gaspiriniEtAl2004', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runa()'],
'cleanup': ['cd ..', 'rm -fr gaspiriniEtAl2004']
},
'44050_3':
{
'variant': 'AMPA + NMDA',
'compile': ['cd gaspiriniEtAl2004', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runm()'],
'cleanup': ['cd ..', 'rm -fr gaspiriniEtAl2004']
},
'144541_1':
{
'variant': 'Control',
'compile': ['cd Ih_current', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("fig-5a.hoc")', 'h.loop()'],
'cleanup': ['cd ..', 'rm -fr Ih_current']
},
'144541_2':
{
'variant': 'Control',
'compile': ['cd Ih_current', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("fig-5a.hoc")', 'h.zd()'],
'cleanup': ['cd ..', 'rm -fr Ih_current']
},
'151949':
{
'compile': ['cd SousaEtAl2014', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ..', 'rm -fr SousaEtAl2014']
},
'7509':
{
'compile': ['cd magee2000'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ..', 'rm -fr magee2000'],
'stopmidsim': False # need this because an xpanel is open until after the sim completes
},
'106551':
{
'compile': ['cd nc-mri', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runm()'],
'cleanup': ['cd ..', 'rm -fr nc-mri']
},
'3507':
{
'compile': ['cd fh', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ..', 'rm -fr fh']
},
'7386':
{
'compile': ['cd boosting', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runc()'],
'cleanup': ['cd ..', 'rm -fr boosting']
},
'125152':
{
'compile': ['cd Uebachs-et-al_2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_sim_graph()'],
'cleanup': ['cd ..', 'rm -fr Uebachs-et-al_2010']
},
'2796_1':
{
'variant': 'Fig 1A',
'compile': ['cd ca1', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("fig_1a.hoc")', 'h.runu()'],
'cleanup': ['cd ..', 'rm -fr ca1']
},
'2796_2':
{
'variant': 'Fig 1C',
'compile': ['cd ca1', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("fig_1c.hoc")', 'h.runu()'],
'cleanup': ['cd ..', 'rm -fr ca1']
},
'144401':
{
'compile': ['cd VladimirovTuTraub2012', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr VladimirovTuTraub2012']
},
'87546':
{
'compile': ['cd olm-int', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr olm-int']
},
'20015':
{
'compile': ['cd k_interneurons', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("kinetics.hoc")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr k_interneurons']
},
'32992':
{
'compile': ['cd synchro-ca1', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ..', 'rm -fr synchro-ca1']
},
'2937_1':
{
'variant': 'Fig 3',
'compile': ['cd slowinact', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run3()'],
'cleanup': ['cd ..', 'rm -fr slowinact']
},
'2937_2':
{
'variant': 'Fig 4bc',
'compile': ['cd slowinact', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run4bc()'],
'cleanup': ['cd ..', 'rm -fr slowinact']
},
'2937_3':
{
'variant': 'Fig 4bd',
'compile': ['cd slowinact', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run4bd()'],
'cleanup': ['cd ..', 'rm -fr slowinact']
},
'139418_1':
{
'variant': 'Fig 11',
'compile': ['cd fietkiewicz2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("figure11.hoc")'],
'cleanup': ['cd ..', 'rm -fr fietkiewicz2011']
},
'139418_2':
{
'variant': 'Fig 13',
'compile': ['cd fietkiewicz2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("figure13.hoc")'],
'cleanup': ['cd ..', 'rm -fr fietkiewicz2011']
},
'46839':
{
'compile': ['cd GranuleCell', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ..', 'rm -fr GranuleCell']
},
'116830':
{
'compile': ['cd b08dec23', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("init.hoc")'],
'cleanup': ['cd ..', 'rm -fr b08dec23']
},
'125689':
{
'compile': ['cd CarvalhoBuonomano/Neuron2009', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.MULTI()'],
'cleanup': ['cd ../..', 'rm -fr CarvalhoBuonomano']
},
'127388':
{
'compile': ['cd BGnet', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_sim()'],
'cleanup': ['cd ../..', 'rm -fr BGnet']
},
'136803':
{
'compile': ['cd JonesEtAl2009', 'nrnivmodl mod_files'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ../..', 'rm -fr JonesEtAl2009']
},
'116096_1':
{
'variant': 'Fig 2A',
'compile': ['cd badoual_stdp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.ampasyn.delta = -100', 'h.set_axis_limits(0.0014, 0.007, 0.7, 0.014)', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr badoual_stdp']
},
'116096_2':
{
'variant': 'Fig 2B',
'compile': ['cd badoual_stdp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.ampasyn.delta = -10', 'h.set_axis_limits(0.0014, 0.007, 0.7, 0.35)', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr badoual_stdp']
},
'116096_3':
{
'variant': 'Fig 2C',
'compile': ['cd badoual_stdp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.ampasyn.delta = 10', 'h.set_axis_limits(0.0045, 0.5, 0.9, 0.014)', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr badoual_stdp']
},
'116096_4':
{
'variant': 'Fig 2D',
'compile': ['cd badoual_stdp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.ampasyn.delta = 200', 'h.ampasyn.onset = 10', 'h.set_axis_limits(0.0016, 0.016, 0.7, 0.014)', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr badoual_stdp']
},
'147538_1':
{
'variant': 'Fig 2A',
'compile': ['cd NarayananJohnston2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Fig2A()'],
'cleanup': ['cd ..', 'rm -fr NarayananJohnston2010']
},
'147538_2':
{
'variant': 'Fig 2B',
'compile': ['cd NarayananJohnston2010', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.Fig2B()'],
'cleanup': ['cd ..', 'rm -fr NarayananJohnston2010']
},
'112834':
{
'compile': ['cd nacb_msp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ..', 'rm -fr nacb_msp']
},
'125378':
{
'compile': ['cd leeEtAl2003', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig8b()'],
'cleanup': ['cd ..', 'rm -fr leeEtAl2003']
},
'115356':
{
'compile': ['cd RoyeckEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run_sim_graph()'],
'cleanup': ['cd ..', 'rm -fr RoyeckEtAl2008']
},
'127021':
{
'compile': ['cd Golgi_cell_NaKATPAse', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.recreate()'],
'cleanup': ['cd ..', 'rm -fr Golgi_cell_NaKATPAse']
},
'147514':
{
'compile': ['cd dendritic_complexity', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ..', 'rm -fr dendritic_complexity']
},
'135838':
{
'compile': ['cd Alle_et_al_2009', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Alle_et_al_2009']
},
'143635':
{
'compile': ['cd CasaleEtAl2011', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.measure()'],
'cleanup': ['cd ..', 'rm -fr CasaleEtAl2011']
},
'87473':
{
'compile': ['cd weaver_SimAnn_ObjFcn', 'nrnivmodl model optmz'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr weaver_SimAnn_ObjFcn']
},
'135839':
{
'compile': ['cd McCormickEtAl2007YuEtAl2008', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.soma_inj()'],
'cleanup': ['cd ..', 'rm -fr McCormickEtAl2007YuEtAl2008']
},
'127992':
{
'compile': ['cd HHcn', 'nrnivmodl mod-files/', 'cp python/* .'],
'launch': ['nrngui -python'],
'run': ['execfile("HHneuron.py")'],
'cleanup': ['cd ..', 'rm -fr HHcn']
},
'145836':
{
'compile': ['cd MoradiEtAl2012', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr MoradiEtAl2012']
},
'28316_1':
{
'variant': '8A Long',
'compile': ['cd OLMmodel', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("initFig8Along")'],
'cleanup': ['cd ..', 'rm -fr OLMmodel']
},
'3785_1':
{
'variant': 'Figure 3 1A in vitro',
'compile': ['cd crane2001', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.cvode_active(1)', 'h.fig1A_vitro()'],
'cleanup': ['cd ..', 'rm -fr crane2001']
},
'3785_2':
{
'variant': 'Figure 4 2A in vitro',
'compile': ['cd crane2001', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.cvode_active(1)', 'h("mcab[0] othervitro(10000)")'],
'cleanup': ['cd ..', 'rm -fr crane2001']
},
'3785_3':
{
'variant': "Figure 4 2A' in vitro",
'compile': ['cd crane2001', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.cvode_active(1)', 'h("ecab[0] othervitro(10000)")'],
'cleanup': ['cd ..', 'rm -fr crane2001']
},
'3785_4':
{
'variant': "Figure 5 3A in vitro",
'compile': ['cd crane2001', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.cvode_active(0)', 'h("mcab[0] othervitro(100)")'],
'cleanup': ['cd ..', 'rm -fr crane2001']
},
'3785_5':
{
'variant': "Figure 5 3A' in vitro",
'compile': ['cd crane2001', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.cvode_active(0)', 'h("ecab[0] othervitro(100)")'],
'cleanup': ['cd ..', 'rm -fr crane2001']
},
'87284_1':
{
'variant': 'Figure 1, 2',
'compile': ['cd CA1_abeta', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig1and2()'],
'cleanup': ['cd ..', 'rm -fr CA1_abeta']
},
'87284_2':
{
'variant': 'Figure 3',
'compile': ['cd CA1_abeta', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig3()', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr CA1_abeta']
},
'87284_3':
{
'variant': 'Figure 4',
'compile': ['cd CA1_abeta', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig4()'],
'cleanup': ['cd ..', 'rm -fr CA1_abeta']
},
'87284_4':
{
'variant': 'Figure 5',
'compile': ['cd CA1_abeta', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig5()'],
'cleanup': ['cd ..', 'rm -fr CA1_abeta']
},
'87284_5':
{
'variant': 'Figure 6',
'compile': ['cd CA1_abeta', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig6()'],
'cleanup': ['cd ..', 'rm -fr CA1_abeta']
},
'18198_1':
{
'variant': 'Synaptic Release',
'compile': ['cd SYN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("release")'],
'cleanup': ['cd ..', 'rm -fr SYN_NEW']
},
'18198_2':
{
'variant': 'AMPA - simple',
'compile': ['cd SYN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("ampa")'],
'cleanup': ['cd ..', 'rm -fr SYN_NEW']
},
'18198_3':
{
'variant': 'AMPA - detailed',
'compile': ['cd SYN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("ampa5")'],
'cleanup': ['cd ..', 'rm -fr SYN_NEW']
},
'18198_4':
{
'variant': 'NMDA - simple',
'compile': ['cd SYN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("nmda")'],
'cleanup': ['cd ..', 'rm -fr SYN_NEW']
},
'18198_5':
{
'variant': 'NMDA - detailed',
'compile': ['cd SYN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("nmda5")'],
'cleanup': ['cd ..', 'rm -fr SYN_NEW']
},
'18198_6':
{
'variant': 'GABA_A - simple',
'compile': ['cd SYN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("gabaa")'],
'cleanup': ['cd ..', 'rm -fr SYN_NEW']
},
'18198_7':
{
'variant': 'GABA_A - detailed',
'compile': ['cd SYN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("gabaa5")'],
'cleanup': ['cd ..', 'rm -fr SYN_NEW']
},
'18198_8':
{
'variant': 'GABA_B - simple',
'compile': ['cd SYN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("gabab")'],
'cleanup': ['cd ..', 'rm -fr SYN_NEW']
},
'18198_9':
{
'variant': 'GABA_B - detailed',
'compile': ['cd SYN_NEW', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("gabab3")'],
'cleanup': ['cd ..', 'rm -fr SYN_NEW']
},
'136715_1':
{
'variant': 'Fig 6B',
'compile': ['cd FleidervishEtAl2010', 'nrnivmodl MechanismsVer7.1/'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("Fig6B.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr FleidervishEtAl2010']
},
'136715_2':
{
'variant': 'Fig 4B 10APs',
'compile': ['cd FleidervishEtAl2010', 'nrnivmodl MechanismsVer7.1/'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("Fig4B 10APs ver7a.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr FleidervishEtAl2010']
},
'136715_3':
{
'variant': 'Fig 4B 100APs',
'compile': ['cd FleidervishEtAl2010', 'nrnivmodl MechanismsVer7.1/'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("Fig4B 100APs ver7a.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr FleidervishEtAl2010']
},
'136715_4':
{
'variant': 'Fig 3A',
'compile': ['cd FleidervishEtAl2010', 'nrnivmodl MechanismsVer7.1/'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.load_file("Fig3A.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr FleidervishEtAl2010']
},
'93321_1':
{
'variant': 'Fig 3A (top left)',
'compile': ['cd liuEtAl1998', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig3topleft()'],
'cleanup': ['cd ..', 'rm -fr liuEtAl1998']
},
'93321_2':
{
'variant': 'Fig 3B (top right)',
'compile': ['cd liuEtAl1998', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig3topright()'],
'cleanup': ['cd ..', 'rm -fr liuEtAl1998']
},
'93321_3':
{
'variant': 'Fig 3A middle (left)',
'compile': ['cd liuEtAl1998', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig3middleleft()'],
'cleanup': ['cd ..', 'rm -fr liuEtAl1998']
},
'93321_4':
{
'variant': 'Fig 3B middle (right)',
'compile': ['cd liuEtAl1998', 'nrnivmodl'],
'launch': ['nrngui -python'],
'stopmidsim': False,
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig3middleright()'],
'cleanup': ['cd ..', 'rm -fr liuEtAl1998']
},
'93321_5':
{
'variant': 'Fig 3 bottom',
'compile': ['cd liuEtAl1998', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.fig3bottom()'],
'cleanup': ['cd ..', 'rm -fr liuEtAl1998']
},
'123897_1':
{
'variant': 'Pyramidal Cell',
'compile': ['cd HuEtAl2009', 'nrnivmodl mechanism/'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.xopen("experiment/Pyramidal_Main.hoc")', 'h.freePlay()', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr HuEtAl2009']
},
'123897_2':
{
'variant': 'Uniform Axon',
'compile': ['cd HuEtAl2009', 'nrnivmodl mechanism/'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.xopen("experiment/UniformAxon_Main.hoc")'],
'cleanup': ['cd ..', 'rm -fr HuEtAl2009']
},
'123897_3':
{
'variant': 'Single Compartment (activation)',
'compile': ['cd HuEtAl2009', 'nrnivmodl mechanism/'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.xopen("experiment/SingleComp_Main.hoc")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr HuEtAl2009']
},
'19176_1':
{
'variant': 'Current Steps',
'compile': ['cd HCN2k', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.experiment1()'],
'cleanup': ['cd ..', 'rm -fr HCN2k']
},
'19176_2':
{
'variant': 'cAMP pulse',
'compile': ['cd HCN2k', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.experiment2()'],
'cleanup': ['cd ..', 'rm -fr HCN2k']
},
'124063':
{
'compile': ['cd PublioEtAl2009', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.start()'],
'cleanup': ['cd ..', 'rm -fr PublioEtAl2009']
},
'54903_1':
{
'variant': 'Fig 7C: hh-dark grey_bar',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7C-hh-dark grey_bar.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_1':
{
'variant': 'Fig 7C: hh-dark grey_bar',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7C-hh-dark grey_bar.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_2':
{
'variant': 'Fig 7C: hh-light grey_bar',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7C-hh-light grey_bar.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_3':
{
'variant': 'Fig 7C: NaCh-black_bar',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7C-NaCh-black_bar.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_4':
{
'variant': 'Fig 7C: NaCh-dark grey_bar',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7C-NaCh-dark grey_bar.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_5':
{
'variant': 'Fig 7C: NaCh-light grey_bar',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7C-NaCh-light grey_bar.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_6':
{
'variant': 'Fig 7C: naf-black_bar',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7C-naf-black_bar.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_7':
{
'variant': 'Fig 7C: naf-dark grey_bar',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7C-naf-dark grey_bar.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_8':
{
'variant': 'Fig 7C: naf-light grey_bar',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7C-naf-light grey_bar.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_9':
{
'variant': 'Fig 7C: naxn-black',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7C-naxn-black.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_10':
{
'variant': 'Fig 7C: naxn-dark grey_bar',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7C-naxn-dark grey_bar.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_11':
{
'variant': 'Fig 7C: naxn-light grey_bar',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7C-naxn-light grey_bar.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_12':
{
'variant': 'Fig 7D',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7D.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_13':
{
'variant': 'Fig 7E',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7E.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_14':
{
'variant': 'Fig 6B',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig6-B.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_15':
{
'variant': 'Fig 6C',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig6-C.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_16':
{
'variant': 'Fig 7B',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7B.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_17':
{
'variant': 'Fig 6D',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig6-D.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_18':
{
'variant': 'Fig 6E',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig6-D.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_19':
{
'variant': 'Fig 6F',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig6-F.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_20':
{
'variant': 'Fig 7A',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig7A.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'54903_21':
{
'variant': 'Fig 6B-inset',
'compile': ['cd Hossain', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("Fig6-B-inset.ses")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr Hossain']
},
'126637_2c':
{
'variant': 'Fig 2C + 2E',
'compile': ['cd purkinje_ppr', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit_spine and spine neck at spinydendrite133.hoc")'],
'cleanup': ['cd ..', 'rm -fr purkinje_ppr']
},
'126637_2d':
{
'variant': 'Fig 2D + 2F',
'compile': ['cd purkinje_ppr', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit_reduced_PPR model.hoc")'],
'cleanup': ['cd ..', 'rm -fr purkinje_ppr']
},
'126637_cvode':
{
'variant': 'CVODE or other solvers',
'compile': ['cd purkinje_ppr', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit_reduced_PPR model_cvode.hoc")'],
'cleanup': ['cd ..', 'rm -fr purkinje_ppr']
},
'146026_ex1':
{
'variant': 'Example 1',
'compile': ['cd BahlEtAl2012', 'nrnivmodl channels/'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("example1.hoc")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr BahlEtAl2012']
},
'146026_ex2':
{
'variant': 'Example 2',
'compile': ['cd BahlEtAl2012', 'nrnivmodl channels/'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("example2.hoc")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr BahlEtAl2012']
},
'146026_ex3':
{
'variant': 'Example 3',
'compile': ['cd BahlEtAl2012', 'nrnivmodl channels/'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("example3.hoc")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr BahlEtAl2012']
},
'137259':
{
'compile': ['cd ca3-synresp', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ..', 'rm -fr ca3-synresp']
},
'53869':
{
'compile': ['cd MSO_Zhouetal_2005', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("MSO_Zhouetal_2005")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr MSO_Zhouetal_2005']
},
'125857_2frb':
{
'variant': '2FRB',
'compile': ['cd FRB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("2FRB")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr FRB']
},
'140249_a1':
{
'variant': 'Fig 4 A1',
'compile': ['cd dLGN_modelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runP1MP()', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr dLGN_modelDB']
},
'140249_b1':
{
'variant': 'Fig 4 B1',
'compile': ['cd dLGN_modelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runP1HP()', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr dLGN_modelDB']
},
'140249_a2':
{
'variant': 'Fig 4 A2',
'compile': ['cd dLGN_modelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runP2MP()', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr dLGN_modelDB']
},
'140249_b2':
{
'variant': 'Fig 4 B2',
'compile': ['cd dLGN_modelDB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.runP2HP()', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr dLGN_modelDB']
},
'125857_frb3':
{
'variant': 'FRB3',
'compile': ['cd FRB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("FRB3")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr FRB']
},
'125857_frb_12_19':
{
'variant': 'FRB_12_19',
'compile': ['cd FRB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("FRB_12_19")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr FRB']
},
'125857_frb_12_21':
{
'variant': 'FRB_12_21',
'compile': ['cd FRB', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")', 'h.restart("FRB_12_21")', 'h.run()'],
'cleanup': ['cd ..', 'rm -fr FRB']
},
'150240':
{
'compile': ['cd TCconvergenceModel', 'nrnivmodl'],
'launch': ['nrngui -python'],
'run': ['from neuron import h, gui', 'h.load_file("mosinit.hoc")'],
'cleanup': ['cd ..', 'rm -fr TCconvergenceModel']
}
}
protocol = dict(automatically_curated_protocols)
protocol.update(manually_curated_protocols)
if __name__ == '__main__':
import json
multi = {}
all_ids = {}
for key in protocol:
split = key.split('_')
all_ids[split[0]] = 0
if len(split) > 1:
if split[0] not in multi:
multi[split[0]] = []
multi[split[0]].append([protocol[key]['variant'], key])
for id in multi:
multi[id] = sorted(multi[id], key=lambda row: row[0])
print json.dumps(multi)
print
print
print 'Protocols for %d models' % len(all_ids.keys())
print 'Number of models with multiple protocols: %d' % len(multi.keys())
print 'Total number of protocols: %d' % len(protocol.keys())