├── .gitignore ├── .travis.yml ├── CNS2017 ├── BluePyOpt │ ├── BluePyOpt.ipynb │ ├── BluePyOpt_exercise.ipynb │ └── simple.swc ├── NEURON │ ├── NEURON_intro.ipynb │ ├── NEURON_morph_synapses.ipynb │ └── morphology │ │ ├── C060114A7.asc │ │ └── LICENSE ├── README.md ├── admin │ ├── Makefile │ ├── Vagrantfile │ ├── neuron.yml │ └── playbook.yml └── eFEL │ ├── data │ ├── exp_APWaveform_ch20_2035.dat │ ├── exp_APWaveform_ch20_3032.dat │ ├── exp_APWaveform_ch20_4036.dat │ ├── exp_APWaveform_ch21_2035.dat │ ├── exp_APWaveform_ch21_3032.dat │ ├── exp_APWaveform_ch21_4036.dat │ ├── exp_IDRest_ch20_2113.dat │ ├── exp_IDRest_ch20_3110.dat │ ├── exp_IDRest_ch20_4114.dat │ ├── exp_IDRest_ch21_2113.dat │ ├── exp_IDRest_ch21_3110.dat │ ├── exp_IDRest_ch21_4114.dat │ ├── exp_IV_ch20_2029.dat │ ├── exp_IV_ch20_3026.dat │ ├── exp_IV_ch20_4030.dat │ ├── exp_IV_ch21_2029.dat │ ├── exp_IV_ch21_3026.dat │ └── exp_IV_ch21_4030.dat │ ├── eFeatures.png │ └── efel.ipynb ├── Dockerfile ├── EBRAINS2022 ├── create_venv.sh ├── ephys.tar ├── tutorial1 │ ├── .DS_Store │ ├── 1.Simple cell.ipynb │ ├── mechanisms │ │ ├── .DS_Store │ │ ├── NaTg.mod │ │ └── SKv3_1.mod │ └── simple.swc └── tutorial2 │ ├── .DS_Store │ ├── bulk_extraction │ └── 2.Bulk extraction.ipynb │ └── l5pc │ ├── .gitignore │ ├── L5PC.ipynb │ ├── checkpoints │ └── .gitignore │ ├── config │ ├── features.json │ ├── fixed_params.json │ ├── mechanisms.json │ ├── parameters.json │ ├── params.json │ └── protocols.json │ ├── figures │ └── .gitignore │ ├── l5pc_analysis.py │ ├── l5pc_evaluator.py │ ├── l5pc_model.py │ ├── mechanisms │ ├── CaDynamics_E2.mod │ ├── Ca_HVA.mod │ ├── Ca_LVAst.mod │ ├── Ih.mod │ ├── Im.mod │ ├── K_Pst.mod │ ├── K_Tst.mod │ ├── LICENSE │ ├── NaTa_t.mod │ ├── NaTs2_t.mod │ ├── Nap_Et2.mod │ ├── SK_E2.mod │ ├── SKv3_1.mod │ └── dummy.inc │ ├── morphology │ ├── C060114A7.asc │ └── LICENSE │ └── opt_l5pc.py ├── FENS2016 ├── .gitignore ├── ABI_model │ ├── Sst-IRES-Cre_Ai14_IVSCC_-183332.05.02.01_486041253_m.swc │ ├── cell_evaluator.py │ ├── cell_model.py │ ├── checkpoints │ │ ├── checkpoint_10.pkl │ │ ├── checkpoint_2.pkl │ │ └── checkpoint_8.pkl │ ├── config │ │ ├── features.json │ │ ├── mechanisms.json │ │ ├── parameters.json │ │ └── protocols.json │ ├── data │ │ └── 475049288.nwb │ ├── modfiles │ │ ├── CaDynamics.mod │ │ ├── Ca_HVA.mod │ │ ├── Ca_LVA.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── Im_v2.mod │ │ ├── K_P.mod │ │ ├── K_T.mod │ │ ├── Kd.mod │ │ ├── Kv2like.mod │ │ ├── Kv3_1.mod │ │ ├── NaTa.mod │ │ ├── NaTs.mod │ │ ├── NaV.mod │ │ ├── Nap.mod │ │ └── SK.mod │ ├── orig_parameters.json │ └── single_cell_model.ipynb ├── LICENSE.txt ├── README.md ├── exercise │ ├── Sst-IRES-Cre_Ai14_IVSCC_-183332.05.02.01_486041253_m.swc │ ├── cell_evaluator.py │ ├── cell_model.py │ ├── checkpoints │ │ ├── checkpoint_10.pkl │ │ ├── checkpoint_2.pkl │ │ └── checkpoint_8.pkl │ ├── config │ │ ├── features.json │ │ ├── mechanisms.json │ │ ├── parameters.json │ │ ├── parameters_start.json │ │ └── protocols.json │ ├── modfiles │ │ ├── CaDynamics.mod │ │ ├── Ca_HVA.mod │ │ ├── Ca_LVA.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── Im_v2.mod │ │ ├── K_P.mod │ │ ├── K_T.mod │ │ ├── Kd.mod │ │ ├── Kv2like.mod │ │ ├── Kv3_1.mod │ │ ├── NaTa.mod │ │ ├── NaTs.mod │ │ ├── NaV.mod │ │ ├── Nap.mod │ │ └── SK.mod │ ├── opt_challenge.ipynb │ └── orig_parameters.json └── scoring │ ├── Sst-IRES-Cre_Ai14_IVSCC_-183332.05.02.01_486041253_m.swc │ ├── cell_evaluator.py │ ├── cell_model.py │ ├── checkpoints │ ├── checkpoint_10.pkl │ ├── checkpoint_2.pkl │ └── checkpoint_8.pkl │ ├── config │ ├── features.json │ ├── mechanisms.json │ ├── parameters.json │ └── protocols.json │ ├── modfiles │ ├── CaDynamics.mod │ ├── Ca_HVA.mod │ ├── Ca_LVA.mod │ ├── Ih.mod │ ├── Im.mod │ ├── Im_v2.mod │ ├── K_P.mod │ ├── K_T.mod │ ├── Kd.mod │ ├── Kv2like.mod │ ├── Kv3_1.mod │ ├── NaTa.mod │ ├── NaTs.mod │ ├── NaV.mod │ ├── Nap.mod │ └── SK.mod │ ├── orig_parameters.json │ ├── scoring.ipynb │ └── students_par │ ├── parameters_Arlindo.json │ ├── parameters_Luis.json │ ├── parameters_Markus.json │ └── parameters_Tansel.json ├── General ├── Installation │ ├── Neuron.md │ └── README.md └── README.md ├── HBPSchool2016 ├── README.md ├── admin │ └── VMs │ │ └── vagrant │ │ ├── .gitignore │ │ ├── Makefile │ │ ├── Vagrantfile │ │ ├── data │ │ └── hbpschool.jpg │ │ ├── neuron.yml │ │ └── playbook.yml ├── demos │ ├── efeatures │ │ ├── L5_TTPC2.zip │ │ ├── L5_TTPC2_cADpyr232_1 │ │ │ ├── .provenance.json │ │ │ ├── CHANGELOG │ │ │ ├── LICENSE │ │ │ ├── README │ │ │ ├── VERSION │ │ │ ├── biophysics.hoc │ │ │ ├── cellinfo.json │ │ │ ├── constants.hoc │ │ │ ├── creategui.hoc │ │ │ ├── createsimulation.hoc │ │ │ ├── current_amps.dat │ │ │ ├── init.hoc │ │ │ ├── mechanisms │ │ │ │ ├── CaDynamics_E2.mod │ │ │ │ ├── Ca_HVA.mod │ │ │ │ ├── Ca_LVAst.mod │ │ │ │ ├── Ih.mod │ │ │ │ ├── Im.mod │ │ │ │ ├── K_Pst.mod │ │ │ │ ├── K_Tst.mod │ │ │ │ ├── NaTa_t.mod │ │ │ │ ├── NaTs2_t.mod │ │ │ │ ├── Nap_Et2.mod │ │ │ │ ├── ProbAMPANMDA_EMS.mod │ │ │ │ ├── ProbGABAAB_EMS.mod │ │ │ │ ├── SK_E2.mod │ │ │ │ └── SKv3_1.mod │ │ │ ├── morphology.hoc │ │ │ ├── morphology │ │ │ │ └── dend-C060114A7_axon-C060116A3_-_Clone_2.asc │ │ │ ├── mosinit.hoc │ │ │ ├── ringplot.hoc │ │ │ ├── run.py │ │ │ ├── run_RmpRiTau.py │ │ │ ├── run_RmpRiTau_py.sh │ │ │ ├── run_hoc.sh │ │ │ ├── run_py.sh │ │ │ ├── synapses │ │ │ │ ├── mtype_map.tsv │ │ │ │ ├── synapses.hoc │ │ │ │ ├── synapses.tsv │ │ │ │ └── synconf.txt │ │ │ └── template.hoc │ │ ├── data │ │ │ ├── exp_APWaveform_ch0_904.V.Step.txt │ │ │ ├── exp_APWaveform_ch0_914.V.Step.txt │ │ │ ├── exp_APWaveform_ch0_924.V.Step.txt │ │ │ ├── exp_IDrest_ch0_944.V.Step.txt │ │ │ ├── exp_IDrest_ch0_999.V.Step.txt │ │ │ ├── exp_IV_ch0_869.V.Step.txt │ │ │ ├── exp_IV_ch0_879.V.Step.txt │ │ │ └── exp_IV_ch0_889.V.Step.txt │ │ └── efel.ipynb │ └── optimisation │ │ ├── BluePyOpt.ipynb │ │ ├── BluePyOpt_exercise.ipynb │ │ ├── data │ │ └── simple.swc └── exercise │ └── config │ └── features.json ├── LICENSE ├── Makefile ├── NSAS2017 ├── BluePyOpt │ ├── BluePyOpt.ipynb │ ├── BluePyOpt_exercise.ipynb │ └── simple.swc ├── NMC_portal │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── NEURON_NMC_nrniv.png │ ├── NEURON_NMC_portal.ipynb │ ├── NEURON_NMC_portal.png │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── hoc_recordings │ │ └── soma_voltage.dat │ ├── init.hoc │ ├── mechanisms │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_HVA.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ │ └── dend-C060114A7_axon-C060116A3_-_Clone_2.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ │ ├── mtype_map.tsv │ │ ├── synapses.all.tsv │ │ ├── synapses.hoc │ │ ├── synapses.paired-patch-clamp.tsv │ │ ├── synapses.tsv │ │ └── synconf.txt │ └── template.hoc ├── README.md └── eFEL │ ├── data │ ├── exp_APWaveform_ch20_2035.dat │ ├── exp_APWaveform_ch20_3032.dat │ ├── exp_APWaveform_ch20_4036.dat │ ├── exp_APWaveform_ch21_2035.dat │ ├── exp_APWaveform_ch21_3032.dat │ ├── exp_APWaveform_ch21_4036.dat │ ├── exp_IDRest_ch20_2113.dat │ ├── exp_IDRest_ch20_3110.dat │ ├── exp_IDRest_ch20_4114.dat │ ├── exp_IDRest_ch21_2113.dat │ ├── exp_IDRest_ch21_3110.dat │ ├── exp_IDRest_ch21_4114.dat │ ├── exp_IV_ch20_2029.dat │ ├── exp_IV_ch20_3026.dat │ ├── exp_IV_ch20_4030.dat │ ├── exp_IV_ch21_2029.dat │ ├── exp_IV_ch21_3026.dat │ └── exp_IV_ch21_4030.dat │ └── efel.ipynb ├── README.md ├── SfN2017 ├── BluePyOpt │ ├── BluePyOpt.ipynb │ └── morphology │ │ ├── C060114A7.asc │ │ └── LICENSE ├── README.md ├── admin │ ├── Vagrantfile │ ├── neuron.yml │ └── playbook.yml └── eFEL │ ├── data │ ├── exp_APWaveform_ch20_2035.dat │ ├── exp_APWaveform_ch20_3032.dat │ ├── exp_APWaveform_ch20_4036.dat │ ├── exp_APWaveform_ch21_2035.dat │ ├── exp_APWaveform_ch21_3032.dat │ ├── exp_APWaveform_ch21_4036.dat │ ├── exp_IDRest_ch20_2113.dat │ ├── exp_IDRest_ch20_3110.dat │ ├── exp_IDRest_ch20_4114.dat │ ├── exp_IDRest_ch21_2113.dat │ ├── exp_IDRest_ch21_3110.dat │ ├── exp_IDRest_ch21_4114.dat │ ├── exp_IV_ch20_2029.dat │ ├── exp_IV_ch20_3026.dat │ ├── exp_IV_ch20_4030.dat │ ├── exp_IV_ch21_2029.dat │ ├── exp_IV_ch21_3026.dat │ └── exp_IV_ch21_4030.dat │ ├── eFeatures.png │ └── efel.ipynb └── YRE2016 ├── BluePyOpt ├── README.md ├── l5pc │ ├── .gitignore │ ├── L5PC.ipynb │ ├── LICENSE │ ├── config │ │ ├── features.json │ │ ├── fixed_params.json │ │ ├── mechanisms.json │ │ ├── parameters.json │ │ ├── params.json │ │ └── protocols.json │ ├── l5pc_evaluator.py │ ├── l5pc_model.py │ ├── mechanisms │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_HVA.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── LICENSE │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ └── morphology │ │ ├── C060114A7.asc │ │ └── LICENSE └── simplecell │ ├── simple.swc │ └── simplecell.ipynb ├── NMC ├── L5_TTPC2_cADpyr232_1.zip ├── L5_TTPC2_cADpyr232_1 │ ├── .provenance.json │ ├── CHANGELOG │ ├── LICENSE │ ├── README │ ├── VERSION │ ├── biophysics.hoc │ ├── cellinfo.json │ ├── constants.hoc │ ├── creategui.hoc │ ├── createsimulation.hoc │ ├── current_amps.dat │ ├── init.hoc │ ├── mechanisms │ │ ├── CaDynamics_E2.mod │ │ ├── Ca_HVA.mod │ │ ├── Ca_LVAst.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── K_Pst.mod │ │ ├── K_Tst.mod │ │ ├── NaTa_t.mod │ │ ├── NaTs2_t.mod │ │ ├── Nap_Et2.mod │ │ ├── ProbAMPANMDA_EMS.mod │ │ ├── ProbGABAAB_EMS.mod │ │ ├── SK_E2.mod │ │ └── SKv3_1.mod │ ├── morphology.hoc │ ├── morphology │ │ └── dend-C060114A7_axon-C060116A3_-_Clone_2.asc │ ├── mosinit.hoc │ ├── ringplot.hoc │ ├── run.py │ ├── run_RmpRiTau.py │ ├── run_RmpRiTau_py.sh │ ├── run_hoc.sh │ ├── run_py.sh │ ├── synapses │ │ ├── mtype_map.tsv │ │ ├── synapses.hoc │ │ ├── synapses.tsv │ │ └── synconf.txt │ └── template.hoc ├── README.md └── nmc_package_gui.png ├── Neuron ├── Neuron simulator tutorial.ipynb └── README.md ├── README.md └── eFEL ├── README.md └── efel.ipynb /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | .ipynb_checkpoints 3 | x86_64 4 | .DS_Store 5 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | script: make test 2 | -------------------------------------------------------------------------------- /CNS2017/BluePyOpt/simple.swc: -------------------------------------------------------------------------------- 1 | # Dummy granule cell morphology 2 | 1 1 -50.0 0.0 0.0 50.0 -1 3 | 2 1 0.0 0.0 0.0 50.0 1 4 | 3 1 50.0 0.0 0.0 50.0 2 5 | -------------------------------------------------------------------------------- /CNS2017/NEURON/morphology/LICENSE: -------------------------------------------------------------------------------- 1 | The CC-BY-NC-SA license applies, as indicated by headers in the 2 | respective source files. 3 | 4 | https://creativecommons.org/licenses/by-nc-sa/4.0/ 5 | 6 | The detailed text is available here 7 | https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode 8 | 9 | or in this tarball in the seperate file LICENSE_CC-BY-CA-SA-4.0 10 | 11 | 12 | The HOC code, Python code, synapse MOD code and cell morphology are licensed with the above mentioned CC-BY-NC-SA license. 13 | 14 | 15 | For models for which the original source is available on ModelDB, any 16 | specific licenses on mentioned on ModelDB, or the generic License of ModelDB 17 | apply: 18 | 19 | 1) Ih model 20 | Author: Stefan Hallermann 21 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=144526&file=\HallermannEtAl2012\h.mod 22 | 23 | 2) StochKv model 24 | Authors: Zach Mainen Adaptations: Kamran Diba, Mickey London, Peter N. Steinmetz, Werner Van Geit 25 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=125385&file=\Sbpap_code\mod\skm.mod 26 | 27 | 3) D-type K current model 28 | Authors: Yuguo Yu 29 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=135898&file=\YuEtAlPNAS2007\kd.mod 30 | 31 | 4) Internal calcium concentration model 32 | Author: Alain Destexhe 33 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=3670&file=\NTW_NEW\capump.mod 34 | 35 | 5) Ca_LVAst, Im, K_Tst, NaTa_t, SK_E2, Ca_HVA, Ih, K_Pst, Nap_Et2, NaTs2_t, SKv3_1 36 | Author: Etay Hay, Shaul Druckmann, Srikanth Ramaswamy, James King, Werner Van Geit 37 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=139653&file=\L5bPCmodelsEH\mod\ 38 | -------------------------------------------------------------------------------- /CNS2017/admin/Makefile: -------------------------------------------------------------------------------- 1 | create: 2 | vagrant up --provider virtualbox 3 | up: 4 | vagrant up 5 | provision: 6 | vagrant provision 7 | clean: 8 | vagrant destroy 9 | ansible: 10 | ansible-playbook -vv --private-key=.vagrant/machines/default/virtualbox/private_key -u vagrant -i .vagrant/provisioners/ansible/inventory/vagrant_ansible_inventory playbook.yml 11 | password: 12 | pip install passlib 13 | python -c 'import crypt, getpass, base64, os; print crypt.crypt(getpass.getpass(), base64.b64encode(os.urandom(16)))' 14 | -------------------------------------------------------------------------------- /CNS2017/admin/Vagrantfile: -------------------------------------------------------------------------------- 1 | # -*- mode: ruby -*- 2 | # vi: set ft=ruby : 3 | 4 | 5 | Vagrant.configure(2) do |config| 6 | # config.vm.define "vb32" do |vb32| 7 | # vb32.vm.box = "ubuntu/trusty32" 8 | # vb32.vm.provider :virtualbox do |vb| 9 | # vb.customize ["modifyvm", :id, "--hwvirtex", "off"] 10 | # vb.name = "cns2017.32bit" 11 | # end 12 | # end 13 | 14 | config.vm.define "vb64" do |vb64| 15 | vb64.vm.box = "ubuntu/trusty64" 16 | vb64.vm.provider :virtualbox do |vb| 17 | vb.customize ["modifyvm", :id, "--hwvirtex", "on"] 18 | vb.name = "cns2017" 19 | end 20 | end 21 | 22 | 23 | config.vm.provider :virtualbox do |vb| 24 | vb.customize ["modifyvm", :id, "--memory", "2048"] 25 | vb.customize ["modifyvm", :id, "--cpus", "4"] 26 | vb.customize ['modifyvm', :id, '--clipboard', 'bidirectional'] 27 | vb.gui = true 28 | end 29 | 30 | 31 | config.vm.provision "ansible" do |ansible| 32 | ansible.playbook = "playbook.yml" 33 | # ansible.verbose = "v" 34 | end 35 | end 36 | 37 | -------------------------------------------------------------------------------- /CNS2017/admin/neuron.yml: -------------------------------------------------------------------------------- 1 | --- 2 | 3 | - name: Get iv Source 4 | get_url: url={{ download_path }}/{{ iv_tarball }} dest={{ src_dir }}/{{ iv_tarball }} 5 | 6 | - name: Get nrn Source 7 | get_url: url={{ download_path }}/{{ nrn_tarball }} dest={{ src_dir }}/{{ nrn_tarball }} 8 | 9 | - name: Untar iv source 10 | unarchive: copy=no src={{ src_dir }}/{{ iv_tarball }} dest={{ src_dir }} 11 | 12 | - name: Untar nrn source 13 | unarchive: copy=no src={{ src_dir }}/{{ nrn_tarball }} dest={{ src_dir }} 14 | 15 | - name: configure iv 16 | shell: "./configure --prefix={{ nrn_prefix }}" 17 | args: 18 | chdir: "{{ iv_src_dir }}" 19 | 20 | - name: build iv 21 | shell: make 22 | args: 23 | chdir: "{{ iv_src_dir }}" 24 | 25 | - name: install iv 26 | shell: make install 27 | args: 28 | chdir: "{{ iv_src_dir }}" 29 | 30 | - name: configure neuron 31 | shell: "./configure --with-iv={{ nrn_prefix }} --with-nrnpython --prefix={{ nrn_prefix }}" 32 | args: 33 | chdir: "{{ nrn_src_dir }}" 34 | 35 | - name: build neuron 36 | shell: make 37 | args: 38 | chdir: "{{ nrn_src_dir }}" 39 | 40 | - name: install neuron 41 | shell: make install 42 | args: 43 | chdir: "{{ nrn_src_dir }}" 44 | 45 | - 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-------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlueBrain/SimulationTutorials/44fa01c22bc83fbbe8a01d3580de75ffadf92ea4/CNS2017/eFEL/eFeatures.png -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 1 | # Copyright (c) 2016, EPFL/Blue Brain Project 2 | # 3 | # This file is part of BluePyOpt 4 | # 5 | # This library is free software; you can redistribute it and/or modify it under 6 | # the terms of the GNU Lesser General Public License version 3.0 as published 7 | # by the Free Software Foundation. 8 | # 9 | # This library is distributed in the hope that it will be useful, but WITHOUT 10 | # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 11 | # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more 12 | # details. 13 | # 14 | # You should have received a copy of the GNU Lesser General Public License 15 | # along with this library; if not, write to the Free Software Foundation, Inc., 16 | # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. 17 | 18 | FROM andrewosh/binder-base 19 | MAINTAINER Werner Van Geit 20 | 21 | USER root 22 | 23 | RUN apt-get update 24 | RUN apt-get install -y unzip wget libx11-6 python-dev git build-essential libncurses-dev 25 | RUN wget https://bootstrap.pypa.io/get-pip.py 26 | RUN python get-pip.py 27 | RUN wget http://www.neuron.yale.edu/ftp/neuron/versions/v7.4/nrn-7.4.x86_64.deb 28 | RUN dpkg -i nrn-7.4.x86_64.deb 29 | RUN rm nrn-7.4.x86_64.deb 30 | 31 | RUN pip install git+git://github.com/BlueBrain/deap 32 | RUN pip install bluepyopt 33 | RUN pip install neurom 34 | RUN pip install allensdk 35 | 36 | RUN wget https://bbp.epfl.ch/nmc-portal/documents/10184/1921755/L5_TTPC2_cADpyr232_1.zip 37 | RUN unzip L5_TTPC2_cADpyr232_1.zip 38 | 39 | ENV PYTHONPATH /usr/local/nrn/lib/python:$PYTHONPATH 40 | -------------------------------------------------------------------------------- /EBRAINS2022/create_venv.sh: -------------------------------------------------------------------------------- 1 | deactivate 2 | 3 | export VENV=myvenv 4 | python3 -m venv $VENV 5 | source $VENV/bin/activate 6 | 7 | ./$VENV/bin/pip install --upgrade setuptools pip 8 | ./$VENV/bin/pip install wheel 9 | ./$VENV/bin/pip install jupyter 10 | ./$VENV/bin/pip install neurom 11 | ./$VENV/bin/pip install bluepyopt 12 | ./$VENV/bin/pip install git+https://github.com/BlueBrain/BluePyEfe@BPE2 13 | 14 | ./$VENV/bin/ipython kernel install --name "EBRAINS2022" --user 15 | -------------------------------------------------------------------------------- /EBRAINS2022/ephys.tar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlueBrain/SimulationTutorials/44fa01c22bc83fbbe8a01d3580de75ffadf92ea4/EBRAINS2022/ephys.tar -------------------------------------------------------------------------------- /EBRAINS2022/tutorial1/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlueBrain/SimulationTutorials/44fa01c22bc83fbbe8a01d3580de75ffadf92ea4/EBRAINS2022/tutorial1/.DS_Store -------------------------------------------------------------------------------- /EBRAINS2022/tutorial1/mechanisms/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlueBrain/SimulationTutorials/44fa01c22bc83fbbe8a01d3580de75ffadf92ea4/EBRAINS2022/tutorial1/mechanisms/.DS_Store -------------------------------------------------------------------------------- /EBRAINS2022/tutorial1/mechanisms/SKv3_1.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Rettig et.al (1992) EMBO J 11, no. 7: 2473-86. 3 | : Methods: Grupe et al. (1990) EMBO J 9, 1749-1756. 4 | : LJP: OK, no LJP, "Patch pipetes were filed with the normal bathing solution in al experiments."" 5 | 6 | NEURON { 7 | SUFFIX SKv3_1 8 | USEION k READ ek WRITE ik 9 | RANGE gSKv3_1bar, gSKv3_1, ik 10 | } 11 | 12 | UNITS { 13 | (S) = (siemens) 14 | (mV) = (millivolt) 15 | (mA) = (milliamp) 16 | } 17 | 18 | PARAMETER { 19 | gSKv3_1bar = 0.00001 (S/cm2) 20 | } 21 | 22 | ASSIGNED { 23 | v (mV) 24 | ek (mV) 25 | ik (mA/cm2) 26 | gSKv3_1 (S/cm2) 27 | mInf 28 | mTau 29 | } 30 | 31 | STATE { 32 | m 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gSKv3_1 = gSKv3_1bar*m 38 | ik = gSKv3_1*(v-ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates() 43 | m' = (mInf-m)/mTau 44 | } 45 | 46 | INITIAL{ 47 | rates() 48 | m = mInf 49 | } 50 | 51 | PROCEDURE rates(){ 52 | UNITSOFF 53 | mInf = 1/(1+exp(((v -(18.700))/(-9.700)))) 54 | mTau = 0.2*20.000/(1+exp(((v -(-46.560))/(-44.140)))) 55 | UNITSON 56 | } 57 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial1/simple.swc: -------------------------------------------------------------------------------- 1 | # Dummy granule cell morphology 2 | 1 1 -10.0 0.0 0.0 10.0 -1 3 | 2 1 0.0 0.0 0.0 10.0 1 4 | 3 1 10.0 0.0 0.0 10.0 2 5 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlueBrain/SimulationTutorials/44fa01c22bc83fbbe8a01d3580de75ffadf92ea4/EBRAINS2022/tutorial2/.DS_Store -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/.gitignore: -------------------------------------------------------------------------------- 1 | /*.pkl 2 | /.ipynb_checkpoints/ 3 | /L5PC.py 4 | /.ipython 5 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/checkpoints/.gitignore: -------------------------------------------------------------------------------- 1 | /* 2 | !.gitignore 3 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/config/fixed_params.json: -------------------------------------------------------------------------------- 1 | { 2 | "global": [ 3 | [ 4 | "v_init", 5 | -65 6 | ], 7 | [ 8 | "celsius", 9 | 34 10 | ] 11 | ], 12 | "all": [ 13 | [ 14 | "g_pas", 15 | 3e-05, 16 | "uniform" 17 | ], 18 | [ 19 | "e_pas", 20 | -75, 21 | "uniform" 22 | ], 23 | [ 24 | "cm", 25 | 1, 26 | "uniform" 27 | ], 28 | [ 29 | "Ra", 30 | 100, 31 | "uniform" 32 | ] 33 | ], 34 | "apical": [ 35 | [ 36 | "ena", 37 | 50, 38 | "uniform" 39 | ], 40 | [ 41 | "ek", 42 | -85, 43 | "uniform" 44 | ], 45 | [ 46 | "cm", 47 | 2, 48 | "uniform" 49 | ] 50 | ], 51 | "somatic": [ 52 | [ 53 | "ena", 54 | 50, 55 | "uniform" 56 | ], 57 | [ 58 | "ek", 59 | -85, 60 | "uniform" 61 | ] 62 | ], 63 | "basal": [ 64 | [ 65 | "cm", 66 | 2, 67 | "uniform" 68 | ] 69 | ], 70 | "axonal": [ 71 | [ 72 | "ena", 73 | 50, 74 | "uniform" 75 | ], 76 | [ 77 | "ek", 78 | -85, 79 | "uniform" 80 | ] 81 | ] 82 | } 83 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/config/mechanisms.json: -------------------------------------------------------------------------------- 1 | { 2 | "basal": [ 3 | "Ih" 4 | ], 5 | "all": [ 6 | "pas" 7 | ], 8 | "apical": [ 9 | "Ih", 10 | "Im", 11 | "SKv3_1", 12 | "NaTs2_t" 13 | ], 14 | "axonal": [ 15 | "Ca_LVAst", 16 | "Ca_HVA", 17 | "CaDynamics_E2", 18 | "SKv3_1", 19 | "SK_E2", 20 | "K_Tst", 21 | "K_Pst", 22 | "Nap_Et2", 23 | "NaTa_t" 24 | ], 25 | "somatic": [ 26 | "NaTs2_t", 27 | "SKv3_1", 28 | "SK_E2", 29 | "CaDynamics_E2", 30 | "Ca_HVA", 31 | "Ca_LVAst", 32 | "Ih" 33 | ] 34 | } 35 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/figures/.gitignore: -------------------------------------------------------------------------------- 1 | /*.eps 2 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/mechanisms/CaDynamics_E2.mod: -------------------------------------------------------------------------------- 1 | : Dynamics that track inside calcium concentration 2 | : modified from Destexhe et al. 1994 3 | 4 | NEURON { 5 | SUFFIX CaDynamics_E2 6 | USEION ca READ ica WRITE cai 7 | RANGE decay, gamma, minCai, depth 8 | } 9 | 10 | UNITS { 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | FARADAY = (faraday) (coulombs) 14 | (molar) = (1/liter) 15 | (mM) = (millimolar) 16 | (um) = (micron) 17 | } 18 | 19 | PARAMETER { 20 | gamma = 0.05 : percent of free calcium (not buffered) 21 | decay = 80 (ms) : rate of removal of calcium 22 | depth = 0.1 (um) : depth of shell 23 | minCai = 1e-4 (mM) 24 | } 25 | 26 | ASSIGNED {ica (mA/cm2)} 27 | 28 | STATE { 29 | cai (mM) 30 | } 31 | 32 | BREAKPOINT { SOLVE states METHOD cnexp } 33 | 34 | DERIVATIVE states { 35 | cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay 36 | } 37 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/mechanisms/Ca_HVA.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993 3 | 4 | NEURON { 5 | SUFFIX Ca_HVA 6 | USEION ca READ eca WRITE ica 7 | RANGE gCa_HVAbar, gCa_HVA, ica 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gCa_HVAbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | eca (mV) 23 | ica (mA/cm2) 24 | gCa (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | hInf 30 | hTau 31 | hAlpha 32 | hBeta 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | gCa = gCa_HVAbar*m*m*h 43 | ica = gCa*(v-eca) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates(){ 59 | UNITSOFF 60 | if((v == -27) ){ 61 | v = v+0.0001 62 | } 63 | mAlpha = (0.055*(-27-v))/(exp((-27-v)/3.8) - 1) 64 | mBeta = (0.94*exp((-75-v)/17)) 65 | mInf = mAlpha/(mAlpha + mBeta) 66 | mTau = 1/(mAlpha + mBeta) 67 | hAlpha = (0.000457*exp((-13-v)/50)) 68 | hBeta = (0.0065/(exp((-v-15)/28)+1)) 69 | hInf = hAlpha/(hAlpha + hBeta) 70 | hTau = 1/(hAlpha + hBeta) 71 | UNITSON 72 | } 73 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/mechanisms/Ca_LVAst.mod: -------------------------------------------------------------------------------- 1 | :Comment : LVA ca channel. Note: mtau is an approximation from the plots 2 | :Reference : : Avery and Johnston 1996, tau from Randall 1997 3 | :Comment: shifted by -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | NEURON { 7 | SUFFIX Ca_LVAst 8 | USEION ca READ eca WRITE ica 9 | RANGE gCa_LVAstbar, gCa_LVAst, ica 10 | } 11 | 12 | UNITS { 13 | (S) = (siemens) 14 | (mV) = (millivolt) 15 | (mA) = (milliamp) 16 | } 17 | 18 | PARAMETER { 19 | gCa_LVAstbar = 0.00001 (S/cm2) 20 | } 21 | 22 | ASSIGNED { 23 | v (mV) 24 | eca (mV) 25 | ica (mA/cm2) 26 | gCa_LVAst (S/cm2) 27 | mInf 28 | mTau 29 | hInf 30 | hTau 31 | } 32 | 33 | STATE { 34 | m 35 | h 36 | } 37 | 38 | BREAKPOINT { 39 | SOLVE states METHOD cnexp 40 | gCa_LVAst = gCa_LVAstbar*m*m*h 41 | ica = gCa_LVAst*(v-eca) 42 | } 43 | 44 | DERIVATIVE states { 45 | rates() 46 | m' = (mInf-m)/mTau 47 | h' = (hInf-h)/hTau 48 | } 49 | 50 | INITIAL{ 51 | rates() 52 | m = mInf 53 | h = hInf 54 | } 55 | 56 | PROCEDURE rates(){ 57 | LOCAL qt 58 | qt = 2.3^((34-21)/10) 59 | 60 | UNITSOFF 61 | v = v + 10 62 | mInf = 1.0000/(1+ exp((v - -30.000)/-6)) 63 | mTau = (5.0000 + 20.0000/(1+exp((v - -25.000)/5)))/qt 64 | hInf = 1.0000/(1+ exp((v - -80.000)/6.4)) 65 | hTau = (20.0000 + 50.0000/(1+exp((v - -40.000)/7)))/qt 66 | v = v - 10 67 | UNITSON 68 | } 69 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/mechanisms/Ih.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Kole,Hallermann,and Stuart, J. Neurosci. 2006 3 | 4 | NEURON { 5 | SUFFIX Ih 6 | NONSPECIFIC_CURRENT ihcn 7 | RANGE gIhbar, gIh, ihcn 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gIhbar = 0.00001 (S/cm2) 18 | ehcn = -45.0 (mV) 19 | } 20 | 21 | ASSIGNED { 22 | v (mV) 23 | ihcn (mA/cm2) 24 | gIh (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | } 30 | 31 | STATE { 32 | m 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gIh = gIhbar*m 38 | ihcn = gIh*(v-ehcn) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates() 43 | m' = (mInf-m)/mTau 44 | } 45 | 46 | INITIAL{ 47 | rates() 48 | m = mInf 49 | } 50 | 51 | PROCEDURE rates(){ 52 | UNITSOFF 53 | if(v == -154.9){ 54 | v = v + 0.0001 55 | } 56 | mAlpha = 0.001*6.43*(v+154.9)/(exp((v+154.9)/11.9)-1) 57 | mBeta = 0.001*193*exp(v/33.1) 58 | mInf = mAlpha/(mAlpha + mBeta) 59 | mTau = 1/(mAlpha + mBeta) 60 | UNITSON 61 | } 62 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/mechanisms/Im.mod: -------------------------------------------------------------------------------- 1 | :Reference : : Adams et al. 1982 - M-currents and other potassium currents in bullfrog sympathetic neurones 2 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 3 | 4 | NEURON { 5 | SUFFIX Im 6 | USEION k READ ek WRITE ik 7 | RANGE gImbar, gIm, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gImbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | gIm (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | } 30 | 31 | STATE { 32 | m 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gIm = gImbar*m 38 | ik = gIm*(v-ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates() 43 | m' = (mInf-m)/mTau 44 | } 45 | 46 | INITIAL{ 47 | rates() 48 | m = mInf 49 | } 50 | 51 | PROCEDURE rates(){ 52 | LOCAL qt 53 | qt = 2.3^((34-21)/10) 54 | 55 | UNITSOFF 56 | mAlpha = 3.3e-3*exp(2.5*0.04*(v - -35)) 57 | mBeta = 3.3e-3*exp(-2.5*0.04*(v - -35)) 58 | mInf = mAlpha/(mAlpha + mBeta) 59 | mTau = (1/(mAlpha + mBeta))/qt 60 | UNITSON 61 | } 62 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/mechanisms/K_Pst.mod: -------------------------------------------------------------------------------- 1 | :Comment : The persistent component of the K current 2 | :Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | :Comment : shifted -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | 7 | NEURON { 8 | SUFFIX K_Pst 9 | USEION k READ ek WRITE ik 10 | RANGE gK_Pstbar, gK_Pst, ik 11 | } 12 | 13 | UNITS { 14 | (S) = (siemens) 15 | (mV) = (millivolt) 16 | (mA) = (milliamp) 17 | } 18 | 19 | PARAMETER { 20 | gK_Pstbar = 0.00001 (S/cm2) 21 | } 22 | 23 | ASSIGNED { 24 | v (mV) 25 | ek (mV) 26 | ik (mA/cm2) 27 | gK_Pst (S/cm2) 28 | mInf 29 | mTau 30 | hInf 31 | hTau 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | gK_Pst = gK_Pstbar*m*m*h 42 | ik = gK_Pst*(v-ek) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | LOCAL qt 59 | qt = 2.3^((34-21)/10) 60 | UNITSOFF 61 | v = v + 10 62 | mInf = (1/(1 + exp(-(v+1)/12))) 63 | if(v<-50){ 64 | mTau = (1.25+175.03*exp(-v * -0.026))/qt 65 | }else{ 66 | mTau = ((1.25+13*exp(-v*0.026)))/qt 67 | } 68 | hInf = 1/(1 + exp(-(v+54)/-11)) 69 | hTau = (360+(1010+24*(v+55))*exp(-((v+75)/48)^2))/qt 70 | v = v - 10 71 | UNITSON 72 | } 73 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/mechanisms/K_Tst.mod: -------------------------------------------------------------------------------- 1 | :Comment : The transient component of the K current 2 | :Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | :Comment : shifted -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | NEURON { 7 | SUFFIX K_Tst 8 | USEION k READ ek WRITE ik 9 | RANGE gK_Tstbar, gK_Tst, ik 10 | } 11 | 12 | UNITS { 13 | (S) = (siemens) 14 | (mV) = (millivolt) 15 | (mA) = (milliamp) 16 | } 17 | 18 | PARAMETER { 19 | gK_Tstbar = 0.00001 (S/cm2) 20 | } 21 | 22 | ASSIGNED { 23 | v (mV) 24 | ek (mV) 25 | ik (mA/cm2) 26 | gK_Tst (S/cm2) 27 | mInf 28 | mTau 29 | hInf 30 | hTau 31 | } 32 | 33 | STATE { 34 | m 35 | h 36 | } 37 | 38 | BREAKPOINT { 39 | SOLVE states METHOD cnexp 40 | gK_Tst = gK_Tstbar*(m^4)*h 41 | ik = gK_Tst*(v-ek) 42 | } 43 | 44 | DERIVATIVE states { 45 | rates() 46 | m' = (mInf-m)/mTau 47 | h' = (hInf-h)/hTau 48 | } 49 | 50 | INITIAL{ 51 | rates() 52 | m = mInf 53 | h = hInf 54 | } 55 | 56 | PROCEDURE rates(){ 57 | LOCAL qt 58 | qt = 2.3^((34-21)/10) 59 | 60 | UNITSOFF 61 | v = v + 10 62 | mInf = 1/(1 + exp(-(v+0)/19)) 63 | mTau = (0.34+0.92*exp(-((v+71)/59)^2))/qt 64 | hInf = 1/(1 + exp(-(v+66)/-10)) 65 | hTau = (8+49*exp(-((v+73)/23)^2))/qt 66 | v = v - 10 67 | UNITSON 68 | } 69 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/mechanisms/LICENSE: -------------------------------------------------------------------------------- 1 | The CC-BY-NC-SA license applies, as indicated by headers in the 2 | respective source files. 3 | 4 | https://creativecommons.org/licenses/by-nc-sa/4.0/ 5 | 6 | The detailed text is available here 7 | https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode 8 | 9 | or in this tarball in the seperate file LICENSE_CC-BY-CA-SA-4.0 10 | 11 | 12 | The HOC code, Python code, synapse MOD code and cell morphology are licensed with the above mentioned CC-BY-NC-SA license. 13 | 14 | 15 | For models for which the original source is available on ModelDB, any 16 | specific licenses on mentioned on ModelDB, or the generic License of ModelDB 17 | apply: 18 | 19 | 1) Ih model 20 | Author: Stefan Hallermann 21 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=144526&file=\HallermannEtAl2012\h.mod 22 | 23 | 2) StochKv model 24 | Authors: Zach Mainen Adaptations: Kamran Diba, Mickey London, Peter N. Steinmetz, Werner Van Geit 25 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=125385&file=\Sbpap_code\mod\skm.mod 26 | 27 | 3) D-type K current model 28 | Authors: Yuguo Yu 29 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=135898&file=\YuEtAlPNAS2007\kd.mod 30 | 31 | 4) Internal calcium concentration model 32 | Author: Alain Destexhe 33 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=3670&file=\NTW_NEW\capump.mod 34 | 35 | 5) Ca_LVAst, Im, K_Tst, NaTa_t, SK_E2, Ca_HVA, Ih, K_Pst, Nap_Et2, NaTs2_t, SKv3_1 36 | Author: Etay Hay, Shaul Druckmann, Srikanth Ramaswamy, James King, Werner Van Geit 37 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=139653&file=\L5bPCmodelsEH\mod\ 38 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/mechanisms/NaTa_t.mod: -------------------------------------------------------------------------------- 1 | :Reference :Colbert and Pan 2002 2 | 3 | NEURON { 4 | SUFFIX NaTa_t 5 | USEION na READ ena WRITE ina 6 | RANGE gNaTa_tbar, gNaTa_t, ina 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gNaTa_tbar = 0.00001 (S/cm2) 17 | } 18 | 19 | ASSIGNED { 20 | v (mV) 21 | ena (mV) 22 | ina (mA/cm2) 23 | gNaTa_t (S/cm2) 24 | mInf 25 | mTau 26 | mAlpha 27 | mBeta 28 | hInf 29 | hTau 30 | hAlpha 31 | hBeta 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | gNaTa_t = gNaTa_tbar*m*m*m*h 42 | ina = gNaTa_t*(v-ena) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | LOCAL qt 59 | qt = 2.3^((34-21)/10) 60 | 61 | UNITSOFF 62 | if(v == -38){ 63 | v = v+0.0001 64 | } 65 | mAlpha = (0.182 * (v- -38))/(1-(exp(-(v- -38)/6))) 66 | mBeta = (0.124 * (-v -38))/(1-(exp(-(-v -38)/6))) 67 | mTau = (1/(mAlpha + mBeta))/qt 68 | mInf = mAlpha/(mAlpha + mBeta) 69 | 70 | if(v == -66){ 71 | v = v + 0.0001 72 | } 73 | 74 | hAlpha = (-0.015 * (v- -66))/(1-(exp((v- -66)/6))) 75 | hBeta = (-0.015 * (-v -66))/(1-(exp((-v -66)/6))) 76 | hTau = (1/(hAlpha + hBeta))/qt 77 | hInf = hAlpha/(hAlpha + hBeta) 78 | UNITSON 79 | } 80 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/mechanisms/NaTs2_t.mod: -------------------------------------------------------------------------------- 1 | :Reference :Colbert and Pan 2002 2 | :comment: took the NaTa and shifted both activation/inactivation by 6 mv 3 | 4 | NEURON { 5 | SUFFIX NaTs2_t 6 | USEION na READ ena WRITE ina 7 | RANGE gNaTs2_tbar, gNaTs2_t, ina 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gNaTs2_tbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ena (mV) 23 | ina (mA/cm2) 24 | gNaTs2_t (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | hInf 30 | hTau 31 | hAlpha 32 | hBeta 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | gNaTs2_t = gNaTs2_tbar*m*m*m*h 43 | ina = gNaTs2_t*(v-ena) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates(){ 59 | LOCAL qt 60 | qt = 2.3^((34-21)/10) 61 | 62 | UNITSOFF 63 | if(v == -32){ 64 | v = v+0.0001 65 | } 66 | mAlpha = (0.182 * (v- -32))/(1-(exp(-(v- -32)/6))) 67 | mBeta = (0.124 * (-v -32))/(1-(exp(-(-v -32)/6))) 68 | mInf = mAlpha/(mAlpha + mBeta) 69 | mTau = (1/(mAlpha + mBeta))/qt 70 | 71 | if(v == -60){ 72 | v = v + 0.0001 73 | } 74 | hAlpha = (-0.015 * (v- -60))/(1-(exp((v- -60)/6))) 75 | hBeta = (-0.015 * (-v -60))/(1-(exp((-v -60)/6))) 76 | hInf = hAlpha/(hAlpha + hBeta) 77 | hTau = (1/(hAlpha + hBeta))/qt 78 | UNITSON 79 | } 80 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/mechanisms/SK_E2.mod: -------------------------------------------------------------------------------- 1 | : SK-type calcium-activated potassium current 2 | : Reference : Kohler et al. 1996 3 | 4 | NEURON { 5 | SUFFIX SK_E2 6 | USEION k READ ek WRITE ik 7 | USEION ca READ cai 8 | RANGE gSK_E2bar, gSK_E2, ik 9 | } 10 | 11 | UNITS { 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | (mM) = (milli/liter) 15 | } 16 | 17 | PARAMETER { 18 | v (mV) 19 | gSK_E2bar = .000001 (mho/cm2) 20 | zTau = 1 (ms) 21 | ek (mV) 22 | cai (mM) 23 | } 24 | 25 | ASSIGNED { 26 | zInf 27 | ik (mA/cm2) 28 | gSK_E2 (S/cm2) 29 | } 30 | 31 | STATE { 32 | z FROM 0 TO 1 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gSK_E2 = gSK_E2bar * z 38 | ik = gSK_E2 * (v - ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates(cai) 43 | z' = (zInf - z) / zTau 44 | } 45 | 46 | PROCEDURE rates(ca(mM)) { 47 | if(ca < 1e-7){ 48 | ca = ca + 1e-07 49 | } 50 | zInf = 1/(1 + (0.00043 / ca)^4.8) 51 | } 52 | 53 | INITIAL { 54 | rates(cai) 55 | z = zInf 56 | } 57 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/mechanisms/SKv3_1.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Characterization of a Shaw-related potassium channel family in rat brain, The EMBO Journal, vol.11, no.7,2473-2486 (1992) 3 | 4 | NEURON { 5 | SUFFIX SKv3_1 6 | USEION k READ ek WRITE ik 7 | RANGE gSKv3_1bar, gSKv3_1, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gSKv3_1bar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | gSKv3_1 (S/cm2) 25 | mInf 26 | mTau 27 | } 28 | 29 | STATE { 30 | m 31 | } 32 | 33 | BREAKPOINT { 34 | SOLVE states METHOD cnexp 35 | gSKv3_1 = gSKv3_1bar*m 36 | ik = gSKv3_1*(v-ek) 37 | } 38 | 39 | DERIVATIVE states { 40 | rates() 41 | m' = (mInf-m)/mTau 42 | } 43 | 44 | INITIAL{ 45 | rates() 46 | m = mInf 47 | } 48 | 49 | PROCEDURE rates(){ 50 | UNITSOFF 51 | mInf = 1/(1+exp(((v -(18.700))/(-9.700)))) 52 | mTau = 0.2*20.000/(1+exp(((v -(-46.560))/(-44.140)))) 53 | UNITSON 54 | } 55 | 56 | -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/mechanisms/dummy.inc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlueBrain/SimulationTutorials/44fa01c22bc83fbbe8a01d3580de75ffadf92ea4/EBRAINS2022/tutorial2/l5pc/mechanisms/dummy.inc -------------------------------------------------------------------------------- /EBRAINS2022/tutorial2/l5pc/morphology/LICENSE: -------------------------------------------------------------------------------- 1 | The CC-BY-NC-SA license applies, as indicated by headers in the 2 | respective source files. 3 | 4 | https://creativecommons.org/licenses/by-nc-sa/4.0/ 5 | 6 | The detailed text is available here 7 | https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode 8 | 9 | or in this tarball in the seperate file LICENSE_CC-BY-CA-SA-4.0 10 | 11 | 12 | The HOC code, Python code, synapse MOD code and cell morphology are licensed with the above mentioned CC-BY-NC-SA license. 13 | 14 | 15 | For models for which the original source is available on ModelDB, any 16 | specific licenses on mentioned on ModelDB, or the generic License of ModelDB 17 | apply: 18 | 19 | 1) Ih model 20 | Author: Stefan Hallermann 21 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=144526&file=\HallermannEtAl2012\h.mod 22 | 23 | 2) StochKv model 24 | Authors: Zach Mainen Adaptations: Kamran Diba, Mickey London, Peter N. Steinmetz, Werner Van Geit 25 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=125385&file=\Sbpap_code\mod\skm.mod 26 | 27 | 3) D-type K current model 28 | Authors: Yuguo Yu 29 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=135898&file=\YuEtAlPNAS2007\kd.mod 30 | 31 | 4) Internal calcium concentration model 32 | Author: Alain Destexhe 33 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=3670&file=\NTW_NEW\capump.mod 34 | 35 | 5) Ca_LVAst, Im, K_Tst, NaTa_t, SK_E2, Ca_HVA, Ih, K_Pst, Nap_Et2, NaTs2_t, SKv3_1 36 | Author: Etay Hay, Shaul Druckmann, Srikanth Ramaswamy, James King, Werner Van Geit 37 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=139653&file=\L5bPCmodelsEH\mod\ 38 | -------------------------------------------------------------------------------- /FENS2016/.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | -------------------------------------------------------------------------------- /FENS2016/ABI_model/config/mechanisms.json: -------------------------------------------------------------------------------- 1 | { 2 | "basal": [ 3 | "Ih", 4 | "NaV", 5 | "Kv3_1", 6 | "Im_v2", 7 | "pas" 8 | ], 9 | "somatic": [ 10 | "NaV", 11 | "SK", 12 | "Kv3_1", 13 | "Ca_HVA", 14 | "Ca_LVA", 15 | "CaDynamics", 16 | "Ih", 17 | "pas" 18 | ], 19 | "axonal": [ 20 | "NaV", 21 | "K_T", 22 | "Kd", 23 | "Kv2like", 24 | "Kv3_1", 25 | "SK", 26 | "Ca_HVA", 27 | "Ca_LVA", 28 | "CaDynamics", 29 | "pas" 30 | ] 31 | } 32 | -------------------------------------------------------------------------------- /FENS2016/ABI_model/config/protocols.json: -------------------------------------------------------------------------------- 1 | { 2 | "StepPos": { 3 | "stimuli": [ 4 | { 5 | "delay": 270, 6 | "amp": 0.15, 7 | "duration": 1000, 8 | "totduration": 1540 9 | } 10 | ] 11 | }, 12 | "StepNeg": { 13 | "stimuli": [ 14 | { 15 | "delay": 270, 16 | "amp": -0.11, 17 | "duration": 1000, 18 | "totduration": 1540 19 | } 20 | ] 21 | } 22 | } 23 | -------------------------------------------------------------------------------- /FENS2016/ABI_model/data/475049288.nwb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlueBrain/SimulationTutorials/44fa01c22bc83fbbe8a01d3580de75ffadf92ea4/FENS2016/ABI_model/data/475049288.nwb -------------------------------------------------------------------------------- /FENS2016/ABI_model/modfiles/CaDynamics.mod: -------------------------------------------------------------------------------- 1 | : Dynamics that track inside calcium concentration 2 | : modified from Destexhe et al. 1994 3 | 4 | NEURON { 5 | SUFFIX CaDynamics 6 | USEION ca READ ica WRITE cai 7 | RANGE decay, gamma, minCai, depth 8 | } 9 | 10 | UNITS { 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | FARADAY = (faraday) (coulombs) 14 | (molar) = (1/liter) 15 | (mM) = (millimolar) 16 | (um) = (micron) 17 | } 18 | 19 | PARAMETER { 20 | gamma = 0.05 : percent of free calcium (not buffered) 21 | decay = 80 (ms) : rate of removal of calcium 22 | depth = 0.1 (um) : depth of shell 23 | minCai = 1e-4 (mM) 24 | } 25 | 26 | ASSIGNED {ica (mA/cm2)} 27 | 28 | INITIAL { 29 | cai = minCai 30 | } 31 | 32 | STATE { 33 | cai (mM) 34 | } 35 | 36 | BREAKPOINT { SOLVE states METHOD cnexp } 37 | 38 | DERIVATIVE states { 39 | cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay 40 | } 41 | -------------------------------------------------------------------------------- /FENS2016/ABI_model/modfiles/Ca_HVA.mod: -------------------------------------------------------------------------------- 1 | : Reference: Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993 2 | 3 | NEURON { 4 | SUFFIX Ca_HVA 5 | USEION ca READ eca WRITE ica 6 | RANGE gbar, g, ica 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | } 18 | 19 | ASSIGNED { 20 | v (mV) 21 | eca (mV) 22 | ica (mA/cm2) 23 | g (S/cm2) 24 | mInf 25 | mTau 26 | mAlpha 27 | mBeta 28 | hInf 29 | hTau 30 | hAlpha 31 | hBeta 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | g = gbar*m*m*h 42 | ica = g*(v-eca) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | UNITSOFF 59 | : if((v == -27) ){ 60 | : v = v+0.0001 61 | : } 62 | :mAlpha = (0.055*(-27-v))/(exp((-27-v)/3.8) - 1) 63 | mAlpha = 0.055 * vtrap(-27 - v, 3.8) 64 | mBeta = (0.94*exp((-75-v)/17)) 65 | mInf = mAlpha/(mAlpha + mBeta) 66 | mTau = 1/(mAlpha + mBeta) 67 | hAlpha = (0.000457*exp((-13-v)/50)) 68 | hBeta = (0.0065/(exp((-v-15)/28)+1)) 69 | hInf = hAlpha/(hAlpha + hBeta) 70 | hTau = 1/(hAlpha + hBeta) 71 | UNITSON 72 | } 73 | 74 | FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations 75 | UNITSOFF 76 | if (fabs(x / y) < 1e-6) { 77 | vtrap = y * (1 - x / y / 2) 78 | } else { 79 | vtrap = x / (exp(x / y) - 1) 80 | } 81 | UNITSON 82 | } -------------------------------------------------------------------------------- /FENS2016/ABI_model/modfiles/Ca_LVA.mod: -------------------------------------------------------------------------------- 1 | : Comment: LVA ca channel. Note: mtau is an approximation from the plots 2 | : Reference: Avery and Johnston 1996, tau from Randall 1997 3 | : Comment: shifted by -10 mv to correct for junction potential 4 | : Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | NEURON { 7 | SUFFIX Ca_LVA 8 | USEION ca READ eca WRITE ica 9 | RANGE gbar, g, ica 10 | } 11 | 12 | UNITS { 13 | (S) = (siemens) 14 | (mV) = (millivolt) 15 | (mA) = (milliamp) 16 | } 17 | 18 | PARAMETER { 19 | gbar = 0.00001 (S/cm2) 20 | } 21 | 22 | ASSIGNED { 23 | v (mV) 24 | eca (mV) 25 | ica (mA/cm2) 26 | g (S/cm2) 27 | celsius (degC) 28 | mInf 29 | mTau 30 | hInf 31 | hTau 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | g = gbar*m*m*h 42 | ica = g*(v-eca) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | LOCAL qt 59 | qt = 2.3^((celsius-21)/10) 60 | 61 | UNITSOFF 62 | v = v + 10 63 | mInf = 1.0000/(1+ exp((v - -30.000)/-6)) 64 | mTau = (5.0000 + 20.0000/(1+exp((v - -25.000)/5)))/qt 65 | hInf = 1.0000/(1+ exp((v - -80.000)/6.4)) 66 | hTau = (20.0000 + 50.0000/(1+exp((v - -40.000)/7)))/qt 67 | v = v - 10 68 | UNITSON 69 | } 70 | -------------------------------------------------------------------------------- /FENS2016/ABI_model/modfiles/Ih.mod: -------------------------------------------------------------------------------- 1 | : Reference: Kole,Hallermann,and Stuart, J. Neurosci. 2006 2 | 3 | NEURON { 4 | SUFFIX Ih 5 | NONSPECIFIC_CURRENT ihcn 6 | RANGE gbar, g, ihcn 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | ehcn = -45.0 (mV) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ihcn (mA/cm2) 23 | g (S/cm2) 24 | mInf 25 | mTau 26 | mAlpha 27 | mBeta 28 | } 29 | 30 | STATE { 31 | m 32 | } 33 | 34 | BREAKPOINT { 35 | SOLVE states METHOD cnexp 36 | g = gbar*m 37 | ihcn = g*(v-ehcn) 38 | } 39 | 40 | DERIVATIVE states { 41 | rates() 42 | m' = (mInf-m)/mTau 43 | } 44 | 45 | INITIAL{ 46 | rates() 47 | m = mInf 48 | } 49 | 50 | PROCEDURE rates(){ 51 | UNITSOFF 52 | : if(v == -154.9){ 53 | : v = v + 0.0001 54 | : } 55 | :mAlpha = 0.001*6.43*(v+154.9)/(exp((v+154.9)/11.9)-1) 56 | mAlpha = 0.001 * 6.43 * vtrap(v + 154.9, 11.9) 57 | mBeta = 0.001*193*exp(v/33.1) 58 | mInf = mAlpha/(mAlpha + mBeta) 59 | mTau = 1/(mAlpha + mBeta) 60 | UNITSON 61 | } 62 | 63 | FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations 64 | UNITSOFF 65 | if (fabs(x / y) < 1e-6) { 66 | vtrap = y * (1 - x / y / 2) 67 | } else { 68 | vtrap = x / (exp(x / y) - 1) 69 | } 70 | UNITSON 71 | } 72 | -------------------------------------------------------------------------------- /FENS2016/ABI_model/modfiles/Im.mod: -------------------------------------------------------------------------------- 1 | : Reference: Adams et al. 1982 - M-currents and other potassium currents in bullfrog sympathetic neurones 2 | : Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 3 | 4 | NEURON { 5 | SUFFIX Im 6 | USEION k READ ek WRITE ik 7 | RANGE gbar, g, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | g (S/cm2) 25 | celsius (degC) 26 | mInf 27 | mTau 28 | mAlpha 29 | mBeta 30 | } 31 | 32 | STATE { 33 | m 34 | } 35 | 36 | BREAKPOINT { 37 | SOLVE states METHOD cnexp 38 | g = gbar*m 39 | ik = g*(v-ek) 40 | } 41 | 42 | DERIVATIVE states { 43 | rates() 44 | m' = (mInf-m)/mTau 45 | } 46 | 47 | INITIAL{ 48 | rates() 49 | m = mInf 50 | } 51 | 52 | PROCEDURE rates(){ 53 | LOCAL qt 54 | qt = 2.3^((celsius-21)/10) 55 | 56 | UNITSOFF 57 | mAlpha = 3.3e-3*exp(2.5*0.04*(v - -35)) 58 | mBeta = 3.3e-3*exp(-2.5*0.04*(v - -35)) 59 | mInf = mAlpha/(mAlpha + mBeta) 60 | mTau = (1/(mAlpha + mBeta))/qt 61 | UNITSON 62 | } 63 | -------------------------------------------------------------------------------- /FENS2016/ABI_model/modfiles/Im_v2.mod: -------------------------------------------------------------------------------- 1 | : Based on Im model of Vervaeke et al. (2006) 2 | 3 | NEURON { 4 | SUFFIX Im_v2 5 | USEION k READ ek WRITE ik 6 | RANGE gbar, g, ik 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | } 18 | 19 | ASSIGNED { 20 | v (mV) 21 | ek (mV) 22 | ik (mA/cm2) 23 | g (S/cm2) 24 | celsius (degC) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | } 30 | 31 | STATE { 32 | m 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | g = gbar * m 38 | ik = g * (v - ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates() 43 | m' = (mInf - m) / mTau 44 | } 45 | 46 | INITIAL{ 47 | rates() 48 | m = mInf 49 | } 50 | 51 | PROCEDURE rates() { 52 | LOCAL qt 53 | qt = 2.3^((celsius-30)/10) 54 | mAlpha = 0.007 * exp( (6 * 0.4 * (v - (-48))) / 26.12 ) 55 | mBeta = 0.007 * exp( (-6 * (1 - 0.4) * (v - (-48))) / 26.12 ) 56 | 57 | mInf = mAlpha / (mAlpha + mBeta) 58 | mTau = (15 + 1 / (mAlpha + mBeta)) / qt 59 | } 60 | -------------------------------------------------------------------------------- /FENS2016/ABI_model/modfiles/K_P.mod: -------------------------------------------------------------------------------- 1 | : Comment: The persistent component of the K current 2 | : Reference: Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | 4 | 5 | NEURON { 6 | SUFFIX K_P 7 | USEION k READ ek WRITE ik 8 | RANGE gbar, g, ik 9 | } 10 | 11 | UNITS { 12 | (S) = (siemens) 13 | (mV) = (millivolt) 14 | (mA) = (milliamp) 15 | } 16 | 17 | PARAMETER { 18 | gbar = 0.00001 (S/cm2) 19 | vshift = 0 (mV) 20 | tauF = 1 21 | } 22 | 23 | ASSIGNED { 24 | v (mV) 25 | ek (mV) 26 | ik (mA/cm2) 27 | g (S/cm2) 28 | celsius (degC) 29 | mInf 30 | mTau 31 | hInf 32 | hTau 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | g = gbar*m*m*h 43 | ik = g*(v-ek) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates() { 59 | LOCAL qt 60 | qt = 2.3^((celsius-21)/10) 61 | UNITSOFF 62 | mInf = 1 / (1 + exp(-(v - (-14.3 + vshift)) / 14.6)) 63 | if (v < -50 + vshift){ 64 | mTau = tauF * (1.25+175.03*exp(-(v - vshift) * -0.026))/qt 65 | } else { 66 | mTau = tauF * (1.25+13*exp(-(v - vshift) * 0.026))/qt 67 | } 68 | hInf = 1/(1 + exp(-(v - (-54 + vshift))/-11)) 69 | hTau = (360+(1010+24*(v - (-55 + vshift)))*exp(-((v - (-75 + vshift))/48)^2))/qt 70 | UNITSON 71 | } 72 | -------------------------------------------------------------------------------- /FENS2016/ABI_model/modfiles/K_T.mod: -------------------------------------------------------------------------------- 1 | : Comment: The transient component of the K current 2 | : Reference: Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | 4 | NEURON { 5 | SUFFIX K_T 6 | USEION k READ ek WRITE ik 7 | RANGE gbar, g, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gbar = 0.00001 (S/cm2) 18 | vshift = 0 (mV) 19 | mTauF = 1.0 20 | hTauF = 1.0 21 | } 22 | 23 | ASSIGNED { 24 | v (mV) 25 | ek (mV) 26 | ik (mA/cm2) 27 | g (S/cm2) 28 | celsius (degC) 29 | mInf 30 | mTau 31 | hInf 32 | hTau 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | g = gbar*m*m*m*m*h 43 | ik = g*(v-ek) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates(){ 59 | LOCAL qt 60 | qt = 2.3^((celsius-21)/10) 61 | 62 | UNITSOFF 63 | mInf = 1/(1 + exp(-(v - (-47 + vshift)) / 29)) 64 | mTau = (0.34 + mTauF * 0.92*exp(-((v+71-vshift)/59)^2))/qt 65 | hInf = 1/(1 + exp(-(v+66-vshift)/-10)) 66 | hTau = (8 + hTauF * 49*exp(-((v+73-vshift)/23)^2))/qt 67 | UNITSON 68 | } 69 | -------------------------------------------------------------------------------- /FENS2016/ABI_model/modfiles/Kd.mod: -------------------------------------------------------------------------------- 1 | : Based on Kd model of Foust et al. (2011) 2 | 3 | 4 | NEURON { 5 | SUFFIX Kd 6 | USEION k READ ek WRITE ik 7 | RANGE gbar, g, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | g (S/cm2) 25 | celsius (degC) 26 | mInf 27 | mTau 28 | hInf 29 | hTau 30 | } 31 | 32 | STATE { 33 | m 34 | h 35 | } 36 | 37 | BREAKPOINT { 38 | SOLVE states METHOD cnexp 39 | g = gbar * m * h 40 | ik = g * (v - ek) 41 | } 42 | 43 | DERIVATIVE states { 44 | rates() 45 | m' = (mInf - m) / mTau 46 | h' = (hInf - h) / hTau 47 | } 48 | 49 | INITIAL{ 50 | rates() 51 | m = mInf 52 | h = hInf 53 | } 54 | 55 | PROCEDURE rates() { 56 | LOCAL qt 57 | qt = 2.3^((celsius-23)/10) 58 | mInf = 1 - 1 / (1 + exp((v - (-43)) / 8)) 59 | mTau = 1 60 | hInf = 1 / (1 + exp((v - (-67)) / 7.3)) 61 | hTau = 1500 62 | } 63 | -------------------------------------------------------------------------------- /FENS2016/ABI_model/modfiles/Kv3_1.mod: -------------------------------------------------------------------------------- 1 | : Comment: Kv3-like potassium current 2 | 3 | NEURON { 4 | SUFFIX Kv3_1 5 | USEION k READ ek WRITE ik 6 | RANGE gbar, g, ik 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | vshift = 0 (mV) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | g (S/cm2) 25 | mInf 26 | mTau 27 | } 28 | 29 | STATE { 30 | m 31 | } 32 | 33 | BREAKPOINT { 34 | SOLVE states METHOD cnexp 35 | g = gbar*m 36 | ik = g*(v-ek) 37 | } 38 | 39 | DERIVATIVE states { 40 | rates() 41 | m' = (mInf-m)/mTau 42 | } 43 | 44 | INITIAL{ 45 | rates() 46 | m = mInf 47 | } 48 | 49 | PROCEDURE rates(){ 50 | UNITSOFF 51 | mInf = 1/(1+exp(((v -(18.700 + vshift))/(-9.700)))) 52 | mTau = 0.2*20.000/(1+exp(((v -(-46.560 + vshift))/(-44.140)))) 53 | UNITSON 54 | } 55 | -------------------------------------------------------------------------------- /FENS2016/ABI_model/modfiles/NaTs.mod: -------------------------------------------------------------------------------- 1 | : Reference: Colbert and Pan 2002 2 | 3 | NEURON { 4 | SUFFIX NaTs 5 | USEION na READ ena WRITE ina 6 | RANGE gbar, g, ina 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | 18 | malphaF = 0.182 19 | mbetaF = 0.124 20 | mvhalf = -40 (mV) 21 | mk = 6 (mV) 22 | 23 | halphaF = 0.015 24 | hbetaF = 0.015 25 | hvhalf = -66 (mV) 26 | hk = 6 (mV) 27 | } 28 | 29 | ASSIGNED { 30 | v (mV) 31 | ena (mV) 32 | ina (mA/cm2) 33 | g (S/cm2) 34 | celsius (degC) 35 | mInf 36 | mTau 37 | mAlpha 38 | mBeta 39 | hInf 40 | hTau 41 | hAlpha 42 | hBeta 43 | } 44 | 45 | STATE { 46 | m 47 | h 48 | } 49 | 50 | BREAKPOINT { 51 | SOLVE states METHOD cnexp 52 | g = gbar*m*m*m*h 53 | ina = g*(v-ena) 54 | } 55 | 56 | DERIVATIVE states { 57 | rates() 58 | m' = (mInf-m)/mTau 59 | h' = (hInf-h)/hTau 60 | } 61 | 62 | INITIAL{ 63 | rates() 64 | m = mInf 65 | h = hInf 66 | } 67 | 68 | PROCEDURE rates(){ 69 | LOCAL qt 70 | qt = 2.3^((celsius-23)/10) 71 | 72 | UNITSOFF 73 | mAlpha = malphaF * vtrap(-(v - mvhalf), mk) 74 | mBeta = mbetaF * vtrap((v - mvhalf), mk) 75 | 76 | mInf = mAlpha/(mAlpha + mBeta) 77 | mTau = (1/(mAlpha + mBeta))/qt 78 | 79 | hAlpha = halphaF * vtrap(v - hvhalf, hk) 80 | hBeta = hbetaF * vtrap(-(v - hvhalf), hk) 81 | 82 | hInf = hAlpha/(hAlpha + hBeta) 83 | hTau = (1/(hAlpha + hBeta))/qt 84 | UNITSON 85 | } 86 | 87 | FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations 88 | UNITSOFF 89 | if (fabs(x / y) < 1e-6) { 90 | vtrap = y * (1 - x / y / 2) 91 | } else { 92 | vtrap = x / (exp(x / y) - 1) 93 | } 94 | UNITSON 95 | } -------------------------------------------------------------------------------- /FENS2016/ABI_model/modfiles/Nap.mod: -------------------------------------------------------------------------------- 1 | :Reference : Modeled according to kinetics derived from Magistretti & Alonso 1999 2 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 3 | 4 | NEURON { 5 | SUFFIX Nap 6 | USEION na READ ena WRITE ina 7 | RANGE gbar, g, ina 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ena (mV) 23 | ina (mA/cm2) 24 | g (S/cm2) 25 | celsius (degC) 26 | mInf 27 | hInf 28 | hTau 29 | hAlpha 30 | hBeta 31 | } 32 | 33 | STATE { 34 | h 35 | } 36 | 37 | BREAKPOINT { 38 | SOLVE states METHOD cnexp 39 | rates() 40 | g = gbar*mInf*h 41 | ina = g*(v-ena) 42 | } 43 | 44 | DERIVATIVE states { 45 | rates() 46 | h' = (hInf-h)/hTau 47 | } 48 | 49 | INITIAL{ 50 | rates() 51 | h = hInf 52 | } 53 | 54 | PROCEDURE rates(){ 55 | LOCAL qt 56 | qt = 2.3^((celsius-21)/10) 57 | 58 | UNITSOFF 59 | mInf = 1.0/(1+exp((v- -52.6)/-4.6)) : assuming instantaneous activation as modeled by Magistretti and Alonso 60 | 61 | hInf = 1.0/(1+exp((v- -48.8)/10)) 62 | hAlpha = 2.88e-6 * vtrap(v + 17, 4.63) 63 | hBeta = 6.94e-6 * vtrap(-(v + 64.4), 2.63) 64 | 65 | hTau = (1/(hAlpha + hBeta))/qt 66 | UNITSON 67 | } 68 | 69 | FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations 70 | UNITSOFF 71 | if (fabs(x / y) < 1e-6) { 72 | vtrap = y * (1 - x / y / 2) 73 | } else { 74 | vtrap = x / (exp(x / y) - 1) 75 | } 76 | UNITSON 77 | } -------------------------------------------------------------------------------- /FENS2016/ABI_model/modfiles/SK.mod: -------------------------------------------------------------------------------- 1 | : SK-type calcium-activated potassium current 2 | : Reference : Kohler et al. 1996 3 | 4 | NEURON { 5 | SUFFIX SK 6 | USEION k READ ek WRITE ik 7 | USEION ca READ cai 8 | RANGE gbar, g, ik 9 | } 10 | 11 | UNITS { 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | (mM) = (milli/liter) 15 | } 16 | 17 | PARAMETER { 18 | v (mV) 19 | gbar = .000001 (mho/cm2) 20 | zTau = 1 (ms) 21 | ek (mV) 22 | cai (mM) 23 | } 24 | 25 | ASSIGNED { 26 | zInf 27 | ik (mA/cm2) 28 | g (S/cm2) 29 | } 30 | 31 | STATE { 32 | z FROM 0 TO 1 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | g = gbar * z 38 | ik = g * (v - ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates(cai) 43 | z' = (zInf - z) / zTau 44 | } 45 | 46 | PROCEDURE rates(ca(mM)) { 47 | if(ca < 1e-7){ 48 | ca = ca + 1e-07 49 | } 50 | zInf = 1/(1 + (0.00043 / ca)^4.8) 51 | } 52 | 53 | INITIAL { 54 | rates(cai) 55 | z = zInf 56 | } 57 | -------------------------------------------------------------------------------- /FENS2016/ABI_model/orig_parameters.json: -------------------------------------------------------------------------------- 1 | 2 | { 3 | "ek.all": -107, 4 | "e_pas.somatic": -63.3146, 5 | "Ra.basal": 50.8833, 6 | "gbar_Kv3_1.axonal": 0.0100065, 7 | "gbar_NaV.basal": 0.0205486, 8 | "gbar_Kv3_1.basal": 0.205458, 9 | "e_pas.basal": -62.7085, 10 | "gbar_K_T.axonal": 0.000124859, 11 | "gamma_CaDynamics.somatic": 0.00169922, 12 | "v_init": -81, 13 | "cm.basal": 7.88877, 14 | "gbar_Ca_HVA.axonal": 3.83558e-05, 15 | "gbar_NaV.somatic": 0.0499769, 16 | "gbar_Kv2like.axonal": 0.0010615, 17 | "gbar_Ca_LVA.somatic": 0.0060162, 18 | "gbar_Im_v2.basal": 0.00949979, 19 | "gbar_SK.somatic": 0.0001051137, 20 | "ena.all": 53.0, 21 | "g_pas.axonal": 0.00200656, 22 | "gbar_NaV.axonal": 0.0156789, 23 | "gamma_CaDynamics.axonal": 0.0477399, 24 | "gbar_SK.axonal": 0.00661877, 25 | "cm.axonal": 9.91715, 26 | "gbar_Ca_HVA.somatic": 5.9455e-05, 27 | "gbar_Kd.axonal": 0.00833495, 28 | "gbar_Ih.basal": 7.75636e-06, 29 | "gbar_Ca_LVA.axonal": 0.00775489, 30 | "Ra.somatic": 72.0757, 31 | "e_pas.axonal": -71.1766, 32 | "g_pas.basal": 1.10433e-07, 33 | "decay_CaDynamics.axonal": 811.497, 34 | "cm.somatic": 3.35066, 35 | "gbar_Ih.somatic": 3.46139e-06, 36 | "g_pas.somatic": 7.60303e-05, 37 | "celsius": 34, 38 | "Ra.axonal": 100.799, 39 | "gbar_Kv3_1.somatic": 0.671067, 40 | "decay_CaDynamics.somatic": 326.442 41 | } 42 | -------------------------------------------------------------------------------- /FENS2016/LICENSE.txt: -------------------------------------------------------------------------------- 1 | The experimental data files in this directory are made available for educational 2 | purposes to speed up downloading. 3 | The original files are located at http://celltypes.brain-map.org, and these 4 | files are still licensed according to the policies on that website. 5 | -------------------------------------------------------------------------------- /FENS2016/README.md: -------------------------------------------------------------------------------- 1 | # HBP Neuroinformatics and Single cell modeling Tutorial @ Cells, Circuit and Computation FENS Workshop 2016 2 | 3 | The main part of this demo consists of : 4 | * [**Optimising parameters of full dendritic model**](ABI_model/) 5 | * [**An exciting challenge for the participants (with amazing prizes !)**](exercise/opt_challenge.ipynb) 6 | 7 | ## Binder instances 8 | 9 | Most examples in this demo can be run from a web browser, thanks to Binder (http://mybinder.org/, supported by The Freeman Lab @ HHMI Janelia Research Campus). 10 | 11 | To access the Binder instance set up for this demo, visit: 12 | http://mybinder.org/repo/BlueBrain/SimulationTutorials/FENS2016 13 | 14 | ## Extra material 15 | 16 | A **Google drive** was created with **extra material** 17 | 18 | https://drive.google.com/drive/u/1/folders/0B5FLVTgErnMSdXZWYjU2SHlXZ3c 19 | 20 | This drive contains a **Virtual Machine** that can be used to run the demoed software. 21 | -------------------------------------------------------------------------------- /FENS2016/exercise/config/features.json: -------------------------------------------------------------------------------- 1 | { 2 | "StepNeg": { 3 | "soma": { 4 | "time_constant": [ 5 | 22.292113705651431, 6 | 1.1146056852825716 7 | ], 8 | "voltage_deflection_begin": [ 9 | -23.270169754041433, 10 | 1.1635084877020716 11 | ] 12 | } 13 | }, 14 | "StepPos": { 15 | "soma": { 16 | "AP_duration": [ 17 | 1.5782608695651734, 18 | 0.078913043478258671 19 | ], 20 | "mean_frequency": [ 21 | 23.866348448688008, 22 | 1.1933174224344005 23 | ], 24 | "AP_amplitude": [ 25 | 53.713316542778955, 26 | 2.6856658271389477 27 | ], 28 | "fast_AHP": [ 29 | 21.846590563652441, 30 | 1.0923295281826222 31 | ], 32 | "min_AHP_values": [ 33 | -68.194293478145681, 34 | 3.4097146739072843 35 | ] 36 | } 37 | } 38 | } -------------------------------------------------------------------------------- /FENS2016/exercise/config/mechanisms.json: -------------------------------------------------------------------------------- 1 | { 2 | "basal": [ 3 | "Ih", 4 | "NaV", 5 | "Kv3_1", 6 | "Im_v2", 7 | "pas" 8 | ], 9 | "somatic": [ 10 | "NaV", 11 | "SK", 12 | "Kv3_1", 13 | "Ca_HVA", 14 | "Ca_LVA", 15 | "CaDynamics", 16 | "Ih", 17 | "pas" 18 | ], 19 | "axonal": [ 20 | "NaV", 21 | "K_T", 22 | "Kd", 23 | "Kv2like", 24 | "Kv3_1", 25 | "SK", 26 | "Ca_HVA", 27 | "Ca_LVA", 28 | "CaDynamics", 29 | "pas" 30 | ] 31 | } 32 | -------------------------------------------------------------------------------- /FENS2016/exercise/config/protocols.json: -------------------------------------------------------------------------------- 1 | { 2 | "StepPos": { 3 | "stimuli": [ 4 | { 5 | "delay": 270, 6 | "amp": 0.15, 7 | "duration": 1000, 8 | "totduration": 1540 9 | } 10 | ] 11 | }, 12 | "StepNeg": { 13 | "stimuli": [ 14 | { 15 | "delay": 270, 16 | "amp": -0.11, 17 | "duration": 1000, 18 | "totduration": 1540 19 | } 20 | ] 21 | } 22 | } 23 | -------------------------------------------------------------------------------- /FENS2016/exercise/modfiles/CaDynamics.mod: -------------------------------------------------------------------------------- 1 | : Dynamics that track inside calcium concentration 2 | : modified from Destexhe et al. 1994 3 | 4 | NEURON { 5 | SUFFIX CaDynamics 6 | USEION ca READ ica WRITE cai 7 | RANGE decay, gamma, minCai, depth 8 | } 9 | 10 | UNITS { 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | FARADAY = (faraday) (coulombs) 14 | (molar) = (1/liter) 15 | (mM) = (millimolar) 16 | (um) = (micron) 17 | } 18 | 19 | PARAMETER { 20 | gamma = 0.05 : percent of free calcium (not buffered) 21 | decay = 80 (ms) : rate of removal of calcium 22 | depth = 0.1 (um) : depth of shell 23 | minCai = 1e-4 (mM) 24 | } 25 | 26 | ASSIGNED {ica (mA/cm2)} 27 | 28 | INITIAL { 29 | cai = minCai 30 | } 31 | 32 | STATE { 33 | cai (mM) 34 | } 35 | 36 | BREAKPOINT { SOLVE states METHOD cnexp } 37 | 38 | DERIVATIVE states { 39 | cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay 40 | } 41 | -------------------------------------------------------------------------------- /FENS2016/exercise/modfiles/Ca_HVA.mod: -------------------------------------------------------------------------------- 1 | : Reference: Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993 2 | 3 | NEURON { 4 | SUFFIX Ca_HVA 5 | USEION ca READ eca WRITE ica 6 | RANGE gbar, g, ica 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | } 18 | 19 | ASSIGNED { 20 | v (mV) 21 | eca (mV) 22 | ica (mA/cm2) 23 | g (S/cm2) 24 | mInf 25 | mTau 26 | mAlpha 27 | mBeta 28 | hInf 29 | hTau 30 | hAlpha 31 | hBeta 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | g = gbar*m*m*h 42 | ica = g*(v-eca) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | UNITSOFF 59 | : if((v == -27) ){ 60 | : v = v+0.0001 61 | : } 62 | :mAlpha = (0.055*(-27-v))/(exp((-27-v)/3.8) - 1) 63 | mAlpha = 0.055 * vtrap(-27 - v, 3.8) 64 | mBeta = (0.94*exp((-75-v)/17)) 65 | mInf = mAlpha/(mAlpha + mBeta) 66 | mTau = 1/(mAlpha + mBeta) 67 | hAlpha = (0.000457*exp((-13-v)/50)) 68 | hBeta = (0.0065/(exp((-v-15)/28)+1)) 69 | hInf = hAlpha/(hAlpha + hBeta) 70 | hTau = 1/(hAlpha + hBeta) 71 | UNITSON 72 | } 73 | 74 | FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations 75 | UNITSOFF 76 | if (fabs(x / y) < 1e-6) { 77 | vtrap = y * (1 - x / y / 2) 78 | } else { 79 | vtrap = x / (exp(x / y) - 1) 80 | } 81 | UNITSON 82 | } -------------------------------------------------------------------------------- /FENS2016/exercise/modfiles/Ca_LVA.mod: -------------------------------------------------------------------------------- 1 | : Comment: LVA ca channel. Note: mtau is an approximation from the plots 2 | : Reference: Avery and Johnston 1996, tau from Randall 1997 3 | : Comment: shifted by -10 mv to correct for junction potential 4 | : Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | NEURON { 7 | SUFFIX Ca_LVA 8 | USEION ca READ eca WRITE ica 9 | RANGE gbar, g, ica 10 | } 11 | 12 | UNITS { 13 | (S) = (siemens) 14 | (mV) = (millivolt) 15 | (mA) = (milliamp) 16 | } 17 | 18 | PARAMETER { 19 | gbar = 0.00001 (S/cm2) 20 | } 21 | 22 | ASSIGNED { 23 | v (mV) 24 | eca (mV) 25 | ica (mA/cm2) 26 | g (S/cm2) 27 | celsius (degC) 28 | mInf 29 | mTau 30 | hInf 31 | hTau 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | g = gbar*m*m*h 42 | ica = g*(v-eca) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | LOCAL qt 59 | qt = 2.3^((celsius-21)/10) 60 | 61 | UNITSOFF 62 | v = v + 10 63 | mInf = 1.0000/(1+ exp((v - -30.000)/-6)) 64 | mTau = (5.0000 + 20.0000/(1+exp((v - -25.000)/5)))/qt 65 | hInf = 1.0000/(1+ exp((v - -80.000)/6.4)) 66 | hTau = (20.0000 + 50.0000/(1+exp((v - -40.000)/7)))/qt 67 | v = v - 10 68 | UNITSON 69 | } 70 | -------------------------------------------------------------------------------- /FENS2016/exercise/modfiles/Ih.mod: -------------------------------------------------------------------------------- 1 | : Reference: Kole,Hallermann,and Stuart, J. Neurosci. 2006 2 | 3 | NEURON { 4 | SUFFIX Ih 5 | NONSPECIFIC_CURRENT ihcn 6 | RANGE gbar, g, ihcn 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | ehcn = -45.0 (mV) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ihcn (mA/cm2) 23 | g (S/cm2) 24 | mInf 25 | mTau 26 | mAlpha 27 | mBeta 28 | } 29 | 30 | STATE { 31 | m 32 | } 33 | 34 | BREAKPOINT { 35 | SOLVE states METHOD cnexp 36 | g = gbar*m 37 | ihcn = g*(v-ehcn) 38 | } 39 | 40 | DERIVATIVE states { 41 | rates() 42 | m' = (mInf-m)/mTau 43 | } 44 | 45 | INITIAL{ 46 | rates() 47 | m = mInf 48 | } 49 | 50 | PROCEDURE rates(){ 51 | UNITSOFF 52 | : if(v == -154.9){ 53 | : v = v + 0.0001 54 | : } 55 | :mAlpha = 0.001*6.43*(v+154.9)/(exp((v+154.9)/11.9)-1) 56 | mAlpha = 0.001 * 6.43 * vtrap(v + 154.9, 11.9) 57 | mBeta = 0.001*193*exp(v/33.1) 58 | mInf = mAlpha/(mAlpha + mBeta) 59 | mTau = 1/(mAlpha + mBeta) 60 | UNITSON 61 | } 62 | 63 | FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations 64 | UNITSOFF 65 | if (fabs(x / y) < 1e-6) { 66 | vtrap = y * (1 - x / y / 2) 67 | } else { 68 | vtrap = x / (exp(x / y) - 1) 69 | } 70 | UNITSON 71 | } 72 | -------------------------------------------------------------------------------- /FENS2016/exercise/modfiles/Im.mod: -------------------------------------------------------------------------------- 1 | : Reference: Adams et al. 1982 - M-currents and other potassium currents in bullfrog sympathetic neurones 2 | : Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 3 | 4 | NEURON { 5 | SUFFIX Im 6 | USEION k READ ek WRITE ik 7 | RANGE gbar, g, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | g (S/cm2) 25 | celsius (degC) 26 | mInf 27 | mTau 28 | mAlpha 29 | mBeta 30 | } 31 | 32 | STATE { 33 | m 34 | } 35 | 36 | BREAKPOINT { 37 | SOLVE states METHOD cnexp 38 | g = gbar*m 39 | ik = g*(v-ek) 40 | } 41 | 42 | DERIVATIVE states { 43 | rates() 44 | m' = (mInf-m)/mTau 45 | } 46 | 47 | INITIAL{ 48 | rates() 49 | m = mInf 50 | } 51 | 52 | PROCEDURE rates(){ 53 | LOCAL qt 54 | qt = 2.3^((celsius-21)/10) 55 | 56 | UNITSOFF 57 | mAlpha = 3.3e-3*exp(2.5*0.04*(v - -35)) 58 | mBeta = 3.3e-3*exp(-2.5*0.04*(v - -35)) 59 | mInf = mAlpha/(mAlpha + mBeta) 60 | mTau = (1/(mAlpha + mBeta))/qt 61 | UNITSON 62 | } 63 | -------------------------------------------------------------------------------- /FENS2016/exercise/modfiles/Im_v2.mod: -------------------------------------------------------------------------------- 1 | : Based on Im model of Vervaeke et al. (2006) 2 | 3 | NEURON { 4 | SUFFIX Im_v2 5 | USEION k READ ek WRITE ik 6 | RANGE gbar, g, ik 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | } 18 | 19 | ASSIGNED { 20 | v (mV) 21 | ek (mV) 22 | ik (mA/cm2) 23 | g (S/cm2) 24 | celsius (degC) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | } 30 | 31 | STATE { 32 | m 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | g = gbar * m 38 | ik = g * (v - ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates() 43 | m' = (mInf - m) / mTau 44 | } 45 | 46 | INITIAL{ 47 | rates() 48 | m = mInf 49 | } 50 | 51 | PROCEDURE rates() { 52 | LOCAL qt 53 | qt = 2.3^((celsius-30)/10) 54 | mAlpha = 0.007 * exp( (6 * 0.4 * (v - (-48))) / 26.12 ) 55 | mBeta = 0.007 * exp( (-6 * (1 - 0.4) * (v - (-48))) / 26.12 ) 56 | 57 | mInf = mAlpha / (mAlpha + mBeta) 58 | mTau = (15 + 1 / (mAlpha + mBeta)) / qt 59 | } 60 | -------------------------------------------------------------------------------- /FENS2016/exercise/modfiles/K_P.mod: -------------------------------------------------------------------------------- 1 | : Comment: The persistent component of the K current 2 | : Reference: Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | 4 | 5 | NEURON { 6 | SUFFIX K_P 7 | USEION k READ ek WRITE ik 8 | RANGE gbar, g, ik 9 | } 10 | 11 | UNITS { 12 | (S) = (siemens) 13 | (mV) = (millivolt) 14 | (mA) = (milliamp) 15 | } 16 | 17 | PARAMETER { 18 | gbar = 0.00001 (S/cm2) 19 | vshift = 0 (mV) 20 | tauF = 1 21 | } 22 | 23 | ASSIGNED { 24 | v (mV) 25 | ek (mV) 26 | ik (mA/cm2) 27 | g (S/cm2) 28 | celsius (degC) 29 | mInf 30 | mTau 31 | hInf 32 | hTau 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | g = gbar*m*m*h 43 | ik = g*(v-ek) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates() { 59 | LOCAL qt 60 | qt = 2.3^((celsius-21)/10) 61 | UNITSOFF 62 | mInf = 1 / (1 + exp(-(v - (-14.3 + vshift)) / 14.6)) 63 | if (v < -50 + vshift){ 64 | mTau = tauF * (1.25+175.03*exp(-(v - vshift) * -0.026))/qt 65 | } else { 66 | mTau = tauF * (1.25+13*exp(-(v - vshift) * 0.026))/qt 67 | } 68 | hInf = 1/(1 + exp(-(v - (-54 + vshift))/-11)) 69 | hTau = (360+(1010+24*(v - (-55 + vshift)))*exp(-((v - (-75 + vshift))/48)^2))/qt 70 | UNITSON 71 | } 72 | -------------------------------------------------------------------------------- /FENS2016/exercise/modfiles/K_T.mod: -------------------------------------------------------------------------------- 1 | : Comment: The transient component of the K current 2 | : Reference: Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | 4 | NEURON { 5 | SUFFIX K_T 6 | USEION k READ ek WRITE ik 7 | RANGE gbar, g, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gbar = 0.00001 (S/cm2) 18 | vshift = 0 (mV) 19 | mTauF = 1.0 20 | hTauF = 1.0 21 | } 22 | 23 | ASSIGNED { 24 | v (mV) 25 | ek (mV) 26 | ik (mA/cm2) 27 | g (S/cm2) 28 | celsius (degC) 29 | mInf 30 | mTau 31 | hInf 32 | hTau 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | g = gbar*m*m*m*m*h 43 | ik = g*(v-ek) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates(){ 59 | LOCAL qt 60 | qt = 2.3^((celsius-21)/10) 61 | 62 | UNITSOFF 63 | mInf = 1/(1 + exp(-(v - (-47 + vshift)) / 29)) 64 | mTau = (0.34 + mTauF * 0.92*exp(-((v+71-vshift)/59)^2))/qt 65 | hInf = 1/(1 + exp(-(v+66-vshift)/-10)) 66 | hTau = (8 + hTauF * 49*exp(-((v+73-vshift)/23)^2))/qt 67 | UNITSON 68 | } 69 | -------------------------------------------------------------------------------- /FENS2016/exercise/modfiles/Kd.mod: -------------------------------------------------------------------------------- 1 | : Based on Kd model of Foust et al. (2011) 2 | 3 | 4 | NEURON { 5 | SUFFIX Kd 6 | USEION k READ ek WRITE ik 7 | RANGE gbar, g, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | g (S/cm2) 25 | celsius (degC) 26 | mInf 27 | mTau 28 | hInf 29 | hTau 30 | } 31 | 32 | STATE { 33 | m 34 | h 35 | } 36 | 37 | BREAKPOINT { 38 | SOLVE states METHOD cnexp 39 | g = gbar * m * h 40 | ik = g * (v - ek) 41 | } 42 | 43 | DERIVATIVE states { 44 | rates() 45 | m' = (mInf - m) / mTau 46 | h' = (hInf - h) / hTau 47 | } 48 | 49 | INITIAL{ 50 | rates() 51 | m = mInf 52 | h = hInf 53 | } 54 | 55 | PROCEDURE rates() { 56 | LOCAL qt 57 | qt = 2.3^((celsius-23)/10) 58 | mInf = 1 - 1 / (1 + exp((v - (-43)) / 8)) 59 | mTau = 1 60 | hInf = 1 / (1 + exp((v - (-67)) / 7.3)) 61 | hTau = 1500 62 | } 63 | -------------------------------------------------------------------------------- /FENS2016/exercise/modfiles/Kv3_1.mod: -------------------------------------------------------------------------------- 1 | : Comment: Kv3-like potassium current 2 | 3 | NEURON { 4 | SUFFIX Kv3_1 5 | USEION k READ ek WRITE ik 6 | RANGE gbar, g, ik 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | vshift = 0 (mV) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | g (S/cm2) 25 | mInf 26 | mTau 27 | } 28 | 29 | STATE { 30 | m 31 | } 32 | 33 | BREAKPOINT { 34 | SOLVE states METHOD cnexp 35 | g = gbar*m 36 | ik = g*(v-ek) 37 | } 38 | 39 | DERIVATIVE states { 40 | rates() 41 | m' = (mInf-m)/mTau 42 | } 43 | 44 | INITIAL{ 45 | rates() 46 | m = mInf 47 | } 48 | 49 | PROCEDURE rates(){ 50 | UNITSOFF 51 | mInf = 1/(1+exp(((v -(18.700 + vshift))/(-9.700)))) 52 | mTau = 0.2*20.000/(1+exp(((v -(-46.560 + vshift))/(-44.140)))) 53 | UNITSON 54 | } 55 | -------------------------------------------------------------------------------- /FENS2016/exercise/modfiles/NaTs.mod: -------------------------------------------------------------------------------- 1 | : Reference: Colbert and Pan 2002 2 | 3 | NEURON { 4 | SUFFIX NaTs 5 | USEION na READ ena WRITE ina 6 | RANGE gbar, g, ina 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | 18 | malphaF = 0.182 19 | mbetaF = 0.124 20 | mvhalf = -40 (mV) 21 | mk = 6 (mV) 22 | 23 | halphaF = 0.015 24 | hbetaF = 0.015 25 | hvhalf = -66 (mV) 26 | hk = 6 (mV) 27 | } 28 | 29 | ASSIGNED { 30 | v (mV) 31 | ena (mV) 32 | ina (mA/cm2) 33 | g (S/cm2) 34 | celsius (degC) 35 | mInf 36 | mTau 37 | mAlpha 38 | mBeta 39 | hInf 40 | hTau 41 | hAlpha 42 | hBeta 43 | } 44 | 45 | STATE { 46 | m 47 | h 48 | } 49 | 50 | BREAKPOINT { 51 | SOLVE states METHOD cnexp 52 | g = gbar*m*m*m*h 53 | ina = g*(v-ena) 54 | } 55 | 56 | DERIVATIVE states { 57 | rates() 58 | m' = (mInf-m)/mTau 59 | h' = (hInf-h)/hTau 60 | } 61 | 62 | INITIAL{ 63 | rates() 64 | m = mInf 65 | h = hInf 66 | } 67 | 68 | PROCEDURE rates(){ 69 | LOCAL qt 70 | qt = 2.3^((celsius-23)/10) 71 | 72 | UNITSOFF 73 | mAlpha = malphaF * vtrap(-(v - mvhalf), mk) 74 | mBeta = mbetaF * vtrap((v - mvhalf), mk) 75 | 76 | mInf = mAlpha/(mAlpha + mBeta) 77 | mTau = (1/(mAlpha + mBeta))/qt 78 | 79 | hAlpha = halphaF * vtrap(v - hvhalf, hk) 80 | hBeta = hbetaF * vtrap(-(v - hvhalf), hk) 81 | 82 | hInf = hAlpha/(hAlpha + hBeta) 83 | hTau = (1/(hAlpha + hBeta))/qt 84 | UNITSON 85 | } 86 | 87 | FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations 88 | UNITSOFF 89 | if (fabs(x / y) < 1e-6) { 90 | vtrap = y * (1 - x / y / 2) 91 | } else { 92 | vtrap = x / (exp(x / y) - 1) 93 | } 94 | UNITSON 95 | } -------------------------------------------------------------------------------- /FENS2016/exercise/modfiles/Nap.mod: -------------------------------------------------------------------------------- 1 | :Reference : Modeled according to kinetics derived from Magistretti & Alonso 1999 2 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 3 | 4 | NEURON { 5 | SUFFIX Nap 6 | USEION na READ ena WRITE ina 7 | RANGE gbar, g, ina 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ena (mV) 23 | ina (mA/cm2) 24 | g (S/cm2) 25 | celsius (degC) 26 | mInf 27 | hInf 28 | hTau 29 | hAlpha 30 | hBeta 31 | } 32 | 33 | STATE { 34 | h 35 | } 36 | 37 | BREAKPOINT { 38 | SOLVE states METHOD cnexp 39 | rates() 40 | g = gbar*mInf*h 41 | ina = g*(v-ena) 42 | } 43 | 44 | DERIVATIVE states { 45 | rates() 46 | h' = (hInf-h)/hTau 47 | } 48 | 49 | INITIAL{ 50 | rates() 51 | h = hInf 52 | } 53 | 54 | PROCEDURE rates(){ 55 | LOCAL qt 56 | qt = 2.3^((celsius-21)/10) 57 | 58 | UNITSOFF 59 | mInf = 1.0/(1+exp((v- -52.6)/-4.6)) : assuming instantaneous activation as modeled by Magistretti and Alonso 60 | 61 | hInf = 1.0/(1+exp((v- -48.8)/10)) 62 | hAlpha = 2.88e-6 * vtrap(v + 17, 4.63) 63 | hBeta = 6.94e-6 * vtrap(-(v + 64.4), 2.63) 64 | 65 | hTau = (1/(hAlpha + hBeta))/qt 66 | UNITSON 67 | } 68 | 69 | FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations 70 | UNITSOFF 71 | if (fabs(x / y) < 1e-6) { 72 | vtrap = y * (1 - x / y / 2) 73 | } else { 74 | vtrap = x / (exp(x / y) - 1) 75 | } 76 | UNITSON 77 | } -------------------------------------------------------------------------------- /FENS2016/exercise/modfiles/SK.mod: -------------------------------------------------------------------------------- 1 | : SK-type calcium-activated potassium current 2 | : Reference : Kohler et al. 1996 3 | 4 | NEURON { 5 | SUFFIX SK 6 | USEION k READ ek WRITE ik 7 | USEION ca READ cai 8 | RANGE gbar, g, ik 9 | } 10 | 11 | UNITS { 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | (mM) = (milli/liter) 15 | } 16 | 17 | PARAMETER { 18 | v (mV) 19 | gbar = .000001 (mho/cm2) 20 | zTau = 1 (ms) 21 | ek (mV) 22 | cai (mM) 23 | } 24 | 25 | ASSIGNED { 26 | zInf 27 | ik (mA/cm2) 28 | g (S/cm2) 29 | } 30 | 31 | STATE { 32 | z FROM 0 TO 1 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | g = gbar * z 38 | ik = g * (v - ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates(cai) 43 | z' = (zInf - z) / zTau 44 | } 45 | 46 | PROCEDURE rates(ca(mM)) { 47 | if(ca < 1e-7){ 48 | ca = ca + 1e-07 49 | } 50 | zInf = 1/(1 + (0.00043 / ca)^4.8) 51 | } 52 | 53 | INITIAL { 54 | rates(cai) 55 | z = zInf 56 | } 57 | -------------------------------------------------------------------------------- /FENS2016/exercise/orig_parameters.json: -------------------------------------------------------------------------------- 1 | 2 | { 3 | "ek.all": -107, 4 | "e_pas.somatic": -63.3146, 5 | "Ra.basal": 50.8833, 6 | "gbar_Kv3_1.axonal": 0.0100065, 7 | "gbar_NaV.basal": 0.0205486, 8 | "gbar_Kv3_1.basal": 0.205458, 9 | "e_pas.basal": -62.7085, 10 | "gbar_K_T.axonal": 0.000124859, 11 | "gamma_CaDynamics.somatic": 0.00169922, 12 | "v_init": -81, 13 | "cm.basal": 7.88877, 14 | "gbar_Ca_HVA.axonal": 3.83558e-05, 15 | "gbar_NaV.somatic": 0.0499769, 16 | "gbar_Kv2like.axonal": 0.0010615, 17 | "gbar_Ca_LVA.somatic": 0.0060162, 18 | "gbar_Im_v2.basal": 0.00949979, 19 | "gbar_SK.somatic": 0.0001051137, 20 | "ena.all": 53.0, 21 | "g_pas.axonal": 0.00200656, 22 | "gbar_NaV.axonal": 0.0156789, 23 | "gamma_CaDynamics.axonal": 0.0477399, 24 | "gbar_SK.axonal": 0.00661877, 25 | "cm.axonal": 9.91715, 26 | "gbar_Ca_HVA.somatic": 5.9455e-05, 27 | "gbar_Kd.axonal": 0.00833495, 28 | "gbar_Ih.basal": 7.75636e-06, 29 | "gbar_Ca_LVA.axonal": 0.00775489, 30 | "Ra.somatic": 72.0757, 31 | "e_pas.axonal": -71.1766, 32 | "g_pas.basal": 1.10433e-07, 33 | "decay_CaDynamics.axonal": 811.497, 34 | "cm.somatic": 3.35066, 35 | "gbar_Ih.somatic": 3.46139e-06, 36 | "g_pas.somatic": 7.60303e-05, 37 | "celsius": 34, 38 | "Ra.axonal": 100.799, 39 | "gbar_Kv3_1.somatic": 0.671067, 40 | "decay_CaDynamics.somatic": 326.442 41 | } 42 | -------------------------------------------------------------------------------- /FENS2016/scoring/config/mechanisms.json: -------------------------------------------------------------------------------- 1 | { 2 | "basal": [ 3 | "Ih", 4 | "NaV", 5 | "Kv3_1", 6 | "Im_v2", 7 | "pas" 8 | ], 9 | "somatic": [ 10 | "NaV", 11 | "SK", 12 | "Kv3_1", 13 | "Ca_HVA", 14 | "Ca_LVA", 15 | "CaDynamics", 16 | "Ih", 17 | "pas" 18 | ], 19 | "axonal": [ 20 | "NaV", 21 | "K_T", 22 | "Kd", 23 | "Kv2like", 24 | "Kv3_1", 25 | "SK", 26 | "Ca_HVA", 27 | "Ca_LVA", 28 | "CaDynamics", 29 | "pas" 30 | ] 31 | } 32 | -------------------------------------------------------------------------------- /FENS2016/scoring/config/protocols.json: -------------------------------------------------------------------------------- 1 | { 2 | "StepPos": { 3 | "stimuli": [ 4 | { 5 | "delay": 270, 6 | "amp": 0.15, 7 | "duration": 1000, 8 | "totduration": 1540 9 | } 10 | ] 11 | }, 12 | "StepNeg": { 13 | "stimuli": [ 14 | { 15 | "delay": 270, 16 | "amp": -0.11, 17 | "duration": 1000, 18 | "totduration": 1540 19 | } 20 | ] 21 | } 22 | } 23 | -------------------------------------------------------------------------------- /FENS2016/scoring/modfiles/CaDynamics.mod: -------------------------------------------------------------------------------- 1 | : Dynamics that track inside calcium concentration 2 | : modified from Destexhe et al. 1994 3 | 4 | NEURON { 5 | SUFFIX CaDynamics 6 | USEION ca READ ica WRITE cai 7 | RANGE decay, gamma, minCai, depth 8 | } 9 | 10 | UNITS { 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | FARADAY = (faraday) (coulombs) 14 | (molar) = (1/liter) 15 | (mM) = (millimolar) 16 | (um) = (micron) 17 | } 18 | 19 | PARAMETER { 20 | gamma = 0.05 : percent of free calcium (not buffered) 21 | decay = 80 (ms) : rate of removal of calcium 22 | depth = 0.1 (um) : depth of shell 23 | minCai = 1e-4 (mM) 24 | } 25 | 26 | ASSIGNED {ica (mA/cm2)} 27 | 28 | INITIAL { 29 | cai = minCai 30 | } 31 | 32 | STATE { 33 | cai (mM) 34 | } 35 | 36 | BREAKPOINT { SOLVE states METHOD cnexp } 37 | 38 | DERIVATIVE states { 39 | cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay 40 | } 41 | -------------------------------------------------------------------------------- /FENS2016/scoring/modfiles/Ca_HVA.mod: -------------------------------------------------------------------------------- 1 | : Reference: Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993 2 | 3 | NEURON { 4 | SUFFIX Ca_HVA 5 | USEION ca READ eca WRITE ica 6 | RANGE gbar, g, ica 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | } 18 | 19 | ASSIGNED { 20 | v (mV) 21 | eca (mV) 22 | ica (mA/cm2) 23 | g (S/cm2) 24 | mInf 25 | mTau 26 | mAlpha 27 | mBeta 28 | hInf 29 | hTau 30 | hAlpha 31 | hBeta 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | g = gbar*m*m*h 42 | ica = g*(v-eca) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | UNITSOFF 59 | : if((v == -27) ){ 60 | : v = v+0.0001 61 | : } 62 | :mAlpha = (0.055*(-27-v))/(exp((-27-v)/3.8) - 1) 63 | mAlpha = 0.055 * vtrap(-27 - v, 3.8) 64 | mBeta = (0.94*exp((-75-v)/17)) 65 | mInf = mAlpha/(mAlpha + mBeta) 66 | mTau = 1/(mAlpha + mBeta) 67 | hAlpha = (0.000457*exp((-13-v)/50)) 68 | hBeta = (0.0065/(exp((-v-15)/28)+1)) 69 | hInf = hAlpha/(hAlpha + hBeta) 70 | hTau = 1/(hAlpha + hBeta) 71 | UNITSON 72 | } 73 | 74 | FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations 75 | UNITSOFF 76 | if (fabs(x / y) < 1e-6) { 77 | vtrap = y * (1 - x / y / 2) 78 | } else { 79 | vtrap = x / (exp(x / y) - 1) 80 | } 81 | UNITSON 82 | } -------------------------------------------------------------------------------- /FENS2016/scoring/modfiles/Ca_LVA.mod: -------------------------------------------------------------------------------- 1 | : Comment: LVA ca channel. Note: mtau is an approximation from the plots 2 | : Reference: Avery and Johnston 1996, tau from Randall 1997 3 | : Comment: shifted by -10 mv to correct for junction potential 4 | : Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | NEURON { 7 | SUFFIX Ca_LVA 8 | USEION ca READ eca WRITE ica 9 | RANGE gbar, g, ica 10 | } 11 | 12 | UNITS { 13 | (S) = (siemens) 14 | (mV) = (millivolt) 15 | (mA) = (milliamp) 16 | } 17 | 18 | PARAMETER { 19 | gbar = 0.00001 (S/cm2) 20 | } 21 | 22 | ASSIGNED { 23 | v (mV) 24 | eca (mV) 25 | ica (mA/cm2) 26 | g (S/cm2) 27 | celsius (degC) 28 | mInf 29 | mTau 30 | hInf 31 | hTau 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | g = gbar*m*m*h 42 | ica = g*(v-eca) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | LOCAL qt 59 | qt = 2.3^((celsius-21)/10) 60 | 61 | UNITSOFF 62 | v = v + 10 63 | mInf = 1.0000/(1+ exp((v - -30.000)/-6)) 64 | mTau = (5.0000 + 20.0000/(1+exp((v - -25.000)/5)))/qt 65 | hInf = 1.0000/(1+ exp((v - -80.000)/6.4)) 66 | hTau = (20.0000 + 50.0000/(1+exp((v - -40.000)/7)))/qt 67 | v = v - 10 68 | UNITSON 69 | } 70 | -------------------------------------------------------------------------------- /FENS2016/scoring/modfiles/Ih.mod: -------------------------------------------------------------------------------- 1 | : Reference: Kole,Hallermann,and Stuart, J. Neurosci. 2006 2 | 3 | NEURON { 4 | SUFFIX Ih 5 | NONSPECIFIC_CURRENT ihcn 6 | RANGE gbar, g, ihcn 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | ehcn = -45.0 (mV) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ihcn (mA/cm2) 23 | g (S/cm2) 24 | mInf 25 | mTau 26 | mAlpha 27 | mBeta 28 | } 29 | 30 | STATE { 31 | m 32 | } 33 | 34 | BREAKPOINT { 35 | SOLVE states METHOD cnexp 36 | g = gbar*m 37 | ihcn = g*(v-ehcn) 38 | } 39 | 40 | DERIVATIVE states { 41 | rates() 42 | m' = (mInf-m)/mTau 43 | } 44 | 45 | INITIAL{ 46 | rates() 47 | m = mInf 48 | } 49 | 50 | PROCEDURE rates(){ 51 | UNITSOFF 52 | : if(v == -154.9){ 53 | : v = v + 0.0001 54 | : } 55 | :mAlpha = 0.001*6.43*(v+154.9)/(exp((v+154.9)/11.9)-1) 56 | mAlpha = 0.001 * 6.43 * vtrap(v + 154.9, 11.9) 57 | mBeta = 0.001*193*exp(v/33.1) 58 | mInf = mAlpha/(mAlpha + mBeta) 59 | mTau = 1/(mAlpha + mBeta) 60 | UNITSON 61 | } 62 | 63 | FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations 64 | UNITSOFF 65 | if (fabs(x / y) < 1e-6) { 66 | vtrap = y * (1 - x / y / 2) 67 | } else { 68 | vtrap = x / (exp(x / y) - 1) 69 | } 70 | UNITSON 71 | } 72 | -------------------------------------------------------------------------------- /FENS2016/scoring/modfiles/Im.mod: -------------------------------------------------------------------------------- 1 | : Reference: Adams et al. 1982 - M-currents and other potassium currents in bullfrog sympathetic neurones 2 | : Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 3 | 4 | NEURON { 5 | SUFFIX Im 6 | USEION k READ ek WRITE ik 7 | RANGE gbar, g, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | g (S/cm2) 25 | celsius (degC) 26 | mInf 27 | mTau 28 | mAlpha 29 | mBeta 30 | } 31 | 32 | STATE { 33 | m 34 | } 35 | 36 | BREAKPOINT { 37 | SOLVE states METHOD cnexp 38 | g = gbar*m 39 | ik = g*(v-ek) 40 | } 41 | 42 | DERIVATIVE states { 43 | rates() 44 | m' = (mInf-m)/mTau 45 | } 46 | 47 | INITIAL{ 48 | rates() 49 | m = mInf 50 | } 51 | 52 | PROCEDURE rates(){ 53 | LOCAL qt 54 | qt = 2.3^((celsius-21)/10) 55 | 56 | UNITSOFF 57 | mAlpha = 3.3e-3*exp(2.5*0.04*(v - -35)) 58 | mBeta = 3.3e-3*exp(-2.5*0.04*(v - -35)) 59 | mInf = mAlpha/(mAlpha + mBeta) 60 | mTau = (1/(mAlpha + mBeta))/qt 61 | UNITSON 62 | } 63 | -------------------------------------------------------------------------------- /FENS2016/scoring/modfiles/Im_v2.mod: -------------------------------------------------------------------------------- 1 | : Based on Im model of Vervaeke et al. (2006) 2 | 3 | NEURON { 4 | SUFFIX Im_v2 5 | USEION k READ ek WRITE ik 6 | RANGE gbar, g, ik 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | } 18 | 19 | ASSIGNED { 20 | v (mV) 21 | ek (mV) 22 | ik (mA/cm2) 23 | g (S/cm2) 24 | celsius (degC) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | } 30 | 31 | STATE { 32 | m 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | g = gbar * m 38 | ik = g * (v - ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates() 43 | m' = (mInf - m) / mTau 44 | } 45 | 46 | INITIAL{ 47 | rates() 48 | m = mInf 49 | } 50 | 51 | PROCEDURE rates() { 52 | LOCAL qt 53 | qt = 2.3^((celsius-30)/10) 54 | mAlpha = 0.007 * exp( (6 * 0.4 * (v - (-48))) / 26.12 ) 55 | mBeta = 0.007 * exp( (-6 * (1 - 0.4) * (v - (-48))) / 26.12 ) 56 | 57 | mInf = mAlpha / (mAlpha + mBeta) 58 | mTau = (15 + 1 / (mAlpha + mBeta)) / qt 59 | } 60 | -------------------------------------------------------------------------------- /FENS2016/scoring/modfiles/K_P.mod: -------------------------------------------------------------------------------- 1 | : Comment: The persistent component of the K current 2 | : Reference: Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | 4 | 5 | NEURON { 6 | SUFFIX K_P 7 | USEION k READ ek WRITE ik 8 | RANGE gbar, g, ik 9 | } 10 | 11 | UNITS { 12 | (S) = (siemens) 13 | (mV) = (millivolt) 14 | (mA) = (milliamp) 15 | } 16 | 17 | PARAMETER { 18 | gbar = 0.00001 (S/cm2) 19 | vshift = 0 (mV) 20 | tauF = 1 21 | } 22 | 23 | ASSIGNED { 24 | v (mV) 25 | ek (mV) 26 | ik (mA/cm2) 27 | g (S/cm2) 28 | celsius (degC) 29 | mInf 30 | mTau 31 | hInf 32 | hTau 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | g = gbar*m*m*h 43 | ik = g*(v-ek) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates() { 59 | LOCAL qt 60 | qt = 2.3^((celsius-21)/10) 61 | UNITSOFF 62 | mInf = 1 / (1 + exp(-(v - (-14.3 + vshift)) / 14.6)) 63 | if (v < -50 + vshift){ 64 | mTau = tauF * (1.25+175.03*exp(-(v - vshift) * -0.026))/qt 65 | } else { 66 | mTau = tauF * (1.25+13*exp(-(v - vshift) * 0.026))/qt 67 | } 68 | hInf = 1/(1 + exp(-(v - (-54 + vshift))/-11)) 69 | hTau = (360+(1010+24*(v - (-55 + vshift)))*exp(-((v - (-75 + vshift))/48)^2))/qt 70 | UNITSON 71 | } 72 | -------------------------------------------------------------------------------- /FENS2016/scoring/modfiles/K_T.mod: -------------------------------------------------------------------------------- 1 | : Comment: The transient component of the K current 2 | : Reference: Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | 4 | NEURON { 5 | SUFFIX K_T 6 | USEION k READ ek WRITE ik 7 | RANGE gbar, g, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gbar = 0.00001 (S/cm2) 18 | vshift = 0 (mV) 19 | mTauF = 1.0 20 | hTauF = 1.0 21 | } 22 | 23 | ASSIGNED { 24 | v (mV) 25 | ek (mV) 26 | ik (mA/cm2) 27 | g (S/cm2) 28 | celsius (degC) 29 | mInf 30 | mTau 31 | hInf 32 | hTau 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | g = gbar*m*m*m*m*h 43 | ik = g*(v-ek) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates(){ 59 | LOCAL qt 60 | qt = 2.3^((celsius-21)/10) 61 | 62 | UNITSOFF 63 | mInf = 1/(1 + exp(-(v - (-47 + vshift)) / 29)) 64 | mTau = (0.34 + mTauF * 0.92*exp(-((v+71-vshift)/59)^2))/qt 65 | hInf = 1/(1 + exp(-(v+66-vshift)/-10)) 66 | hTau = (8 + hTauF * 49*exp(-((v+73-vshift)/23)^2))/qt 67 | UNITSON 68 | } 69 | -------------------------------------------------------------------------------- /FENS2016/scoring/modfiles/Kd.mod: -------------------------------------------------------------------------------- 1 | : Based on Kd model of Foust et al. (2011) 2 | 3 | 4 | NEURON { 5 | SUFFIX Kd 6 | USEION k READ ek WRITE ik 7 | RANGE gbar, g, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | g (S/cm2) 25 | celsius (degC) 26 | mInf 27 | mTau 28 | hInf 29 | hTau 30 | } 31 | 32 | STATE { 33 | m 34 | h 35 | } 36 | 37 | BREAKPOINT { 38 | SOLVE states METHOD cnexp 39 | g = gbar * m * h 40 | ik = g * (v - ek) 41 | } 42 | 43 | DERIVATIVE states { 44 | rates() 45 | m' = (mInf - m) / mTau 46 | h' = (hInf - h) / hTau 47 | } 48 | 49 | INITIAL{ 50 | rates() 51 | m = mInf 52 | h = hInf 53 | } 54 | 55 | PROCEDURE rates() { 56 | LOCAL qt 57 | qt = 2.3^((celsius-23)/10) 58 | mInf = 1 - 1 / (1 + exp((v - (-43)) / 8)) 59 | mTau = 1 60 | hInf = 1 / (1 + exp((v - (-67)) / 7.3)) 61 | hTau = 1500 62 | } 63 | -------------------------------------------------------------------------------- /FENS2016/scoring/modfiles/Kv3_1.mod: -------------------------------------------------------------------------------- 1 | : Comment: Kv3-like potassium current 2 | 3 | NEURON { 4 | SUFFIX Kv3_1 5 | USEION k READ ek WRITE ik 6 | RANGE gbar, g, ik 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | vshift = 0 (mV) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | g (S/cm2) 25 | mInf 26 | mTau 27 | } 28 | 29 | STATE { 30 | m 31 | } 32 | 33 | BREAKPOINT { 34 | SOLVE states METHOD cnexp 35 | g = gbar*m 36 | ik = g*(v-ek) 37 | } 38 | 39 | DERIVATIVE states { 40 | rates() 41 | m' = (mInf-m)/mTau 42 | } 43 | 44 | INITIAL{ 45 | rates() 46 | m = mInf 47 | } 48 | 49 | PROCEDURE rates(){ 50 | UNITSOFF 51 | mInf = 1/(1+exp(((v -(18.700 + vshift))/(-9.700)))) 52 | mTau = 0.2*20.000/(1+exp(((v -(-46.560 + vshift))/(-44.140)))) 53 | UNITSON 54 | } 55 | -------------------------------------------------------------------------------- /FENS2016/scoring/modfiles/NaTs.mod: -------------------------------------------------------------------------------- 1 | : Reference: Colbert and Pan 2002 2 | 3 | NEURON { 4 | SUFFIX NaTs 5 | USEION na READ ena WRITE ina 6 | RANGE gbar, g, ina 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gbar = 0.00001 (S/cm2) 17 | 18 | malphaF = 0.182 19 | mbetaF = 0.124 20 | mvhalf = -40 (mV) 21 | mk = 6 (mV) 22 | 23 | halphaF = 0.015 24 | hbetaF = 0.015 25 | hvhalf = -66 (mV) 26 | hk = 6 (mV) 27 | } 28 | 29 | ASSIGNED { 30 | v (mV) 31 | ena (mV) 32 | ina (mA/cm2) 33 | g (S/cm2) 34 | celsius (degC) 35 | mInf 36 | mTau 37 | mAlpha 38 | mBeta 39 | hInf 40 | hTau 41 | hAlpha 42 | hBeta 43 | } 44 | 45 | STATE { 46 | m 47 | h 48 | } 49 | 50 | BREAKPOINT { 51 | SOLVE states METHOD cnexp 52 | g = gbar*m*m*m*h 53 | ina = g*(v-ena) 54 | } 55 | 56 | DERIVATIVE states { 57 | rates() 58 | m' = (mInf-m)/mTau 59 | h' = (hInf-h)/hTau 60 | } 61 | 62 | INITIAL{ 63 | rates() 64 | m = mInf 65 | h = hInf 66 | } 67 | 68 | PROCEDURE rates(){ 69 | LOCAL qt 70 | qt = 2.3^((celsius-23)/10) 71 | 72 | UNITSOFF 73 | mAlpha = malphaF * vtrap(-(v - mvhalf), mk) 74 | mBeta = mbetaF * vtrap((v - mvhalf), mk) 75 | 76 | mInf = mAlpha/(mAlpha + mBeta) 77 | mTau = (1/(mAlpha + mBeta))/qt 78 | 79 | hAlpha = halphaF * vtrap(v - hvhalf, hk) 80 | hBeta = hbetaF * vtrap(-(v - hvhalf), hk) 81 | 82 | hInf = hAlpha/(hAlpha + hBeta) 83 | hTau = (1/(hAlpha + hBeta))/qt 84 | UNITSON 85 | } 86 | 87 | FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations 88 | UNITSOFF 89 | if (fabs(x / y) < 1e-6) { 90 | vtrap = y * (1 - x / y / 2) 91 | } else { 92 | vtrap = x / (exp(x / y) - 1) 93 | } 94 | UNITSON 95 | } -------------------------------------------------------------------------------- /FENS2016/scoring/modfiles/Nap.mod: -------------------------------------------------------------------------------- 1 | :Reference : Modeled according to kinetics derived from Magistretti & Alonso 1999 2 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 3 | 4 | NEURON { 5 | SUFFIX Nap 6 | USEION na READ ena WRITE ina 7 | RANGE gbar, g, ina 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ena (mV) 23 | ina (mA/cm2) 24 | g (S/cm2) 25 | celsius (degC) 26 | mInf 27 | hInf 28 | hTau 29 | hAlpha 30 | hBeta 31 | } 32 | 33 | STATE { 34 | h 35 | } 36 | 37 | BREAKPOINT { 38 | SOLVE states METHOD cnexp 39 | rates() 40 | g = gbar*mInf*h 41 | ina = g*(v-ena) 42 | } 43 | 44 | DERIVATIVE states { 45 | rates() 46 | h' = (hInf-h)/hTau 47 | } 48 | 49 | INITIAL{ 50 | rates() 51 | h = hInf 52 | } 53 | 54 | PROCEDURE rates(){ 55 | LOCAL qt 56 | qt = 2.3^((celsius-21)/10) 57 | 58 | UNITSOFF 59 | mInf = 1.0/(1+exp((v- -52.6)/-4.6)) : assuming instantaneous activation as modeled by Magistretti and Alonso 60 | 61 | hInf = 1.0/(1+exp((v- -48.8)/10)) 62 | hAlpha = 2.88e-6 * vtrap(v + 17, 4.63) 63 | hBeta = 6.94e-6 * vtrap(-(v + 64.4), 2.63) 64 | 65 | hTau = (1/(hAlpha + hBeta))/qt 66 | UNITSON 67 | } 68 | 69 | FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations 70 | UNITSOFF 71 | if (fabs(x / y) < 1e-6) { 72 | vtrap = y * (1 - x / y / 2) 73 | } else { 74 | vtrap = x / (exp(x / y) - 1) 75 | } 76 | UNITSON 77 | } -------------------------------------------------------------------------------- /FENS2016/scoring/modfiles/SK.mod: -------------------------------------------------------------------------------- 1 | : SK-type calcium-activated potassium current 2 | : Reference : Kohler et al. 1996 3 | 4 | NEURON { 5 | SUFFIX SK 6 | USEION k READ ek WRITE ik 7 | USEION ca READ cai 8 | RANGE gbar, g, ik 9 | } 10 | 11 | UNITS { 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | (mM) = (milli/liter) 15 | } 16 | 17 | PARAMETER { 18 | v (mV) 19 | gbar = .000001 (mho/cm2) 20 | zTau = 1 (ms) 21 | ek (mV) 22 | cai (mM) 23 | } 24 | 25 | ASSIGNED { 26 | zInf 27 | ik (mA/cm2) 28 | g (S/cm2) 29 | } 30 | 31 | STATE { 32 | z FROM 0 TO 1 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | g = gbar * z 38 | ik = g * (v - ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates(cai) 43 | z' = (zInf - z) / zTau 44 | } 45 | 46 | PROCEDURE rates(ca(mM)) { 47 | if(ca < 1e-7){ 48 | ca = ca + 1e-07 49 | } 50 | zInf = 1/(1 + (0.00043 / ca)^4.8) 51 | } 52 | 53 | INITIAL { 54 | rates(cai) 55 | z = zInf 56 | } 57 | -------------------------------------------------------------------------------- /FENS2016/scoring/orig_parameters.json: -------------------------------------------------------------------------------- 1 | 2 | { 3 | "ek.all": -107, 4 | "e_pas.somatic": -63.3146, 5 | "Ra.basal": 50.8833, 6 | "gbar_Kv3_1.axonal": 0.0100065, 7 | "gbar_NaV.basal": 0.0205486, 8 | "gbar_Kv3_1.basal": 0.205458, 9 | "e_pas.basal": -62.7085, 10 | "gbar_K_T.axonal": 0.000124859, 11 | "gamma_CaDynamics.somatic": 0.00169922, 12 | "v_init": -81, 13 | "cm.basal": 7.88877, 14 | "gbar_Ca_HVA.axonal": 3.83558e-05, 15 | "gbar_NaV.somatic": 0.0499769, 16 | "gbar_Kv2like.axonal": 0.0010615, 17 | "gbar_Ca_LVA.somatic": 0.0060162, 18 | "gbar_Im_v2.basal": 0.00949979, 19 | "gbar_SK.somatic": 0.0001051137, 20 | "ena.all": 53.0, 21 | "g_pas.axonal": 0.00200656, 22 | "gbar_NaV.axonal": 0.0156789, 23 | "gamma_CaDynamics.axonal": 0.0477399, 24 | "gbar_SK.axonal": 0.00661877, 25 | "cm.axonal": 9.91715, 26 | "gbar_Ca_HVA.somatic": 5.9455e-05, 27 | "gbar_Kd.axonal": 0.00833495, 28 | "gbar_Ih.basal": 7.75636e-06, 29 | "gbar_Ca_LVA.axonal": 0.00775489, 30 | "Ra.somatic": 72.0757, 31 | "e_pas.axonal": -71.1766, 32 | "g_pas.basal": 1.10433e-07, 33 | "decay_CaDynamics.axonal": 811.497, 34 | "cm.somatic": 3.35066, 35 | "gbar_Ih.somatic": 3.46139e-06, 36 | "g_pas.somatic": 7.60303e-05, 37 | "celsius": 34, 38 | "Ra.axonal": 100.799, 39 | "gbar_Kv3_1.somatic": 0.671067, 40 | "decay_CaDynamics.somatic": 326.442 41 | } 42 | -------------------------------------------------------------------------------- /FENS2016/scoring/students_par/parameters_Arlindo.json: -------------------------------------------------------------------------------- 1 | { 2 | "ek.all": -107, 3 | "gbar_NaV.somatic": 0.04595, 4 | "e_pas.somatic": -63.3146, 5 | "Ra.basal": 50.8833, 6 | "gamma_CaDynamics.axonal": 0.0477399, 7 | "gbar_Kv3_1.axonal": 0.0100065, 8 | "v_init": -81, 9 | "e_pas.basal": -62.7085, 10 | "gbar_Kv3_1.basal": 0.205458, 11 | "cm.axonal": 7.6668, 12 | "gbar_K_T.axonal": 0.0013593, 13 | "gamma_CaDynamics.somatic": 0.00169922, 14 | "gbar_Im_v2.basal": 0.01, 15 | "celsius": 34, 16 | "gbar_SK.axonal": 0.00661877, 17 | "gbar_Ca_HVA.somatic": 5.9455e-05, 18 | "gbar_Ih.basal": 7e-05, 19 | "gbar_Ca_HVA.axonal": 3.83558e-05, 20 | "gbar_Kd.axonal": 0.00833495, 21 | "gbar_Ca_LVA.axonal": 0.00775489, 22 | "gbar_Kv2like.axonal": 0.00848501700778672, 23 | "Ra.somatic": 72.0757, 24 | "e_pas.axonal": -71.1766, 25 | "g_pas.basal": 1.10433e-07, 26 | "decay_CaDynamics.axonal": 811.497, 27 | "cm.somatic": 2.1356, 28 | "gbar_Ca_LVA.somatic": 0.0060162, 29 | "gbar_Ih.somatic": 3.46139e-06, 30 | "g_pas.somatic": 7.60303e-05, 31 | "cm.basal": 1.4357, 32 | "Ra.axonal": 100.799, 33 | "gbar_NaV.basal": 0.0205486, 34 | "gbar_NaV.axonal": 0.013436510974815711, 35 | "gbar_Kv3_1.somatic": 0.7294, 36 | "gbar_SK.somatic": 0.0001051137, 37 | "decay_CaDynamics.somatic": 326.442, 38 | "ena.all": 53.0, 39 | "g_pas.axonal": 0.00200656 40 | } -------------------------------------------------------------------------------- /FENS2016/scoring/students_par/parameters_Luis.json: -------------------------------------------------------------------------------- 1 | { 2 | "ek.all": -107, 3 | "gbar_NaV.somatic": 0.04595, 4 | "e_pas.somatic": -63.3146, 5 | "Ra.basal": 50.8833, 6 | "gamma_CaDynamics.axonal": 0.0477399, 7 | "gbar_Kv3_1.axonal": 0.0100065, 8 | "v_init": -81, 9 | "e_pas.basal": -62.7085, 10 | "gbar_Kv3_1.basal": 0.205458, 11 | "cm.axonal": 7.6668, 12 | "gbar_K_T.axonal": 0.0013593, 13 | "gamma_CaDynamics.somatic": 0.00169922, 14 | "gbar_Im_v2.basal": 0.01, 15 | "celsius": 34, 16 | "gbar_SK.axonal": 0.00661877, 17 | "gbar_Ca_HVA.somatic": 5.9455e-05, 18 | "gbar_Ih.basal": 5.346422332836298e-05, 19 | "gbar_Ca_HVA.axonal": 3.83558e-05, 20 | "gbar_Kd.axonal": 0.00833495, 21 | "gbar_Ca_LVA.axonal": 0.00775489, 22 | "gbar_Kv2like.axonal": 0.00848501700778672, 23 | "Ra.somatic": 72.0757, 24 | "e_pas.axonal": -71.1766, 25 | "g_pas.basal": 1.10433e-07, 26 | "decay_CaDynamics.axonal": 811.497, 27 | "cm.somatic": 2.1356, 28 | "gbar_Ca_LVA.somatic": 0.0060162, 29 | "gbar_Ih.somatic": 3.46139e-06, 30 | "g_pas.somatic": 7.60303e-05, 31 | "cm.basal": 1.4357, 32 | "Ra.axonal": 100.799, 33 | "gbar_NaV.basal": 0.0205486, 34 | "gbar_NaV.axonal": 0.013436510974815711, 35 | "gbar_Kv3_1.somatic": 0.7294, 36 | "gbar_SK.somatic": 0.0001051137, 37 | "decay_CaDynamics.somatic": 326.442, 38 | "ena.all": 53.0, 39 | "g_pas.axonal": 0.00200656 40 | } -------------------------------------------------------------------------------- /FENS2016/scoring/students_par/parameters_Markus.json: -------------------------------------------------------------------------------- 1 | { 2 | "ek.all": -107, 3 | "gbar_NaV.somatic": 0.04595, 4 | "e_pas.somatic": -63.3146, 5 | "Ra.basal": 50.8833, 6 | "gamma_CaDynamics.axonal": 0.0477399, 7 | "gbar_Kv3_1.axonal": 0.022947474961030473, 8 | "v_init": -81, 9 | "e_pas.basal": -62.7085, 10 | "gbar_Kv3_1.basal": 0.5008541189680321, 11 | "cm.axonal": 7.6668, 12 | "gbar_K_T.axonal": 0.0013593, 13 | "gamma_CaDynamics.somatic": 0.00169922, 14 | "gbar_Im_v2.basal": 0.01, 15 | "celsius": 34, 16 | "gbar_SK.axonal": 0.00661877, 17 | "gbar_Ca_HVA.somatic": 5.9455e-05, 18 | "gbar_Ih.basal": 7e-05, 19 | "gbar_Ca_HVA.axonal": 3.83558e-05, 20 | "gbar_Kd.axonal": 0.00833495, 21 | "gbar_Ca_LVA.axonal": 0.00775489, 22 | "gbar_Kv2like.axonal": 0.00692472190574025, 23 | "Ra.somatic": 72.0757, 24 | "e_pas.axonal": -71.1766, 25 | "g_pas.basal": 1.10433e-07, 26 | "decay_CaDynamics.axonal": 811.497, 27 | "cm.somatic": 2.1356, 28 | "gbar_Ca_LVA.somatic": 0.0060162, 29 | "gbar_Ih.somatic": 3.46139e-06, 30 | "g_pas.somatic": 7.60303e-05, 31 | "cm.basal": 1.4357, 32 | "Ra.axonal": 100.799, 33 | "gbar_NaV.basal": 0.0205486, 34 | "gbar_NaV.axonal": 0.0011645794914983177, 35 | "gbar_Kv3_1.somatic": 0.5109308141941027, 36 | "gbar_SK.somatic": 0.0001051137, 37 | "decay_CaDynamics.somatic": 326.442, 38 | "ena.all": 53.0, 39 | "g_pas.axonal": 0.00200656 40 | } -------------------------------------------------------------------------------- /FENS2016/scoring/students_par/parameters_Tansel.json: -------------------------------------------------------------------------------- 1 | { 2 | "ek.all": -107, 3 | "gbar_NaV.somatic": 0.04595, 4 | "e_pas.somatic": -63.3146, 5 | "Ra.basal": 50.8833, 6 | "gamma_CaDynamics.axonal": 0.0477399, 7 | "gbar_Kv3_1.axonal": 0.0100065, 8 | "v_init": -81, 9 | "e_pas.basal": -62.7085, 10 | "gbar_Kv3_1.basal": 0.205458, 11 | "cm.axonal": 7.6668, 12 | "gbar_K_T.axonal": 0.0013593, 13 | "gamma_CaDynamics.somatic": 0.00169922, 14 | "gbar_Im_v2.basal": 0.01, 15 | "celsius": 34, 16 | "gbar_SK.axonal": 0.00661877, 17 | "gbar_Ca_HVA.somatic": 5.9455e-05, 18 | "gbar_Ih.basal": 7e-05, 19 | "gbar_Ca_HVA.axonal": 3.83558e-05, 20 | "gbar_Kd.axonal": 0.00833495, 21 | "gbar_Ca_LVA.axonal": 0.00775489, 22 | "gbar_Kv2like.axonal": 0.004970523780681963, 23 | "Ra.somatic": 72.0757, 24 | "e_pas.axonal": -71.1766, 25 | "g_pas.basal": 1.10433e-07, 26 | "decay_CaDynamics.axonal": 811.497, 27 | "cm.somatic": 2.1356, 28 | "gbar_Ca_LVA.somatic": 0.0060162, 29 | "gbar_Ih.somatic": 3.46139e-06, 30 | "g_pas.somatic": 7.60303e-05, 31 | "cm.basal": 1.4357, 32 | "Ra.axonal": 100.799, 33 | "gbar_NaV.basal": 0.0205486, 34 | "gbar_NaV.axonal": 0.01243901497054983, 35 | "gbar_Kv3_1.somatic": 0.7294, 36 | "gbar_SK.somatic": 0.0001051137, 37 | "decay_CaDynamics.somatic": 326.442, 38 | "ena.all": 53.0, 39 | "g_pas.axonal": 0.00200656 40 | } -------------------------------------------------------------------------------- /General/Installation/Neuron.md: -------------------------------------------------------------------------------- 1 | # Neuron simulator 2 | -------------------------------------------------------------------------------- /General/README.md: -------------------------------------------------------------------------------- 1 | # General 2 | 3 | Content shared among the tutorials 4 | 5 | ## Installation instructions 6 | 7 | Installation instructions for the software used during the tutorials are in [this subdirectory](Installation/README.md) 8 | -------------------------------------------------------------------------------- /HBPSchool2016/admin/VMs/vagrant/.gitignore: -------------------------------------------------------------------------------- 1 | /*.log 2 | /.vagrant 3 | -------------------------------------------------------------------------------- /HBPSchool2016/admin/VMs/vagrant/Makefile: -------------------------------------------------------------------------------- 1 | create: 2 | vagrant up --provider virtualbox 3 | up: 4 | vagrant up 5 | provision: 6 | vagrant provision 7 | clean: 8 | vagrant destroy 9 | ansible: 10 | ansible-playbook -vv --private-key=.vagrant/machines/default/virtualbox/private_key -u vagrant -i .vagrant/provisioners/ansible/inventory/vagrant_ansible_inventory playbook.yml 11 | password: 12 | pip install passlib 13 | python -c 'import crypt, getpass, base64, os; print crypt.crypt(getpass.getpass(), base64.b64encode(os.urandom(16)))' 14 | -------------------------------------------------------------------------------- /HBPSchool2016/admin/VMs/vagrant/Vagrantfile: -------------------------------------------------------------------------------- 1 | # -*- mode: ruby -*- 2 | # vi: set ft=ruby : 3 | 4 | 5 | Vagrant.configure(2) do |config| 6 | config.vm.define "vb32" do |vb32| 7 | vb32.vm.box = "ubuntu/trusty32" 8 | vb32.vm.provider :virtualbox do |vb| 9 | vb.customize ["modifyvm", :id, "--hwvirtex", "off"] 10 | vb.name = "hbpschool2016.32bit" 11 | end 12 | end 13 | 14 | config.vm.define "vb64" do |vb64| 15 | vb64.vm.box = "ubuntu/trusty64" 16 | vb64.vm.provider :virtualbox do |vb| 17 | vb.customize ["modifyvm", :id, "--hwvirtex", "off"] 18 | vb.name = "hbpschool2016" 19 | end 20 | end 21 | 22 | 23 | config.vm.provider :virtualbox do |vb| 24 | vb.customize ["modifyvm", :id, "--memory", "2048"] 25 | vb.customize ["modifyvm", :id, "--cpus", "4"] 26 | vb.customize ['modifyvm', :id, '--clipboard', 'bidirectional'] 27 | vb.gui = true 28 | end 29 | 30 | 31 | config.vm.provision "ansible" do |ansible| 32 | ansible.playbook = "playbook.yml" 33 | # ansible.verbose = "v" 34 | end 35 | end 36 | 37 | -------------------------------------------------------------------------------- /HBPSchool2016/admin/VMs/vagrant/data/hbpschool.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlueBrain/SimulationTutorials/44fa01c22bc83fbbe8a01d3580de75ffadf92ea4/HBPSchool2016/admin/VMs/vagrant/data/hbpschool.jpg -------------------------------------------------------------------------------- /HBPSchool2016/admin/VMs/vagrant/neuron.yml: -------------------------------------------------------------------------------- 1 | --- 2 | 3 | - name: Get iv Source 4 | get_url: url={{ download_path }}/{{ iv_tarball }} dest={{ src_dir }}/{{ iv_tarball }} 5 | 6 | - name: Get nrn Source 7 | get_url: url={{ download_path }}/{{ nrn_tarball }} dest={{ src_dir }}/{{ nrn_tarball }} 8 | 9 | - name: Untar iv source 10 | unarchive: copy=no src={{ src_dir }}/{{ iv_tarball }} dest={{ src_dir }} 11 | 12 | - name: Untar nrn source 13 | unarchive: copy=no src={{ src_dir }}/{{ nrn_tarball }} dest={{ src_dir }} 14 | 15 | - name: configure iv 16 | shell: "./configure --prefix={{ nrn_prefix }}" 17 | args: 18 | chdir: "{{ iv_src_dir }}" 19 | 20 | - name: build iv 21 | shell: make 22 | args: 23 | chdir: "{{ iv_src_dir }}" 24 | 25 | - name: install iv 26 | shell: make install 27 | args: 28 | chdir: "{{ iv_src_dir }}" 29 | 30 | - name: configure neuron 31 | shell: "./configure --with-iv={{ nrn_prefix }} --with-nrnpython --prefix={{ nrn_prefix }}" 32 | args: 33 | chdir: "{{ nrn_src_dir }}" 34 | 35 | - name: build neuron 36 | shell: make 37 | args: 38 | chdir: "{{ nrn_src_dir }}" 39 | 40 | - name: install neuron 41 | shell: make install 42 | args: 43 | chdir: "{{ nrn_src_dir }}" 44 | 45 | - name: install nrnpython 46 | shell: "{{ venv }}/bin/python setup.py install" 47 | args: 48 | chdir: "{{ nrn_src_dir }}/src/nrnpython" 49 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlueBrain/SimulationTutorials/44fa01c22bc83fbbe8a01d3580de75ffadf92ea4/HBPSchool2016/demos/efeatures/L5_TTPC2.zip -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/.provenance.json: -------------------------------------------------------------------------------- 1 | { 2 | "gid": 17636, 3 | "blueconfig": "/gpfs/bbp.cscs.ch/project/proj1/simulations/ReNCCv2/k_ca_scan_dense/K5p0/Ca2p00/BlueConfig" 4 | } -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/CHANGELOG: -------------------------------------------------------------------------------- 1 | 1.0.11: Made compatible with python3. Improved README 2 | 1.0.10: Increased the current to calculate the Rin to get above the noise level 3 | for models with stochastic channels 4 | 1.0.9: Every model package now contains a cellinfo.json file with e.g. the 5 | m-type, e-type, etc. 6 | 1.0.8: Code was added to calculate the Resting Membrane Potential, 7 | Input Resitance and Time constant 8 | 1.0.6: Make random number generators use exact same seed as in large network 9 | simulation 10 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/VERSION: -------------------------------------------------------------------------------- 1 | 1.0.11 2 | 2015/10/07 3 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/cellinfo.json: -------------------------------------------------------------------------------- 1 | { 2 | "cell name": "cADpyr232_L5_TTPC2_5_dend-C060114A7_axon-C060116A3_-_Clone_2", 3 | "e-type": "L5PC", 4 | "gid": "17636", 5 | "layer": "L5", 6 | "m-type": "L5_TTPC2", 7 | "me-type": "L5_TTPC2_L5PC", 8 | "morphology": "dend-C060114A7_axon-C060116A3_-_Clone_2" 9 | } -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/current_amps.dat: -------------------------------------------------------------------------------- 1 | -0.286011 0.5930628 0.6424847 0.6919066 -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/mechanisms/CaDynamics_E2.mod: -------------------------------------------------------------------------------- 1 | : Dynamics that track inside calcium concentration 2 | : modified from Destexhe et al. 1994 3 | 4 | NEURON { 5 | SUFFIX CaDynamics_E2 6 | USEION ca READ ica WRITE cai 7 | RANGE decay, gamma, minCai, depth 8 | } 9 | 10 | UNITS { 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | FARADAY = (faraday) (coulombs) 14 | (molar) = (1/liter) 15 | (mM) = (millimolar) 16 | (um) = (micron) 17 | } 18 | 19 | PARAMETER { 20 | gamma = 0.05 : percent of free calcium (not buffered) 21 | decay = 80 (ms) : rate of removal of calcium 22 | depth = 0.1 (um) : depth of shell 23 | minCai = 1e-4 (mM) 24 | } 25 | 26 | ASSIGNED {ica (mA/cm2)} 27 | 28 | STATE { 29 | cai (mM) 30 | } 31 | 32 | BREAKPOINT { SOLVE states METHOD cnexp } 33 | 34 | DERIVATIVE states { 35 | cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay 36 | } 37 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/mechanisms/Ca_HVA.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993 3 | 4 | NEURON { 5 | SUFFIX Ca_HVA 6 | USEION ca READ eca WRITE ica 7 | RANGE gCa_HVAbar, gCa_HVA, ica 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gCa_HVAbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | eca (mV) 23 | ica (mA/cm2) 24 | gCa (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | hInf 30 | hTau 31 | hAlpha 32 | hBeta 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | gCa = gCa_HVAbar*m*m*h 43 | ica = gCa*(v-eca) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates(){ 59 | UNITSOFF 60 | if((v == -27) ){ 61 | v = v+0.0001 62 | } 63 | mAlpha = (0.055*(-27-v))/(exp((-27-v)/3.8) - 1) 64 | mBeta = (0.94*exp((-75-v)/17)) 65 | mInf = mAlpha/(mAlpha + mBeta) 66 | mTau = 1/(mAlpha + mBeta) 67 | hAlpha = (0.000457*exp((-13-v)/50)) 68 | hBeta = (0.0065/(exp((-v-15)/28)+1)) 69 | hInf = hAlpha/(hAlpha + hBeta) 70 | hTau = 1/(hAlpha + hBeta) 71 | UNITSON 72 | } 73 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/mechanisms/Ca_LVAst.mod: -------------------------------------------------------------------------------- 1 | :Comment : LVA ca channel. Note: mtau is an approximation from the plots 2 | :Reference : : Avery and Johnston 1996, tau from Randall 1997 3 | :Comment: shifted by -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | NEURON { 7 | SUFFIX Ca_LVAst 8 | USEION ca READ eca WRITE ica 9 | RANGE gCa_LVAstbar, gCa_LVAst, ica 10 | } 11 | 12 | UNITS { 13 | (S) = (siemens) 14 | (mV) = (millivolt) 15 | (mA) = (milliamp) 16 | } 17 | 18 | PARAMETER { 19 | gCa_LVAstbar = 0.00001 (S/cm2) 20 | } 21 | 22 | ASSIGNED { 23 | v (mV) 24 | eca (mV) 25 | ica (mA/cm2) 26 | gCa_LVAst (S/cm2) 27 | mInf 28 | mTau 29 | hInf 30 | hTau 31 | } 32 | 33 | STATE { 34 | m 35 | h 36 | } 37 | 38 | BREAKPOINT { 39 | SOLVE states METHOD cnexp 40 | gCa_LVAst = gCa_LVAstbar*m*m*h 41 | ica = gCa_LVAst*(v-eca) 42 | } 43 | 44 | DERIVATIVE states { 45 | rates() 46 | m' = (mInf-m)/mTau 47 | h' = (hInf-h)/hTau 48 | } 49 | 50 | INITIAL{ 51 | rates() 52 | m = mInf 53 | h = hInf 54 | } 55 | 56 | PROCEDURE rates(){ 57 | LOCAL qt 58 | qt = 2.3^((34-21)/10) 59 | 60 | UNITSOFF 61 | v = v + 10 62 | mInf = 1.0000/(1+ exp((v - -30.000)/-6)) 63 | mTau = (5.0000 + 20.0000/(1+exp((v - -25.000)/5)))/qt 64 | hInf = 1.0000/(1+ exp((v - -80.000)/6.4)) 65 | hTau = (20.0000 + 50.0000/(1+exp((v - -40.000)/7)))/qt 66 | v = v - 10 67 | UNITSON 68 | } 69 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/mechanisms/Ih.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Kole,Hallermann,and Stuart, J. Neurosci. 2006 3 | 4 | NEURON { 5 | SUFFIX Ih 6 | NONSPECIFIC_CURRENT ihcn 7 | RANGE gIhbar, gIh, ihcn 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gIhbar = 0.00001 (S/cm2) 18 | ehcn = -45.0 (mV) 19 | } 20 | 21 | ASSIGNED { 22 | v (mV) 23 | ihcn (mA/cm2) 24 | gIh (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | } 30 | 31 | STATE { 32 | m 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gIh = gIhbar*m 38 | ihcn = gIh*(v-ehcn) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates() 43 | m' = (mInf-m)/mTau 44 | } 45 | 46 | INITIAL{ 47 | rates() 48 | m = mInf 49 | } 50 | 51 | PROCEDURE rates(){ 52 | UNITSOFF 53 | if(v == -154.9){ 54 | v = v + 0.0001 55 | } 56 | mAlpha = 0.001*6.43*(v+154.9)/(exp((v+154.9)/11.9)-1) 57 | mBeta = 0.001*193*exp(v/33.1) 58 | mInf = mAlpha/(mAlpha + mBeta) 59 | mTau = 1/(mAlpha + mBeta) 60 | UNITSON 61 | } 62 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/mechanisms/Im.mod: -------------------------------------------------------------------------------- 1 | :Reference : : Adams et al. 1982 - M-currents and other potassium currents in bullfrog sympathetic neurones 2 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 3 | 4 | NEURON { 5 | SUFFIX Im 6 | USEION k READ ek WRITE ik 7 | RANGE gImbar, gIm, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gImbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | gIm (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | } 30 | 31 | STATE { 32 | m 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gIm = gImbar*m 38 | ik = gIm*(v-ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates() 43 | m' = (mInf-m)/mTau 44 | } 45 | 46 | INITIAL{ 47 | rates() 48 | m = mInf 49 | } 50 | 51 | PROCEDURE rates(){ 52 | LOCAL qt 53 | qt = 2.3^((34-21)/10) 54 | 55 | UNITSOFF 56 | mAlpha = 3.3e-3*exp(2.5*0.04*(v - -35)) 57 | mBeta = 3.3e-3*exp(-2.5*0.04*(v - -35)) 58 | mInf = mAlpha/(mAlpha + mBeta) 59 | mTau = (1/(mAlpha + mBeta))/qt 60 | UNITSON 61 | } 62 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/mechanisms/K_Pst.mod: -------------------------------------------------------------------------------- 1 | :Comment : The persistent component of the K current 2 | :Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | :Comment : shifted -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | 7 | NEURON { 8 | SUFFIX K_Pst 9 | USEION k READ ek WRITE ik 10 | RANGE gK_Pstbar, gK_Pst, ik 11 | } 12 | 13 | UNITS { 14 | (S) = (siemens) 15 | (mV) = (millivolt) 16 | (mA) = (milliamp) 17 | } 18 | 19 | PARAMETER { 20 | gK_Pstbar = 0.00001 (S/cm2) 21 | } 22 | 23 | ASSIGNED { 24 | v (mV) 25 | ek (mV) 26 | ik (mA/cm2) 27 | gK_Pst (S/cm2) 28 | mInf 29 | mTau 30 | hInf 31 | hTau 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | gK_Pst = gK_Pstbar*m*m*h 42 | ik = gK_Pst*(v-ek) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | LOCAL qt 59 | qt = 2.3^((34-21)/10) 60 | UNITSOFF 61 | v = v + 10 62 | mInf = (1/(1 + exp(-(v+1)/12))) 63 | if(v<-50){ 64 | mTau = (1.25+175.03*exp(-v * -0.026))/qt 65 | }else{ 66 | mTau = ((1.25+13*exp(-v*0.026)))/qt 67 | } 68 | hInf = 1/(1 + exp(-(v+54)/-11)) 69 | hTau = (360+(1010+24*(v+55))*exp(-((v+75)/48)^2))/qt 70 | v = v - 10 71 | UNITSON 72 | } 73 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/mechanisms/K_Tst.mod: -------------------------------------------------------------------------------- 1 | :Comment : The transient component of the K current 2 | :Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | :Comment : shifted -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | NEURON { 7 | SUFFIX K_Tst 8 | USEION k READ ek WRITE ik 9 | RANGE gK_Tstbar, gK_Tst, ik 10 | } 11 | 12 | UNITS { 13 | (S) = (siemens) 14 | (mV) = (millivolt) 15 | (mA) = (milliamp) 16 | } 17 | 18 | PARAMETER { 19 | gK_Tstbar = 0.00001 (S/cm2) 20 | } 21 | 22 | ASSIGNED { 23 | v (mV) 24 | ek (mV) 25 | ik (mA/cm2) 26 | gK_Tst (S/cm2) 27 | mInf 28 | mTau 29 | hInf 30 | hTau 31 | } 32 | 33 | STATE { 34 | m 35 | h 36 | } 37 | 38 | BREAKPOINT { 39 | SOLVE states METHOD cnexp 40 | gK_Tst = gK_Tstbar*(m^4)*h 41 | ik = gK_Tst*(v-ek) 42 | } 43 | 44 | DERIVATIVE states { 45 | rates() 46 | m' = (mInf-m)/mTau 47 | h' = (hInf-h)/hTau 48 | } 49 | 50 | INITIAL{ 51 | rates() 52 | m = mInf 53 | h = hInf 54 | } 55 | 56 | PROCEDURE rates(){ 57 | LOCAL qt 58 | qt = 2.3^((34-21)/10) 59 | 60 | UNITSOFF 61 | v = v + 10 62 | mInf = 1/(1 + exp(-(v+0)/19)) 63 | mTau = (0.34+0.92*exp(-((v+71)/59)^2))/qt 64 | hInf = 1/(1 + exp(-(v+66)/-10)) 65 | hTau = (8+49*exp(-((v+73)/23)^2))/qt 66 | v = v - 10 67 | UNITSON 68 | } 69 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/mechanisms/NaTa_t.mod: -------------------------------------------------------------------------------- 1 | :Reference :Colbert and Pan 2002 2 | 3 | NEURON { 4 | SUFFIX NaTa_t 5 | USEION na READ ena WRITE ina 6 | RANGE gNaTa_tbar, gNaTa_t, ina 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gNaTa_tbar = 0.00001 (S/cm2) 17 | } 18 | 19 | ASSIGNED { 20 | v (mV) 21 | ena (mV) 22 | ina (mA/cm2) 23 | gNaTa_t (S/cm2) 24 | mInf 25 | mTau 26 | mAlpha 27 | mBeta 28 | hInf 29 | hTau 30 | hAlpha 31 | hBeta 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | gNaTa_t = gNaTa_tbar*m*m*m*h 42 | ina = gNaTa_t*(v-ena) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | LOCAL qt 59 | qt = 2.3^((34-21)/10) 60 | 61 | UNITSOFF 62 | if(v == -38){ 63 | v = v+0.0001 64 | } 65 | mAlpha = (0.182 * (v- -38))/(1-(exp(-(v- -38)/6))) 66 | mBeta = (0.124 * (-v -38))/(1-(exp(-(-v -38)/6))) 67 | mTau = (1/(mAlpha + mBeta))/qt 68 | mInf = mAlpha/(mAlpha + mBeta) 69 | 70 | if(v == -66){ 71 | v = v + 0.0001 72 | } 73 | 74 | hAlpha = (-0.015 * (v- -66))/(1-(exp((v- -66)/6))) 75 | hBeta = (-0.015 * (-v -66))/(1-(exp((-v -66)/6))) 76 | hTau = (1/(hAlpha + hBeta))/qt 77 | hInf = hAlpha/(hAlpha + hBeta) 78 | UNITSON 79 | } -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/mechanisms/NaTs2_t.mod: -------------------------------------------------------------------------------- 1 | :Reference :Colbert and Pan 2002 2 | :comment: took the NaTa and shifted both activation/inactivation by 6 mv 3 | 4 | NEURON { 5 | SUFFIX NaTs2_t 6 | USEION na READ ena WRITE ina 7 | RANGE gNaTs2_tbar, gNaTs2_t, ina 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gNaTs2_tbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ena (mV) 23 | ina (mA/cm2) 24 | gNaTs2_t (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | hInf 30 | hTau 31 | hAlpha 32 | hBeta 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | gNaTs2_t = gNaTs2_tbar*m*m*m*h 43 | ina = gNaTs2_t*(v-ena) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates(){ 59 | LOCAL qt 60 | qt = 2.3^((34-21)/10) 61 | 62 | UNITSOFF 63 | if(v == -32){ 64 | v = v+0.0001 65 | } 66 | mAlpha = (0.182 * (v- -32))/(1-(exp(-(v- -32)/6))) 67 | mBeta = (0.124 * (-v -32))/(1-(exp(-(-v -32)/6))) 68 | mInf = mAlpha/(mAlpha + mBeta) 69 | mTau = (1/(mAlpha + mBeta))/qt 70 | 71 | if(v == -60){ 72 | v = v + 0.0001 73 | } 74 | hAlpha = (-0.015 * (v- -60))/(1-(exp((v- -60)/6))) 75 | hBeta = (-0.015 * (-v -60))/(1-(exp((-v -60)/6))) 76 | hInf = hAlpha/(hAlpha + hBeta) 77 | hTau = (1/(hAlpha + hBeta))/qt 78 | UNITSON 79 | } -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/mechanisms/SK_E2.mod: -------------------------------------------------------------------------------- 1 | : SK-type calcium-activated potassium current 2 | : Reference : Kohler et al. 1996 3 | 4 | NEURON { 5 | SUFFIX SK_E2 6 | USEION k READ ek WRITE ik 7 | USEION ca READ cai 8 | RANGE gSK_E2bar, gSK_E2, ik 9 | } 10 | 11 | UNITS { 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | (mM) = (milli/liter) 15 | } 16 | 17 | PARAMETER { 18 | v (mV) 19 | gSK_E2bar = .000001 (mho/cm2) 20 | zTau = 1 (ms) 21 | ek (mV) 22 | cai (mM) 23 | } 24 | 25 | ASSIGNED { 26 | zInf 27 | ik (mA/cm2) 28 | gSK_E2 (S/cm2) 29 | } 30 | 31 | STATE { 32 | z FROM 0 TO 1 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gSK_E2 = gSK_E2bar * z 38 | ik = gSK_E2 * (v - ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates(cai) 43 | z' = (zInf - z) / zTau 44 | } 45 | 46 | PROCEDURE rates(ca(mM)) { 47 | if(ca < 1e-7){ 48 | ca = ca + 1e-07 49 | } 50 | zInf = 1/(1 + (0.00043 / ca)^4.8) 51 | } 52 | 53 | INITIAL { 54 | rates(cai) 55 | z = zInf 56 | } 57 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/mechanisms/SKv3_1.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Characterization of a Shaw-related potassium channel family in rat brain, The EMBO Journal, vol.11, no.7,2473-2486 (1992) 3 | 4 | NEURON { 5 | SUFFIX SKv3_1 6 | USEION k READ ek WRITE ik 7 | RANGE gSKv3_1bar, gSKv3_1, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gSKv3_1bar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | gSKv3_1 (S/cm2) 25 | mInf 26 | mTau 27 | } 28 | 29 | STATE { 30 | m 31 | } 32 | 33 | BREAKPOINT { 34 | SOLVE states METHOD cnexp 35 | gSKv3_1 = gSKv3_1bar*m 36 | ik = gSKv3_1*(v-ek) 37 | } 38 | 39 | DERIVATIVE states { 40 | rates() 41 | m' = (mInf-m)/mTau 42 | } 43 | 44 | INITIAL{ 45 | rates() 46 | m = mInf 47 | } 48 | 49 | PROCEDURE rates(){ 50 | UNITSOFF 51 | mInf = 1/(1+exp(((v -(18.700))/(-9.700)))) 52 | mTau = 0.2*20.000/(1+exp(((v -(-46.560))/(-44.140)))) 53 | UNITSON 54 | } 55 | 56 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/run_RmpRiTau_py.sh: -------------------------------------------------------------------------------- 1 | nrnivmodl ./mechanisms 2 | ./run_RmpRiTau.py "$@" 3 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/run_hoc.sh: -------------------------------------------------------------------------------- 1 | nrnivmodl ./mechanisms 2 | nrngui mosinit.hoc 3 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/run_py.sh: -------------------------------------------------------------------------------- 1 | nrnivmodl ./mechanisms 2 | 3 | # Use for python 2.6+ 4 | python ./run.py "$@" 5 | 6 | # Use for python 3.4+ 7 | # python3 ./run.py "$@" 8 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/efeatures/L5_TTPC2_cADpyr232_1/synapses/mtype_map.tsv: -------------------------------------------------------------------------------- 1 | 0 L1_DAC 2 | 1 L1_NGC-DA 3 | 2 L1_NGC-SA 4 | 3 L1_HAC 5 | 4 L1_DLAC 6 | 5 L1_SLAC 7 | 6 L23_PC 8 | 7 L23_MC 9 | 8 L23_BTC 10 | 9 L23_DBC 11 | 10 L23_BP 12 | 11 L23_NGC 13 | 12 L23_LBC 14 | 13 L23_NBC 15 | 14 L23_SBC 16 | 15 L23_ChC 17 | 16 L4_PC 18 | 17 L4_SP 19 | 18 L4_SS 20 | 19 L4_MC 21 | 20 L4_BTC 22 | 21 L4_DBC 23 | 22 L4_BP 24 | 23 L4_NGC 25 | 24 L4_LBC 26 | 25 L4_NBC 27 | 26 L4_SBC 28 | 27 L4_ChC 29 | 28 L5_TTPC1 30 | 29 L5_TTPC2 31 | 30 L5_UTPC 32 | 31 L5_STPC 33 | 32 L5_MC 34 | 33 L5_BTC 35 | 34 L5_DBC 36 | 35 L5_BP 37 | 36 L5_NGC 38 | 37 L5_LBC 39 | 38 L5_NBC 40 | 39 L5_SBC 41 | 40 L5_ChC 42 | 41 L6_TPC_L1 43 | 42 L6_TPC_L4 44 | 43 L6_UTPC 45 | 44 L6_IPC 46 | 45 L6_BPC 47 | 46 L6_MC 48 | 47 L6_BTC 49 | 48 L6_DBC 50 | 49 L6_BP 51 | 50 L6_NGC 52 | 51 L6_LBC 53 | 52 L6_NBC 54 | 53 L6_SBC 55 | 54 L6_ChC 56 | -------------------------------------------------------------------------------- /HBPSchool2016/demos/optimisation/data: -------------------------------------------------------------------------------- 1 | ../efeatures/data -------------------------------------------------------------------------------- /HBPSchool2016/demos/optimisation/simple.swc: -------------------------------------------------------------------------------- 1 | # Dummy granule cell morphology 2 | 1 1 -50.0 0.0 0.0 50.0 -1 3 | 2 1 0.0 0.0 0.0 50.0 1 4 | 3 1 50.0 0.0 0.0 50.0 2 5 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | test: 2 | ! find . -name x86_64 | grep x86_64 3 | -------------------------------------------------------------------------------- /NSAS2017/BluePyOpt/simple.swc: -------------------------------------------------------------------------------- 1 | # Dummy granule cell morphology 2 | 1 1 -50.0 0.0 0.0 50.0 -1 3 | 2 1 0.0 0.0 0.0 50.0 1 4 | 3 1 50.0 0.0 0.0 50.0 2 5 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/.provenance.json: -------------------------------------------------------------------------------- 1 | { 2 | "gid": 17636, 3 | "blueconfig": "/gpfs/bbp.cscs.ch/project/proj1/simulations/ReNCCv2/k_ca_scan_dense/K5p0/Ca2p00/BlueConfig" 4 | } -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/CHANGELOG: -------------------------------------------------------------------------------- 1 | 1.0.11: Made compatible with python3. Improved README 2 | 1.0.10: Increased the current to calculate the Rin to get above the noise level 3 | for models with stochastic channels 4 | 1.0.9: Every model package now contains a cellinfo.json file with e.g. the 5 | m-type, e-type, etc. 6 | 1.0.8: Code was added to calculate the Resting Membrane Potential, 7 | Input Resitance and Time constant 8 | 1.0.6: Make random number generators use exact same seed as in large network 9 | simulation 10 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/LICENSE: -------------------------------------------------------------------------------- 1 | The CC-BY-NC-SA license applies, as indicated by headers in the 2 | respective source files. 3 | 4 | https://creativecommons.org/licenses/by-nc-sa/4.0/ 5 | 6 | The detailed text is available here 7 | https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode 8 | 9 | or in this tarball in the seperate file LICENSE_CC-BY-CA-SA-4.0 10 | 11 | 12 | The HOC code, Python code, synapse MOD code and cell morphology are licensed with the above mentioned CC-BY-NC-SA license. 13 | 14 | 15 | For models for which the original source is available on ModelDB, any 16 | specific licenses on mentioned on ModelDB, or the generic License of ModelDB 17 | apply: 18 | 19 | 1) Ih model 20 | Author: Stefan Hallermann 21 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=144526&file=\HallermannEtAl2012\h.mod 22 | 23 | 2) StochKv model 24 | Authors: Zach Mainen Adaptations: Kamran Diba, Mickey London, Peter N. Steinmetz, Werner Van Geit 25 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=125385&file=\Sbpap_code\mod\skm.mod 26 | 27 | 3) D-type K current model 28 | Authors: Yuguo Yu 29 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=135898&file=\YuEtAlPNAS2007\kd.mod 30 | 31 | 4) Internal calcium concentration model 32 | Author: Alain Destexhe 33 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=3670&file=\NTW_NEW\capump.mod 34 | 35 | 5) Ca_LVAst, Im, K_Tst, NaTa_t, SK_E2, Ca_HVA, Ih, K_Pst, Nap_Et2, NaTs2_t, SKv3_1 36 | Author: Etay Hay, Shaul Druckmann, Srikanth Ramaswamy, James King, Werner Van Geit 37 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=139653&file=\L5bPCmodelsEH\mod\ 38 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/NEURON_NMC_nrniv.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlueBrain/SimulationTutorials/44fa01c22bc83fbbe8a01d3580de75ffadf92ea4/NSAS2017/NMC_portal/NEURON_NMC_nrniv.png -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/NEURON_NMC_portal.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlueBrain/SimulationTutorials/44fa01c22bc83fbbe8a01d3580de75ffadf92ea4/NSAS2017/NMC_portal/NEURON_NMC_portal.png -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/VERSION: -------------------------------------------------------------------------------- 1 | 1.0.11 2 | 2015/10/07 3 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/cellinfo.json: -------------------------------------------------------------------------------- 1 | { 2 | "cell name": "cADpyr232_L5_TTPC2_5_dend-C060114A7_axon-C060116A3_-_Clone_2", 3 | "e-type": "L5PC", 4 | "gid": "17636", 5 | "layer": "L5", 6 | "m-type": "L5_TTPC2", 7 | "me-type": "L5_TTPC2_L5PC", 8 | "morphology": "dend-C060114A7_axon-C060116A3_-_Clone_2" 9 | } -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/constants.hoc: -------------------------------------------------------------------------------- 1 | /* Copyright (c) 2015 EPFL-BBP, All rights reserved. 2 | 3 | THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS'' 4 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 5 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 6 | PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BLUE BRAIN PROJECT 7 | BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 8 | CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 9 | SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR 10 | BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 11 | WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE 12 | OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN 13 | IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 14 | 15 | This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. 16 | To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/legalcode or send a letter to Creative Commons, 171 17 | Second Street, Suite 300, San Francisco, California, 94105, USA. 18 | */ 19 | 20 | /* 21 | * @file constants.hoc 22 | * @brief Define constants used in the simulation 23 | * @author Werner Van Geit @ BBP 24 | * @date 2015 25 | */ 26 | 27 | celsius=34 28 | {printf("Setting temperature to %f C\n", celsius)} 29 | tstop=30000 30 | dt=0.025 31 | {printf("Setting simulation time step to %f ms\n", dt)} 32 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/current_amps.dat: -------------------------------------------------------------------------------- 1 | -0.286011 0.5930628 0.6424847 0.6919066 -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/mechanisms/CaDynamics_E2.mod: -------------------------------------------------------------------------------- 1 | : Dynamics that track inside calcium concentration 2 | : modified from Destexhe et al. 1994 3 | 4 | NEURON { 5 | SUFFIX CaDynamics_E2 6 | USEION ca READ ica WRITE cai 7 | RANGE decay, gamma, minCai, depth 8 | } 9 | 10 | UNITS { 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | FARADAY = (faraday) (coulombs) 14 | (molar) = (1/liter) 15 | (mM) = (millimolar) 16 | (um) = (micron) 17 | } 18 | 19 | PARAMETER { 20 | gamma = 0.05 : percent of free calcium (not buffered) 21 | decay = 80 (ms) : rate of removal of calcium 22 | depth = 0.1 (um) : depth of shell 23 | minCai = 1e-4 (mM) 24 | } 25 | 26 | ASSIGNED {ica (mA/cm2)} 27 | 28 | STATE { 29 | cai (mM) 30 | } 31 | 32 | BREAKPOINT { SOLVE states METHOD cnexp } 33 | 34 | DERIVATIVE states { 35 | cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay 36 | } 37 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/mechanisms/Ca_HVA.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993 3 | 4 | NEURON { 5 | SUFFIX Ca_HVA 6 | USEION ca READ eca WRITE ica 7 | RANGE gCa_HVAbar, gCa_HVA, ica 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gCa_HVAbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | eca (mV) 23 | ica (mA/cm2) 24 | gCa (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | hInf 30 | hTau 31 | hAlpha 32 | hBeta 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | gCa = gCa_HVAbar*m*m*h 43 | ica = gCa*(v-eca) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates(){ 59 | UNITSOFF 60 | if((v == -27) ){ 61 | v = v+0.0001 62 | } 63 | mAlpha = (0.055*(-27-v))/(exp((-27-v)/3.8) - 1) 64 | mBeta = (0.94*exp((-75-v)/17)) 65 | mInf = mAlpha/(mAlpha + mBeta) 66 | mTau = 1/(mAlpha + mBeta) 67 | hAlpha = (0.000457*exp((-13-v)/50)) 68 | hBeta = (0.0065/(exp((-v-15)/28)+1)) 69 | hInf = hAlpha/(hAlpha + hBeta) 70 | hTau = 1/(hAlpha + hBeta) 71 | UNITSON 72 | } 73 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/mechanisms/Ca_LVAst.mod: -------------------------------------------------------------------------------- 1 | :Comment : LVA ca channel. Note: mtau is an approximation from the plots 2 | :Reference : : Avery and Johnston 1996, tau from Randall 1997 3 | :Comment: shifted by -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | NEURON { 7 | SUFFIX Ca_LVAst 8 | USEION ca READ eca WRITE ica 9 | RANGE gCa_LVAstbar, gCa_LVAst, ica 10 | } 11 | 12 | UNITS { 13 | (S) = (siemens) 14 | (mV) = (millivolt) 15 | (mA) = (milliamp) 16 | } 17 | 18 | PARAMETER { 19 | gCa_LVAstbar = 0.00001 (S/cm2) 20 | } 21 | 22 | ASSIGNED { 23 | v (mV) 24 | eca (mV) 25 | ica (mA/cm2) 26 | gCa_LVAst (S/cm2) 27 | mInf 28 | mTau 29 | hInf 30 | hTau 31 | } 32 | 33 | STATE { 34 | m 35 | h 36 | } 37 | 38 | BREAKPOINT { 39 | SOLVE states METHOD cnexp 40 | gCa_LVAst = gCa_LVAstbar*m*m*h 41 | ica = gCa_LVAst*(v-eca) 42 | } 43 | 44 | DERIVATIVE states { 45 | rates() 46 | m' = (mInf-m)/mTau 47 | h' = (hInf-h)/hTau 48 | } 49 | 50 | INITIAL{ 51 | rates() 52 | m = mInf 53 | h = hInf 54 | } 55 | 56 | PROCEDURE rates(){ 57 | LOCAL qt 58 | qt = 2.3^((34-21)/10) 59 | 60 | UNITSOFF 61 | v = v + 10 62 | mInf = 1.0000/(1+ exp((v - -30.000)/-6)) 63 | mTau = (5.0000 + 20.0000/(1+exp((v - -25.000)/5)))/qt 64 | hInf = 1.0000/(1+ exp((v - -80.000)/6.4)) 65 | hTau = (20.0000 + 50.0000/(1+exp((v - -40.000)/7)))/qt 66 | v = v - 10 67 | UNITSON 68 | } 69 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/mechanisms/Ih.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Kole,Hallermann,and Stuart, J. Neurosci. 2006 3 | 4 | NEURON { 5 | SUFFIX Ih 6 | NONSPECIFIC_CURRENT ihcn 7 | RANGE gIhbar, gIh, ihcn 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gIhbar = 0.00001 (S/cm2) 18 | ehcn = -45.0 (mV) 19 | } 20 | 21 | ASSIGNED { 22 | v (mV) 23 | ihcn (mA/cm2) 24 | gIh (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | } 30 | 31 | STATE { 32 | m 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gIh = gIhbar*m 38 | ihcn = gIh*(v-ehcn) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates() 43 | m' = (mInf-m)/mTau 44 | } 45 | 46 | INITIAL{ 47 | rates() 48 | m = mInf 49 | } 50 | 51 | PROCEDURE rates(){ 52 | UNITSOFF 53 | if(v == -154.9){ 54 | v = v + 0.0001 55 | } 56 | mAlpha = 0.001*6.43*(v+154.9)/(exp((v+154.9)/11.9)-1) 57 | mBeta = 0.001*193*exp(v/33.1) 58 | mInf = mAlpha/(mAlpha + mBeta) 59 | mTau = 1/(mAlpha + mBeta) 60 | UNITSON 61 | } 62 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/mechanisms/Im.mod: -------------------------------------------------------------------------------- 1 | :Reference : : Adams et al. 1982 - M-currents and other potassium currents in bullfrog sympathetic neurones 2 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 3 | 4 | NEURON { 5 | SUFFIX Im 6 | USEION k READ ek WRITE ik 7 | RANGE gImbar, gIm, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gImbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | gIm (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | } 30 | 31 | STATE { 32 | m 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gIm = gImbar*m 38 | ik = gIm*(v-ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates() 43 | m' = (mInf-m)/mTau 44 | } 45 | 46 | INITIAL{ 47 | rates() 48 | m = mInf 49 | } 50 | 51 | PROCEDURE rates(){ 52 | LOCAL qt 53 | qt = 2.3^((34-21)/10) 54 | 55 | UNITSOFF 56 | mAlpha = 3.3e-3*exp(2.5*0.04*(v - -35)) 57 | mBeta = 3.3e-3*exp(-2.5*0.04*(v - -35)) 58 | mInf = mAlpha/(mAlpha + mBeta) 59 | mTau = (1/(mAlpha + mBeta))/qt 60 | UNITSON 61 | } 62 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/mechanisms/K_Pst.mod: -------------------------------------------------------------------------------- 1 | :Comment : The persistent component of the K current 2 | :Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | :Comment : shifted -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | 7 | NEURON { 8 | SUFFIX K_Pst 9 | USEION k READ ek WRITE ik 10 | RANGE gK_Pstbar, gK_Pst, ik 11 | } 12 | 13 | UNITS { 14 | (S) = (siemens) 15 | (mV) = (millivolt) 16 | (mA) = (milliamp) 17 | } 18 | 19 | PARAMETER { 20 | gK_Pstbar = 0.00001 (S/cm2) 21 | } 22 | 23 | ASSIGNED { 24 | v (mV) 25 | ek (mV) 26 | ik (mA/cm2) 27 | gK_Pst (S/cm2) 28 | mInf 29 | mTau 30 | hInf 31 | hTau 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | gK_Pst = gK_Pstbar*m*m*h 42 | ik = gK_Pst*(v-ek) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | LOCAL qt 59 | qt = 2.3^((34-21)/10) 60 | UNITSOFF 61 | v = v + 10 62 | mInf = (1/(1 + exp(-(v+1)/12))) 63 | if(v<-50){ 64 | mTau = (1.25+175.03*exp(-v * -0.026))/qt 65 | }else{ 66 | mTau = ((1.25+13*exp(-v*0.026)))/qt 67 | } 68 | hInf = 1/(1 + exp(-(v+54)/-11)) 69 | hTau = (360+(1010+24*(v+55))*exp(-((v+75)/48)^2))/qt 70 | v = v - 10 71 | UNITSON 72 | } 73 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/mechanisms/K_Tst.mod: -------------------------------------------------------------------------------- 1 | :Comment : The transient component of the K current 2 | :Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | :Comment : shifted -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | NEURON { 7 | SUFFIX K_Tst 8 | USEION k READ ek WRITE ik 9 | RANGE gK_Tstbar, gK_Tst, ik 10 | } 11 | 12 | UNITS { 13 | (S) = (siemens) 14 | (mV) = (millivolt) 15 | (mA) = (milliamp) 16 | } 17 | 18 | PARAMETER { 19 | gK_Tstbar = 0.00001 (S/cm2) 20 | } 21 | 22 | ASSIGNED { 23 | v (mV) 24 | ek (mV) 25 | ik (mA/cm2) 26 | gK_Tst (S/cm2) 27 | mInf 28 | mTau 29 | hInf 30 | hTau 31 | } 32 | 33 | STATE { 34 | m 35 | h 36 | } 37 | 38 | BREAKPOINT { 39 | SOLVE states METHOD cnexp 40 | gK_Tst = gK_Tstbar*(m^4)*h 41 | ik = gK_Tst*(v-ek) 42 | } 43 | 44 | DERIVATIVE states { 45 | rates() 46 | m' = (mInf-m)/mTau 47 | h' = (hInf-h)/hTau 48 | } 49 | 50 | INITIAL{ 51 | rates() 52 | m = mInf 53 | h = hInf 54 | } 55 | 56 | PROCEDURE rates(){ 57 | LOCAL qt 58 | qt = 2.3^((34-21)/10) 59 | 60 | UNITSOFF 61 | v = v + 10 62 | mInf = 1/(1 + exp(-(v+0)/19)) 63 | mTau = (0.34+0.92*exp(-((v+71)/59)^2))/qt 64 | hInf = 1/(1 + exp(-(v+66)/-10)) 65 | hTau = (8+49*exp(-((v+73)/23)^2))/qt 66 | v = v - 10 67 | UNITSON 68 | } 69 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/mechanisms/NaTa_t.mod: -------------------------------------------------------------------------------- 1 | :Reference :Colbert and Pan 2002 2 | 3 | NEURON { 4 | SUFFIX NaTa_t 5 | USEION na READ ena WRITE ina 6 | RANGE gNaTa_tbar, gNaTa_t, ina 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gNaTa_tbar = 0.00001 (S/cm2) 17 | } 18 | 19 | ASSIGNED { 20 | v (mV) 21 | ena (mV) 22 | ina (mA/cm2) 23 | gNaTa_t (S/cm2) 24 | mInf 25 | mTau 26 | mAlpha 27 | mBeta 28 | hInf 29 | hTau 30 | hAlpha 31 | hBeta 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | gNaTa_t = gNaTa_tbar*m*m*m*h 42 | ina = gNaTa_t*(v-ena) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | LOCAL qt 59 | qt = 2.3^((34-21)/10) 60 | 61 | UNITSOFF 62 | if(v == -38){ 63 | v = v+0.0001 64 | } 65 | mAlpha = (0.182 * (v- -38))/(1-(exp(-(v- -38)/6))) 66 | mBeta = (0.124 * (-v -38))/(1-(exp(-(-v -38)/6))) 67 | mTau = (1/(mAlpha + mBeta))/qt 68 | mInf = mAlpha/(mAlpha + mBeta) 69 | 70 | if(v == -66){ 71 | v = v + 0.0001 72 | } 73 | 74 | hAlpha = (-0.015 * (v- -66))/(1-(exp((v- -66)/6))) 75 | hBeta = (-0.015 * (-v -66))/(1-(exp((-v -66)/6))) 76 | hTau = (1/(hAlpha + hBeta))/qt 77 | hInf = hAlpha/(hAlpha + hBeta) 78 | UNITSON 79 | } -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/mechanisms/NaTs2_t.mod: -------------------------------------------------------------------------------- 1 | :Reference :Colbert and Pan 2002 2 | :comment: took the NaTa and shifted both activation/inactivation by 6 mv 3 | 4 | NEURON { 5 | SUFFIX NaTs2_t 6 | USEION na READ ena WRITE ina 7 | RANGE gNaTs2_tbar, gNaTs2_t, ina 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gNaTs2_tbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ena (mV) 23 | ina (mA/cm2) 24 | gNaTs2_t (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | hInf 30 | hTau 31 | hAlpha 32 | hBeta 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | gNaTs2_t = gNaTs2_tbar*m*m*m*h 43 | ina = gNaTs2_t*(v-ena) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates(){ 59 | LOCAL qt 60 | qt = 2.3^((34-21)/10) 61 | 62 | UNITSOFF 63 | if(v == -32){ 64 | v = v+0.0001 65 | } 66 | mAlpha = (0.182 * (v- -32))/(1-(exp(-(v- -32)/6))) 67 | mBeta = (0.124 * (-v -32))/(1-(exp(-(-v -32)/6))) 68 | mInf = mAlpha/(mAlpha + mBeta) 69 | mTau = (1/(mAlpha + mBeta))/qt 70 | 71 | if(v == -60){ 72 | v = v + 0.0001 73 | } 74 | hAlpha = (-0.015 * (v- -60))/(1-(exp((v- -60)/6))) 75 | hBeta = (-0.015 * (-v -60))/(1-(exp((-v -60)/6))) 76 | hInf = hAlpha/(hAlpha + hBeta) 77 | hTau = (1/(hAlpha + hBeta))/qt 78 | UNITSON 79 | } -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/mechanisms/SK_E2.mod: -------------------------------------------------------------------------------- 1 | : SK-type calcium-activated potassium current 2 | : Reference : Kohler et al. 1996 3 | 4 | NEURON { 5 | SUFFIX SK_E2 6 | USEION k READ ek WRITE ik 7 | USEION ca READ cai 8 | RANGE gSK_E2bar, gSK_E2, ik 9 | } 10 | 11 | UNITS { 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | (mM) = (milli/liter) 15 | } 16 | 17 | PARAMETER { 18 | v (mV) 19 | gSK_E2bar = .000001 (mho/cm2) 20 | zTau = 1 (ms) 21 | ek (mV) 22 | cai (mM) 23 | } 24 | 25 | ASSIGNED { 26 | zInf 27 | ik (mA/cm2) 28 | gSK_E2 (S/cm2) 29 | } 30 | 31 | STATE { 32 | z FROM 0 TO 1 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gSK_E2 = gSK_E2bar * z 38 | ik = gSK_E2 * (v - ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates(cai) 43 | z' = (zInf - z) / zTau 44 | } 45 | 46 | PROCEDURE rates(ca(mM)) { 47 | if(ca < 1e-7){ 48 | ca = ca + 1e-07 49 | } 50 | zInf = 1/(1 + (0.00043 / ca)^4.8) 51 | } 52 | 53 | INITIAL { 54 | rates(cai) 55 | z = zInf 56 | } 57 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/mechanisms/SKv3_1.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Characterization of a Shaw-related potassium channel family in rat brain, The EMBO Journal, vol.11, no.7,2473-2486 (1992) 3 | 4 | NEURON { 5 | SUFFIX SKv3_1 6 | USEION k READ ek WRITE ik 7 | RANGE gSKv3_1bar, gSKv3_1, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gSKv3_1bar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | gSKv3_1 (S/cm2) 25 | mInf 26 | mTau 27 | } 28 | 29 | STATE { 30 | m 31 | } 32 | 33 | BREAKPOINT { 34 | SOLVE states METHOD cnexp 35 | gSKv3_1 = gSKv3_1bar*m 36 | ik = gSKv3_1*(v-ek) 37 | } 38 | 39 | DERIVATIVE states { 40 | rates() 41 | m' = (mInf-m)/mTau 42 | } 43 | 44 | INITIAL{ 45 | rates() 46 | m = mInf 47 | } 48 | 49 | PROCEDURE rates(){ 50 | UNITSOFF 51 | mInf = 1/(1+exp(((v -(18.700))/(-9.700)))) 52 | mTau = 0.2*20.000/(1+exp(((v -(-46.560))/(-44.140)))) 53 | UNITSON 54 | } 55 | 56 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/run_RmpRiTau_py.sh: -------------------------------------------------------------------------------- 1 | nrnivmodl ./mechanisms 2 | ./run_RmpRiTau.py "$@" 3 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/run_hoc.sh: -------------------------------------------------------------------------------- 1 | nrnivmodl ./mechanisms 2 | nrngui mosinit.hoc 3 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/run_py.sh: -------------------------------------------------------------------------------- 1 | nrnivmodl ./mechanisms 2 | 3 | # Use for python 2.6+ 4 | python ./run.py "$@" 5 | 6 | # Use for python 3.4+ 7 | # python3 ./run.py "$@" 8 | -------------------------------------------------------------------------------- /NSAS2017/NMC_portal/synapses/mtype_map.tsv: -------------------------------------------------------------------------------- 1 | 0 L1_DAC 2 | 1 L1_NGC-DA 3 | 2 L1_NGC-SA 4 | 3 L1_HAC 5 | 4 L1_DLAC 6 | 5 L1_SLAC 7 | 6 L23_PC 8 | 7 L23_MC 9 | 8 L23_BTC 10 | 9 L23_DBC 11 | 10 L23_BP 12 | 11 L23_NGC 13 | 12 L23_LBC 14 | 13 L23_NBC 15 | 14 L23_SBC 16 | 15 L23_ChC 17 | 16 L4_PC 18 | 17 L4_SP 19 | 18 L4_SS 20 | 19 L4_MC 21 | 20 L4_BTC 22 | 21 L4_DBC 23 | 22 L4_BP 24 | 23 L4_NGC 25 | 24 L4_LBC 26 | 25 L4_NBC 27 | 26 L4_SBC 28 | 27 L4_ChC 29 | 28 L5_TTPC1 30 | 29 L5_TTPC2 31 | 30 L5_UTPC 32 | 31 L5_STPC 33 | 32 L5_MC 34 | 33 L5_BTC 35 | 34 L5_DBC 36 | 35 L5_BP 37 | 36 L5_NGC 38 | 37 L5_LBC 39 | 38 L5_NBC 40 | 39 L5_SBC 41 | 40 L5_ChC 42 | 41 L6_TPC_L1 43 | 42 L6_TPC_L4 44 | 43 L6_UTPC 45 | 44 L6_IPC 46 | 45 L6_BPC 47 | 46 L6_MC 48 | 47 L6_BTC 49 | 48 L6_DBC 50 | 49 L6_BP 51 | 50 L6_NGC 52 | 51 L6_LBC 53 | 52 L6_NBC 54 | 53 L6_SBC 55 | 54 L6_ChC 56 | -------------------------------------------------------------------------------- /NSAS2017/eFEL/data/exp_APWaveform_ch20_2035.dat: -------------------------------------------------------------------------------- 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https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode 8 | 9 | or in this tarball in the seperate file LICENSE_CC-BY-CA-SA-4.0 10 | 11 | 12 | The HOC code, Python code, synapse MOD code and cell morphology are licensed with the above mentioned CC-BY-NC-SA license. 13 | 14 | 15 | For models for which the original source is available on ModelDB, any 16 | specific licenses on mentioned on ModelDB, or the generic License of ModelDB 17 | apply: 18 | 19 | 1) Ih model 20 | Author: Stefan Hallermann 21 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=144526&file=\HallermannEtAl2012\h.mod 22 | 23 | 2) StochKv model 24 | Authors: Zach Mainen Adaptations: Kamran Diba, Mickey London, Peter N. Steinmetz, Werner Van Geit 25 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=125385&file=\Sbpap_code\mod\skm.mod 26 | 27 | 3) D-type K current model 28 | Authors: Yuguo Yu 29 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=135898&file=\YuEtAlPNAS2007\kd.mod 30 | 31 | 4) Internal calcium concentration model 32 | Author: Alain Destexhe 33 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=3670&file=\NTW_NEW\capump.mod 34 | 35 | 5) Ca_LVAst, Im, K_Tst, NaTa_t, SK_E2, Ca_HVA, Ih, K_Pst, Nap_Et2, NaTs2_t, SKv3_1 36 | Author: Etay Hay, Shaul Druckmann, Srikanth Ramaswamy, James King, Werner Van Geit 37 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=139653&file=\L5bPCmodelsEH\mod\ 38 | -------------------------------------------------------------------------------- /SfN2017/README.md: -------------------------------------------------------------------------------- 1 | # Data-Driven Neurophysiology and Neuronal Modelling @ SfN 2017 2 | 3 | The main parts of this demo consists of : 4 | * **Extracting electrical features from in vitro recordings** 5 | * **Optimising parameters of neuron models** 6 | 7 | This tutorial is presented by Elisabetta Iavarone (@ Blue Brain Project, Geneva, Switzerland) 8 | 9 | ## Schedule 10 | 11 | Date: November 10 2017 12 | * Session 1: 15:45 - 16:45 13 | * Session 2: 17:00 - 18:00 14 | 15 | 16 | ## Virtual Machine 17 | 18 | A **Google drive** was created with **material** for the tutorial: 19 | https://drive.google.com/drive/folders/0B_t-Q_iriAyARUxnNElDdkxDMEU?usp=sharing 20 | 21 | This drive contains a **Virtual Machine** (.ova file) that can be used to run the demoed software, donwload the file with "final" in the filename. 22 | 23 | Please follow the **instructions** [here](https://github.com/BlueBrain/SimulationTutorials/tree/master/General/Installation) to install VirtualBox so that you can run the VM on your machine. 24 | 25 | The **login information** for the VM: username=sfn2017 password=sfn2017 26 | 27 | Please **ignore** all **update requests** from the OS inside the VM. 28 | 29 | ### FAQ 30 | 31 | * You might get an error about 'shared folder' when first opening the .ova file, you can ignore these. 32 | 33 | ## Support 34 | 35 | If you have any questions/comments regarding this tutorial, 36 | please let us know on [our chat channel](https://gitter.im/BlueBrain/SimulationTutorials). 37 | -------------------------------------------------------------------------------- /SfN2017/admin/Vagrantfile: -------------------------------------------------------------------------------- 1 | # -*- mode: ruby -*- 2 | # vi: set ft=ruby : 3 | 4 | 5 | Vagrant.configure(2) do |config| 6 | # config.vm.define "vb32" do |vb32| 7 | # vb32.vm.box = "ubuntu/trusty32" 8 | # vb32.vm.provider :virtualbox do |vb| 9 | # vb.customize ["modifyvm", :id, "--hwvirtex", "off"] 10 | # vb.name = "cns2017.32bit" 11 | # end 12 | # end 13 | 14 | config.vm.define "vb64" do |vb64| 15 | vb64.vm.box = "ubuntu/trusty64" 16 | vb64.vm.provider :virtualbox do |vb| 17 | vb.customize ["modifyvm", :id, "--hwvirtex", "on"] 18 | vb.name = "cns2017" 19 | end 20 | end 21 | 22 | 23 | config.vm.provider :virtualbox do |vb| 24 | vb.customize ["modifyvm", :id, "--memory", "2048"] 25 | vb.customize ["modifyvm", :id, "--cpus", "4"] 26 | vb.customize ['modifyvm', :id, '--clipboard', 'bidirectional'] 27 | vb.gui = true 28 | end 29 | 30 | 31 | config.vm.provision "ansible" do |ansible| 32 | ansible.playbook = "playbook.yml" 33 | # ansible.verbose = "v" 34 | end 35 | end 36 | 37 | -------------------------------------------------------------------------------- /SfN2017/admin/neuron.yml: -------------------------------------------------------------------------------- 1 | --- 2 | 3 | - name: Get iv Source 4 | get_url: url={{ download_path }}/{{ iv_tarball }} dest={{ src_dir }}/{{ iv_tarball }} 5 | 6 | - name: Get nrn Source 7 | get_url: url={{ download_path }}/{{ nrn_tarball }} dest={{ src_dir }}/{{ nrn_tarball }} 8 | 9 | - name: Untar iv source 10 | unarchive: copy=no src={{ src_dir }}/{{ iv_tarball }} dest={{ src_dir }} 11 | 12 | - name: Untar nrn source 13 | unarchive: copy=no src={{ src_dir }}/{{ nrn_tarball }} dest={{ src_dir }} 14 | 15 | - name: configure iv 16 | shell: "./configure --prefix={{ nrn_prefix }}" 17 | args: 18 | chdir: "{{ iv_src_dir }}" 19 | 20 | - name: build iv 21 | shell: make 22 | args: 23 | chdir: "{{ iv_src_dir }}" 24 | 25 | - name: install iv 26 | shell: make install 27 | args: 28 | chdir: "{{ iv_src_dir }}" 29 | 30 | - name: configure neuron 31 | shell: "./configure --with-iv={{ nrn_prefix }} --with-nrnpython --prefix={{ nrn_prefix }}" 32 | args: 33 | chdir: "{{ nrn_src_dir }}" 34 | 35 | - name: build neuron 36 | shell: make 37 | args: 38 | chdir: "{{ nrn_src_dir }}" 39 | 40 | - name: install neuron 41 | shell: make install 42 | args: 43 | chdir: "{{ nrn_src_dir }}" 44 | 45 | - name: install 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-------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlueBrain/SimulationTutorials/44fa01c22bc83fbbe8a01d3580de75ffadf92ea4/SfN2017/eFEL/eFeatures.png -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/README.md: -------------------------------------------------------------------------------- 1 | ## BluePyOpt 2 | 3 | The **Blue Brain Python Optimisation Library** (BluePyOpt) is an extensible framework for data-driven model parameter optimisation that wraps and standardises several existing open-source tools. It simplifies the task of creating and sharing these optimisations, and the associated techniques and knowledge. This is achieved by abstracting the optimisation and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. Further, BluePyOpt provides methods for setting up both small- and large-scale optimisations on a variety of platforms, ranging from laptops to Linux clusters and cloud-based compute infrastructures. 4 | 5 | https://github.com/BlueBrain/BluePyOpt 6 | 7 | The demo is explained in the following notebooks: 8 | - An optimisation of two parameters of a single compartmental cell: [simplecell/simplecell.ipynb](simplecell/simplecell.ipynb) 9 | - Optimisation of Rat Neocortical Layer 5 Pyramidal Cell: [l5pc/L5PC.ipynb](l5pc/L5PC.ipynb) 10 | 11 | These notebooks can be run from a browser: [binder instance](http://mybinder.org/repo/BlueBrain/SimulationTutorials/YRE2016/BluePyOpt) 12 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/.gitignore: -------------------------------------------------------------------------------- 1 | /x86_64 2 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/LICENSE: -------------------------------------------------------------------------------- 1 | The CC-BY-NC-SA license applies, as indicated by headers in the 2 | respective source files. 3 | 4 | https://creativecommons.org/licenses/by-nc-sa/4.0/ 5 | 6 | The detailed text is available here 7 | https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode 8 | 9 | or in this tarball in the seperate file LICENSE_CC-BY-CA-SA-4.0 10 | 11 | 12 | The HOC code, Python code, synapse MOD code and cell morphology are licensed with the above mentioned CC-BY-NC-SA license. 13 | 14 | 15 | For models for which the original source is available on ModelDB, any 16 | specific licenses on mentioned on ModelDB, or the generic License of ModelDB 17 | apply: 18 | 19 | 1) Ih model 20 | Author: Stefan Hallermann 21 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=144526&file=\HallermannEtAl2012\h.mod 22 | 23 | 2) StochKv model 24 | Authors: Zach Mainen Adaptations: Kamran Diba, Mickey London, Peter N. Steinmetz, Werner Van Geit 25 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=125385&file=\Sbpap_code\mod\skm.mod 26 | 27 | 3) D-type K current model 28 | Authors: Yuguo Yu 29 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=135898&file=\YuEtAlPNAS2007\kd.mod 30 | 31 | 4) Internal calcium concentration model 32 | Author: Alain Destexhe 33 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=3670&file=\NTW_NEW\capump.mod 34 | 35 | 5) Ca_LVAst, Im, K_Tst, NaTa_t, SK_E2, Ca_HVA, Ih, K_Pst, Nap_Et2, NaTs2_t, SKv3_1 36 | Author: Etay Hay, Shaul Druckmann, Srikanth Ramaswamy, James King, Werner Van Geit 37 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=139653&file=\L5bPCmodelsEH\mod\ 38 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/config/fixed_params.json: -------------------------------------------------------------------------------- 1 | { 2 | "global": [ 3 | [ 4 | "v_init", 5 | -65 6 | ], 7 | [ 8 | "celsius", 9 | 34 10 | ] 11 | ], 12 | "all": [ 13 | [ 14 | "g_pas", 15 | 3e-05, 16 | "uniform" 17 | ], 18 | [ 19 | "e_pas", 20 | -75, 21 | "uniform" 22 | ], 23 | [ 24 | "cm", 25 | 1, 26 | "uniform" 27 | ], 28 | [ 29 | "Ra", 30 | 100, 31 | "uniform" 32 | ] 33 | ], 34 | "apical": [ 35 | [ 36 | "ena", 37 | 50, 38 | "uniform" 39 | ], 40 | [ 41 | "ek", 42 | -85, 43 | "uniform" 44 | ], 45 | [ 46 | "cm", 47 | 2, 48 | "uniform" 49 | ] 50 | ], 51 | "somatic": [ 52 | [ 53 | "ena", 54 | 50, 55 | "uniform" 56 | ], 57 | [ 58 | "ek", 59 | -85, 60 | "uniform" 61 | ] 62 | ], 63 | "basal": [ 64 | [ 65 | "cm", 66 | 2, 67 | "uniform" 68 | ] 69 | ], 70 | "axonal": [ 71 | [ 72 | "ena", 73 | 50, 74 | "uniform" 75 | ], 76 | [ 77 | "ek", 78 | -85, 79 | "uniform" 80 | ] 81 | ] 82 | } 83 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/config/mechanisms.json: -------------------------------------------------------------------------------- 1 | { 2 | "basal": [ 3 | "Ih" 4 | ], 5 | "all": [ 6 | "pas" 7 | ], 8 | "apical": [ 9 | "Ih", 10 | "Im", 11 | "SKv3_1", 12 | "NaTs2_t" 13 | ], 14 | "axonal": [ 15 | "Ca_LVAst", 16 | "Ca_HVA", 17 | "CaDynamics_E2", 18 | "SKv3_1", 19 | "SK_E2", 20 | "K_Tst", 21 | "K_Pst", 22 | "Nap_Et2", 23 | "NaTa_t" 24 | ], 25 | "somatic": [ 26 | "NaTs2_t", 27 | "SKv3_1", 28 | "SK_E2", 29 | "CaDynamics_E2", 30 | "Ca_HVA", 31 | "Ca_LVAst", 32 | "Ih" 33 | ] 34 | } 35 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/mechanisms/CaDynamics_E2.mod: -------------------------------------------------------------------------------- 1 | : Dynamics that track inside calcium concentration 2 | : modified from Destexhe et al. 1994 3 | 4 | NEURON { 5 | SUFFIX CaDynamics_E2 6 | USEION ca READ ica WRITE cai 7 | RANGE decay, gamma, minCai, depth 8 | } 9 | 10 | UNITS { 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | FARADAY = (faraday) (coulombs) 14 | (molar) = (1/liter) 15 | (mM) = (millimolar) 16 | (um) = (micron) 17 | } 18 | 19 | PARAMETER { 20 | gamma = 0.05 : percent of free calcium (not buffered) 21 | decay = 80 (ms) : rate of removal of calcium 22 | depth = 0.1 (um) : depth of shell 23 | minCai = 1e-4 (mM) 24 | } 25 | 26 | ASSIGNED {ica (mA/cm2)} 27 | 28 | STATE { 29 | cai (mM) 30 | } 31 | 32 | BREAKPOINT { SOLVE states METHOD cnexp } 33 | 34 | DERIVATIVE states { 35 | cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay 36 | } 37 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/mechanisms/Ca_HVA.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993 3 | 4 | NEURON { 5 | SUFFIX Ca_HVA 6 | USEION ca READ eca WRITE ica 7 | RANGE gCa_HVAbar, gCa_HVA, ica 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gCa_HVAbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | eca (mV) 23 | ica (mA/cm2) 24 | gCa (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | hInf 30 | hTau 31 | hAlpha 32 | hBeta 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | gCa = gCa_HVAbar*m*m*h 43 | ica = gCa*(v-eca) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates(){ 59 | UNITSOFF 60 | if((v == -27) ){ 61 | v = v+0.0001 62 | } 63 | mAlpha = (0.055*(-27-v))/(exp((-27-v)/3.8) - 1) 64 | mBeta = (0.94*exp((-75-v)/17)) 65 | mInf = mAlpha/(mAlpha + mBeta) 66 | mTau = 1/(mAlpha + mBeta) 67 | hAlpha = (0.000457*exp((-13-v)/50)) 68 | hBeta = (0.0065/(exp((-v-15)/28)+1)) 69 | hInf = hAlpha/(hAlpha + hBeta) 70 | hTau = 1/(hAlpha + hBeta) 71 | UNITSON 72 | } 73 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/mechanisms/Ca_LVAst.mod: -------------------------------------------------------------------------------- 1 | :Comment : LVA ca channel. Note: mtau is an approximation from the plots 2 | :Reference : : Avery and Johnston 1996, tau from Randall 1997 3 | :Comment: shifted by -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | NEURON { 7 | SUFFIX Ca_LVAst 8 | USEION ca READ eca WRITE ica 9 | RANGE gCa_LVAstbar, gCa_LVAst, ica 10 | } 11 | 12 | UNITS { 13 | (S) = (siemens) 14 | (mV) = (millivolt) 15 | (mA) = (milliamp) 16 | } 17 | 18 | PARAMETER { 19 | gCa_LVAstbar = 0.00001 (S/cm2) 20 | } 21 | 22 | ASSIGNED { 23 | v (mV) 24 | eca (mV) 25 | ica (mA/cm2) 26 | gCa_LVAst (S/cm2) 27 | mInf 28 | mTau 29 | hInf 30 | hTau 31 | } 32 | 33 | STATE { 34 | m 35 | h 36 | } 37 | 38 | BREAKPOINT { 39 | SOLVE states METHOD cnexp 40 | gCa_LVAst = gCa_LVAstbar*m*m*h 41 | ica = gCa_LVAst*(v-eca) 42 | } 43 | 44 | DERIVATIVE states { 45 | rates() 46 | m' = (mInf-m)/mTau 47 | h' = (hInf-h)/hTau 48 | } 49 | 50 | INITIAL{ 51 | rates() 52 | m = mInf 53 | h = hInf 54 | } 55 | 56 | PROCEDURE rates(){ 57 | LOCAL qt 58 | qt = 2.3^((34-21)/10) 59 | 60 | UNITSOFF 61 | v = v + 10 62 | mInf = 1.0000/(1+ exp((v - -30.000)/-6)) 63 | mTau = (5.0000 + 20.0000/(1+exp((v - -25.000)/5)))/qt 64 | hInf = 1.0000/(1+ exp((v - -80.000)/6.4)) 65 | hTau = (20.0000 + 50.0000/(1+exp((v - -40.000)/7)))/qt 66 | v = v - 10 67 | UNITSON 68 | } 69 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/mechanisms/Ih.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Kole,Hallermann,and Stuart, J. Neurosci. 2006 3 | 4 | NEURON { 5 | SUFFIX Ih 6 | NONSPECIFIC_CURRENT ihcn 7 | RANGE gIhbar, gIh, ihcn 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gIhbar = 0.00001 (S/cm2) 18 | ehcn = -45.0 (mV) 19 | } 20 | 21 | ASSIGNED { 22 | v (mV) 23 | ihcn (mA/cm2) 24 | gIh (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | } 30 | 31 | STATE { 32 | m 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gIh = gIhbar*m 38 | ihcn = gIh*(v-ehcn) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates() 43 | m' = (mInf-m)/mTau 44 | } 45 | 46 | INITIAL{ 47 | rates() 48 | m = mInf 49 | } 50 | 51 | PROCEDURE rates(){ 52 | UNITSOFF 53 | if(v == -154.9){ 54 | v = v + 0.0001 55 | } 56 | mAlpha = 0.001*6.43*(v+154.9)/(exp((v+154.9)/11.9)-1) 57 | mBeta = 0.001*193*exp(v/33.1) 58 | mInf = mAlpha/(mAlpha + mBeta) 59 | mTau = 1/(mAlpha + mBeta) 60 | UNITSON 61 | } 62 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/mechanisms/Im.mod: -------------------------------------------------------------------------------- 1 | :Reference : : Adams et al. 1982 - M-currents and other potassium currents in bullfrog sympathetic neurones 2 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 3 | 4 | NEURON { 5 | SUFFIX Im 6 | USEION k READ ek WRITE ik 7 | RANGE gImbar, gIm, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gImbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | gIm (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | } 30 | 31 | STATE { 32 | m 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gIm = gImbar*m 38 | ik = gIm*(v-ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates() 43 | m' = (mInf-m)/mTau 44 | } 45 | 46 | INITIAL{ 47 | rates() 48 | m = mInf 49 | } 50 | 51 | PROCEDURE rates(){ 52 | LOCAL qt 53 | qt = 2.3^((34-21)/10) 54 | 55 | UNITSOFF 56 | mAlpha = 3.3e-3*exp(2.5*0.04*(v - -35)) 57 | mBeta = 3.3e-3*exp(-2.5*0.04*(v - -35)) 58 | mInf = mAlpha/(mAlpha + mBeta) 59 | mTau = (1/(mAlpha + mBeta))/qt 60 | UNITSON 61 | } 62 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/mechanisms/K_Pst.mod: -------------------------------------------------------------------------------- 1 | :Comment : The persistent component of the K current 2 | :Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | :Comment : shifted -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | 7 | NEURON { 8 | SUFFIX K_Pst 9 | USEION k READ ek WRITE ik 10 | RANGE gK_Pstbar, gK_Pst, ik 11 | } 12 | 13 | UNITS { 14 | (S) = (siemens) 15 | (mV) = (millivolt) 16 | (mA) = (milliamp) 17 | } 18 | 19 | PARAMETER { 20 | gK_Pstbar = 0.00001 (S/cm2) 21 | } 22 | 23 | ASSIGNED { 24 | v (mV) 25 | ek (mV) 26 | ik (mA/cm2) 27 | gK_Pst (S/cm2) 28 | mInf 29 | mTau 30 | hInf 31 | hTau 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | gK_Pst = gK_Pstbar*m*m*h 42 | ik = gK_Pst*(v-ek) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | LOCAL qt 59 | qt = 2.3^((34-21)/10) 60 | UNITSOFF 61 | v = v + 10 62 | mInf = (1/(1 + exp(-(v+1)/12))) 63 | if(v<-50){ 64 | mTau = (1.25+175.03*exp(-v * -0.026))/qt 65 | }else{ 66 | mTau = ((1.25+13*exp(-v*0.026)))/qt 67 | } 68 | hInf = 1/(1 + exp(-(v+54)/-11)) 69 | hTau = (360+(1010+24*(v+55))*exp(-((v+75)/48)^2))/qt 70 | v = v - 10 71 | UNITSON 72 | } 73 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/mechanisms/K_Tst.mod: -------------------------------------------------------------------------------- 1 | :Comment : The transient component of the K current 2 | :Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | :Comment : shifted -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | NEURON { 7 | SUFFIX K_Tst 8 | USEION k READ ek WRITE ik 9 | RANGE gK_Tstbar, gK_Tst, ik 10 | } 11 | 12 | UNITS { 13 | (S) = (siemens) 14 | (mV) = (millivolt) 15 | (mA) = (milliamp) 16 | } 17 | 18 | PARAMETER { 19 | gK_Tstbar = 0.00001 (S/cm2) 20 | } 21 | 22 | ASSIGNED { 23 | v (mV) 24 | ek (mV) 25 | ik (mA/cm2) 26 | gK_Tst (S/cm2) 27 | mInf 28 | mTau 29 | hInf 30 | hTau 31 | } 32 | 33 | STATE { 34 | m 35 | h 36 | } 37 | 38 | BREAKPOINT { 39 | SOLVE states METHOD cnexp 40 | gK_Tst = gK_Tstbar*(m^4)*h 41 | ik = gK_Tst*(v-ek) 42 | } 43 | 44 | DERIVATIVE states { 45 | rates() 46 | m' = (mInf-m)/mTau 47 | h' = (hInf-h)/hTau 48 | } 49 | 50 | INITIAL{ 51 | rates() 52 | m = mInf 53 | h = hInf 54 | } 55 | 56 | PROCEDURE rates(){ 57 | LOCAL qt 58 | qt = 2.3^((34-21)/10) 59 | 60 | UNITSOFF 61 | v = v + 10 62 | mInf = 1/(1 + exp(-(v+0)/19)) 63 | mTau = (0.34+0.92*exp(-((v+71)/59)^2))/qt 64 | hInf = 1/(1 + exp(-(v+66)/-10)) 65 | hTau = (8+49*exp(-((v+73)/23)^2))/qt 66 | v = v - 10 67 | UNITSON 68 | } 69 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/mechanisms/LICENSE: -------------------------------------------------------------------------------- 1 | The CC-BY-NC-SA license applies, as indicated by headers in the 2 | respective source files. 3 | 4 | https://creativecommons.org/licenses/by-nc-sa/4.0/ 5 | 6 | The detailed text is available here 7 | https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode 8 | 9 | or in this tarball in the seperate file LICENSE_CC-BY-CA-SA-4.0 10 | 11 | 12 | The HOC code, Python code, synapse MOD code and cell morphology are licensed with the above mentioned CC-BY-NC-SA license. 13 | 14 | 15 | For models for which the original source is available on ModelDB, any 16 | specific licenses on mentioned on ModelDB, or the generic License of ModelDB 17 | apply: 18 | 19 | 1) Ih model 20 | Author: Stefan Hallermann 21 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=144526&file=\HallermannEtAl2012\h.mod 22 | 23 | 2) StochKv model 24 | Authors: Zach Mainen Adaptations: Kamran Diba, Mickey London, Peter N. Steinmetz, Werner Van Geit 25 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=125385&file=\Sbpap_code\mod\skm.mod 26 | 27 | 3) D-type K current model 28 | Authors: Yuguo Yu 29 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=135898&file=\YuEtAlPNAS2007\kd.mod 30 | 31 | 4) Internal calcium concentration model 32 | Author: Alain Destexhe 33 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=3670&file=\NTW_NEW\capump.mod 34 | 35 | 5) Ca_LVAst, Im, K_Tst, NaTa_t, SK_E2, Ca_HVA, Ih, K_Pst, Nap_Et2, NaTs2_t, SKv3_1 36 | Author: Etay Hay, Shaul Druckmann, Srikanth Ramaswamy, James King, Werner Van Geit 37 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=139653&file=\L5bPCmodelsEH\mod\ 38 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/mechanisms/NaTa_t.mod: -------------------------------------------------------------------------------- 1 | :Reference :Colbert and Pan 2002 2 | 3 | NEURON { 4 | SUFFIX NaTa_t 5 | USEION na READ ena WRITE ina 6 | RANGE gNaTa_tbar, gNaTa_t, ina 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gNaTa_tbar = 0.00001 (S/cm2) 17 | } 18 | 19 | ASSIGNED { 20 | v (mV) 21 | ena (mV) 22 | ina (mA/cm2) 23 | gNaTa_t (S/cm2) 24 | mInf 25 | mTau 26 | mAlpha 27 | mBeta 28 | hInf 29 | hTau 30 | hAlpha 31 | hBeta 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | gNaTa_t = gNaTa_tbar*m*m*m*h 42 | ina = gNaTa_t*(v-ena) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | LOCAL qt 59 | qt = 2.3^((34-21)/10) 60 | 61 | UNITSOFF 62 | if(v == -38){ 63 | v = v+0.0001 64 | } 65 | mAlpha = (0.182 * (v- -38))/(1-(exp(-(v- -38)/6))) 66 | mBeta = (0.124 * (-v -38))/(1-(exp(-(-v -38)/6))) 67 | mTau = (1/(mAlpha + mBeta))/qt 68 | mInf = mAlpha/(mAlpha + mBeta) 69 | 70 | if(v == -66){ 71 | v = v + 0.0001 72 | } 73 | 74 | hAlpha = (-0.015 * (v- -66))/(1-(exp((v- -66)/6))) 75 | hBeta = (-0.015 * (-v -66))/(1-(exp((-v -66)/6))) 76 | hTau = (1/(hAlpha + hBeta))/qt 77 | hInf = hAlpha/(hAlpha + hBeta) 78 | UNITSON 79 | } 80 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/mechanisms/NaTs2_t.mod: -------------------------------------------------------------------------------- 1 | :Reference :Colbert and Pan 2002 2 | :comment: took the NaTa and shifted both activation/inactivation by 6 mv 3 | 4 | NEURON { 5 | SUFFIX NaTs2_t 6 | USEION na READ ena WRITE ina 7 | RANGE gNaTs2_tbar, gNaTs2_t, ina 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gNaTs2_tbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ena (mV) 23 | ina (mA/cm2) 24 | gNaTs2_t (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | hInf 30 | hTau 31 | hAlpha 32 | hBeta 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | gNaTs2_t = gNaTs2_tbar*m*m*m*h 43 | ina = gNaTs2_t*(v-ena) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates(){ 59 | LOCAL qt 60 | qt = 2.3^((34-21)/10) 61 | 62 | UNITSOFF 63 | if(v == -32){ 64 | v = v+0.0001 65 | } 66 | mAlpha = (0.182 * (v- -32))/(1-(exp(-(v- -32)/6))) 67 | mBeta = (0.124 * (-v -32))/(1-(exp(-(-v -32)/6))) 68 | mInf = mAlpha/(mAlpha + mBeta) 69 | mTau = (1/(mAlpha + mBeta))/qt 70 | 71 | if(v == -60){ 72 | v = v + 0.0001 73 | } 74 | hAlpha = (-0.015 * (v- -60))/(1-(exp((v- -60)/6))) 75 | hBeta = (-0.015 * (-v -60))/(1-(exp((-v -60)/6))) 76 | hInf = hAlpha/(hAlpha + hBeta) 77 | hTau = (1/(hAlpha + hBeta))/qt 78 | UNITSON 79 | } 80 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/mechanisms/SK_E2.mod: -------------------------------------------------------------------------------- 1 | : SK-type calcium-activated potassium current 2 | : Reference : Kohler et al. 1996 3 | 4 | NEURON { 5 | SUFFIX SK_E2 6 | USEION k READ ek WRITE ik 7 | USEION ca READ cai 8 | RANGE gSK_E2bar, gSK_E2, ik 9 | } 10 | 11 | UNITS { 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | (mM) = (milli/liter) 15 | } 16 | 17 | PARAMETER { 18 | v (mV) 19 | gSK_E2bar = .000001 (mho/cm2) 20 | zTau = 1 (ms) 21 | ek (mV) 22 | cai (mM) 23 | } 24 | 25 | ASSIGNED { 26 | zInf 27 | ik (mA/cm2) 28 | gSK_E2 (S/cm2) 29 | } 30 | 31 | STATE { 32 | z FROM 0 TO 1 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gSK_E2 = gSK_E2bar * z 38 | ik = gSK_E2 * (v - ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates(cai) 43 | z' = (zInf - z) / zTau 44 | } 45 | 46 | PROCEDURE rates(ca(mM)) { 47 | if(ca < 1e-7){ 48 | ca = ca + 1e-07 49 | } 50 | zInf = 1/(1 + (0.00043 / ca)^4.8) 51 | } 52 | 53 | INITIAL { 54 | rates(cai) 55 | z = zInf 56 | } 57 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/mechanisms/SKv3_1.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Characterization of a Shaw-related potassium channel family in rat brain, The EMBO Journal, vol.11, no.7,2473-2486 (1992) 3 | 4 | NEURON { 5 | SUFFIX SKv3_1 6 | USEION k READ ek WRITE ik 7 | RANGE gSKv3_1bar, gSKv3_1, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gSKv3_1bar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | gSKv3_1 (S/cm2) 25 | mInf 26 | mTau 27 | } 28 | 29 | STATE { 30 | m 31 | } 32 | 33 | BREAKPOINT { 34 | SOLVE states METHOD cnexp 35 | gSKv3_1 = gSKv3_1bar*m 36 | ik = gSKv3_1*(v-ek) 37 | } 38 | 39 | DERIVATIVE states { 40 | rates() 41 | m' = (mInf-m)/mTau 42 | } 43 | 44 | INITIAL{ 45 | rates() 46 | m = mInf 47 | } 48 | 49 | PROCEDURE rates(){ 50 | UNITSOFF 51 | mInf = 1/(1+exp(((v -(18.700))/(-9.700)))) 52 | mTau = 0.2*20.000/(1+exp(((v -(-46.560))/(-44.140)))) 53 | UNITSON 54 | } 55 | 56 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/l5pc/morphology/LICENSE: -------------------------------------------------------------------------------- 1 | The CC-BY-NC-SA license applies, as indicated by headers in the 2 | respective source files. 3 | 4 | https://creativecommons.org/licenses/by-nc-sa/4.0/ 5 | 6 | The detailed text is available here 7 | https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode 8 | 9 | or in this tarball in the seperate file LICENSE_CC-BY-CA-SA-4.0 10 | 11 | 12 | The HOC code, Python code, synapse MOD code and cell morphology are licensed with the above mentioned CC-BY-NC-SA license. 13 | 14 | 15 | For models for which the original source is available on ModelDB, any 16 | specific licenses on mentioned on ModelDB, or the generic License of ModelDB 17 | apply: 18 | 19 | 1) Ih model 20 | Author: Stefan Hallermann 21 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=144526&file=\HallermannEtAl2012\h.mod 22 | 23 | 2) StochKv model 24 | Authors: Zach Mainen Adaptations: Kamran Diba, Mickey London, Peter N. Steinmetz, Werner Van Geit 25 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=125385&file=\Sbpap_code\mod\skm.mod 26 | 27 | 3) D-type K current model 28 | Authors: Yuguo Yu 29 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=135898&file=\YuEtAlPNAS2007\kd.mod 30 | 31 | 4) Internal calcium concentration model 32 | Author: Alain Destexhe 33 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=3670&file=\NTW_NEW\capump.mod 34 | 35 | 5) Ca_LVAst, Im, K_Tst, NaTa_t, SK_E2, Ca_HVA, Ih, K_Pst, Nap_Et2, NaTs2_t, SKv3_1 36 | Author: Etay Hay, Shaul Druckmann, Srikanth Ramaswamy, James King, Werner Van Geit 37 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=139653&file=\L5bPCmodelsEH\mod\ 38 | -------------------------------------------------------------------------------- /YRE2016/BluePyOpt/simplecell/simple.swc: -------------------------------------------------------------------------------- 1 | # Dummy granule cell morphology 2 | 1 1 -5.0 0.0 0.0 5.0 -1 3 | 2 1 0.0 0.0 0.0 5.0 1 4 | 3 1 5.0 0.0 0.0 5.0 2 5 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlueBrain/SimulationTutorials/44fa01c22bc83fbbe8a01d3580de75ffadf92ea4/YRE2016/NMC/L5_TTPC2_cADpyr232_1.zip -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/.provenance.json: -------------------------------------------------------------------------------- 1 | { 2 | "gid": 17636, 3 | "blueconfig": "/gpfs/bbp.cscs.ch/project/proj1/simulations/ReNCCv2/k_ca_scan_dense/K5p0/Ca2p00/BlueConfig" 4 | } -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/CHANGELOG: -------------------------------------------------------------------------------- 1 | 1.0.11: Made compatible with python3. Improved README 2 | 1.0.10: Increased the current to calculate the Rin to get above the noise level 3 | for models with stochastic channels 4 | 1.0.9: Every model package now contains a cellinfo.json file with e.g. the 5 | m-type, e-type, etc. 6 | 1.0.8: Code was added to calculate the Resting Membrane Potential, 7 | Input Resitance and Time constant 8 | 1.0.6: Make random number generators use exact same seed as in large network 9 | simulation 10 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/LICENSE: -------------------------------------------------------------------------------- 1 | The CC-BY-NC-SA license applies, as indicated by headers in the 2 | respective source files. 3 | 4 | https://creativecommons.org/licenses/by-nc-sa/4.0/ 5 | 6 | The detailed text is available here 7 | https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode 8 | 9 | or in this tarball in the seperate file LICENSE_CC-BY-CA-SA-4.0 10 | 11 | 12 | The HOC code, Python code, synapse MOD code and cell morphology are licensed with the above mentioned CC-BY-NC-SA license. 13 | 14 | 15 | For models for which the original source is available on ModelDB, any 16 | specific licenses on mentioned on ModelDB, or the generic License of ModelDB 17 | apply: 18 | 19 | 1) Ih model 20 | Author: Stefan Hallermann 21 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=144526&file=\HallermannEtAl2012\h.mod 22 | 23 | 2) StochKv model 24 | Authors: Zach Mainen Adaptations: Kamran Diba, Mickey London, Peter N. Steinmetz, Werner Van Geit 25 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=125385&file=\Sbpap_code\mod\skm.mod 26 | 27 | 3) D-type K current model 28 | Authors: Yuguo Yu 29 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=135898&file=\YuEtAlPNAS2007\kd.mod 30 | 31 | 4) Internal calcium concentration model 32 | Author: Alain Destexhe 33 | Original URL: http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=3670&file=\NTW_NEW\capump.mod 34 | 35 | 5) Ca_LVAst, Im, K_Tst, NaTa_t, SK_E2, Ca_HVA, Ih, K_Pst, Nap_Et2, NaTs2_t, SKv3_1 36 | Author: Etay Hay, Shaul Druckmann, Srikanth Ramaswamy, James King, Werner Van Geit 37 | Original URL: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=139653&file=\L5bPCmodelsEH\mod\ 38 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/VERSION: -------------------------------------------------------------------------------- 1 | 1.0.11 2 | 2015/10/07 3 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/cellinfo.json: -------------------------------------------------------------------------------- 1 | { 2 | "cell name": "cADpyr232_L5_TTPC2_5_dend-C060114A7_axon-C060116A3_-_Clone_2", 3 | "e-type": "L5PC", 4 | "gid": "17636", 5 | "layer": "L5", 6 | "m-type": "L5_TTPC2", 7 | "me-type": "L5_TTPC2_L5PC", 8 | "morphology": "dend-C060114A7_axon-C060116A3_-_Clone_2" 9 | } -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/current_amps.dat: -------------------------------------------------------------------------------- 1 | -0.286011 0.5930628 0.6424847 0.6919066 -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/mechanisms/CaDynamics_E2.mod: -------------------------------------------------------------------------------- 1 | : Dynamics that track inside calcium concentration 2 | : modified from Destexhe et al. 1994 3 | 4 | NEURON { 5 | SUFFIX CaDynamics_E2 6 | USEION ca READ ica WRITE cai 7 | RANGE decay, gamma, minCai, depth 8 | } 9 | 10 | UNITS { 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | FARADAY = (faraday) (coulombs) 14 | (molar) = (1/liter) 15 | (mM) = (millimolar) 16 | (um) = (micron) 17 | } 18 | 19 | PARAMETER { 20 | gamma = 0.05 : percent of free calcium (not buffered) 21 | decay = 80 (ms) : rate of removal of calcium 22 | depth = 0.1 (um) : depth of shell 23 | minCai = 1e-4 (mM) 24 | } 25 | 26 | ASSIGNED {ica (mA/cm2)} 27 | 28 | STATE { 29 | cai (mM) 30 | } 31 | 32 | BREAKPOINT { SOLVE states METHOD cnexp } 33 | 34 | DERIVATIVE states { 35 | cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay 36 | } 37 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/mechanisms/Ca_HVA.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993 3 | 4 | NEURON { 5 | SUFFIX Ca_HVA 6 | USEION ca READ eca WRITE ica 7 | RANGE gCa_HVAbar, gCa_HVA, ica 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gCa_HVAbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | eca (mV) 23 | ica (mA/cm2) 24 | gCa (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | hInf 30 | hTau 31 | hAlpha 32 | hBeta 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | gCa = gCa_HVAbar*m*m*h 43 | ica = gCa*(v-eca) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates(){ 59 | UNITSOFF 60 | if((v == -27) ){ 61 | v = v+0.0001 62 | } 63 | mAlpha = (0.055*(-27-v))/(exp((-27-v)/3.8) - 1) 64 | mBeta = (0.94*exp((-75-v)/17)) 65 | mInf = mAlpha/(mAlpha + mBeta) 66 | mTau = 1/(mAlpha + mBeta) 67 | hAlpha = (0.000457*exp((-13-v)/50)) 68 | hBeta = (0.0065/(exp((-v-15)/28)+1)) 69 | hInf = hAlpha/(hAlpha + hBeta) 70 | hTau = 1/(hAlpha + hBeta) 71 | UNITSON 72 | } 73 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/mechanisms/Ca_LVAst.mod: -------------------------------------------------------------------------------- 1 | :Comment : LVA ca channel. Note: mtau is an approximation from the plots 2 | :Reference : : Avery and Johnston 1996, tau from Randall 1997 3 | :Comment: shifted by -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | NEURON { 7 | SUFFIX Ca_LVAst 8 | USEION ca READ eca WRITE ica 9 | RANGE gCa_LVAstbar, gCa_LVAst, ica 10 | } 11 | 12 | UNITS { 13 | (S) = (siemens) 14 | (mV) = (millivolt) 15 | (mA) = (milliamp) 16 | } 17 | 18 | PARAMETER { 19 | gCa_LVAstbar = 0.00001 (S/cm2) 20 | } 21 | 22 | ASSIGNED { 23 | v (mV) 24 | eca (mV) 25 | ica (mA/cm2) 26 | gCa_LVAst (S/cm2) 27 | mInf 28 | mTau 29 | hInf 30 | hTau 31 | } 32 | 33 | STATE { 34 | m 35 | h 36 | } 37 | 38 | BREAKPOINT { 39 | SOLVE states METHOD cnexp 40 | gCa_LVAst = gCa_LVAstbar*m*m*h 41 | ica = gCa_LVAst*(v-eca) 42 | } 43 | 44 | DERIVATIVE states { 45 | rates() 46 | m' = (mInf-m)/mTau 47 | h' = (hInf-h)/hTau 48 | } 49 | 50 | INITIAL{ 51 | rates() 52 | m = mInf 53 | h = hInf 54 | } 55 | 56 | PROCEDURE rates(){ 57 | LOCAL qt 58 | qt = 2.3^((34-21)/10) 59 | 60 | UNITSOFF 61 | v = v + 10 62 | mInf = 1.0000/(1+ exp((v - -30.000)/-6)) 63 | mTau = (5.0000 + 20.0000/(1+exp((v - -25.000)/5)))/qt 64 | hInf = 1.0000/(1+ exp((v - -80.000)/6.4)) 65 | hTau = (20.0000 + 50.0000/(1+exp((v - -40.000)/7)))/qt 66 | v = v - 10 67 | UNITSON 68 | } 69 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/mechanisms/Ih.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Kole,Hallermann,and Stuart, J. Neurosci. 2006 3 | 4 | NEURON { 5 | SUFFIX Ih 6 | NONSPECIFIC_CURRENT ihcn 7 | RANGE gIhbar, gIh, ihcn 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gIhbar = 0.00001 (S/cm2) 18 | ehcn = -45.0 (mV) 19 | } 20 | 21 | ASSIGNED { 22 | v (mV) 23 | ihcn (mA/cm2) 24 | gIh (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | } 30 | 31 | STATE { 32 | m 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gIh = gIhbar*m 38 | ihcn = gIh*(v-ehcn) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates() 43 | m' = (mInf-m)/mTau 44 | } 45 | 46 | INITIAL{ 47 | rates() 48 | m = mInf 49 | } 50 | 51 | PROCEDURE rates(){ 52 | UNITSOFF 53 | if(v == -154.9){ 54 | v = v + 0.0001 55 | } 56 | mAlpha = 0.001*6.43*(v+154.9)/(exp((v+154.9)/11.9)-1) 57 | mBeta = 0.001*193*exp(v/33.1) 58 | mInf = mAlpha/(mAlpha + mBeta) 59 | mTau = 1/(mAlpha + mBeta) 60 | UNITSON 61 | } 62 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/mechanisms/Im.mod: -------------------------------------------------------------------------------- 1 | :Reference : : Adams et al. 1982 - M-currents and other potassium currents in bullfrog sympathetic neurones 2 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 3 | 4 | NEURON { 5 | SUFFIX Im 6 | USEION k READ ek WRITE ik 7 | RANGE gImbar, gIm, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gImbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | gIm (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | } 30 | 31 | STATE { 32 | m 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gIm = gImbar*m 38 | ik = gIm*(v-ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates() 43 | m' = (mInf-m)/mTau 44 | } 45 | 46 | INITIAL{ 47 | rates() 48 | m = mInf 49 | } 50 | 51 | PROCEDURE rates(){ 52 | LOCAL qt 53 | qt = 2.3^((34-21)/10) 54 | 55 | UNITSOFF 56 | mAlpha = 3.3e-3*exp(2.5*0.04*(v - -35)) 57 | mBeta = 3.3e-3*exp(-2.5*0.04*(v - -35)) 58 | mInf = mAlpha/(mAlpha + mBeta) 59 | mTau = (1/(mAlpha + mBeta))/qt 60 | UNITSON 61 | } 62 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/mechanisms/K_Pst.mod: -------------------------------------------------------------------------------- 1 | :Comment : The persistent component of the K current 2 | :Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | :Comment : shifted -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | 7 | NEURON { 8 | SUFFIX K_Pst 9 | USEION k READ ek WRITE ik 10 | RANGE gK_Pstbar, gK_Pst, ik 11 | } 12 | 13 | UNITS { 14 | (S) = (siemens) 15 | (mV) = (millivolt) 16 | (mA) = (milliamp) 17 | } 18 | 19 | PARAMETER { 20 | gK_Pstbar = 0.00001 (S/cm2) 21 | } 22 | 23 | ASSIGNED { 24 | v (mV) 25 | ek (mV) 26 | ik (mA/cm2) 27 | gK_Pst (S/cm2) 28 | mInf 29 | mTau 30 | hInf 31 | hTau 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | gK_Pst = gK_Pstbar*m*m*h 42 | ik = gK_Pst*(v-ek) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | LOCAL qt 59 | qt = 2.3^((34-21)/10) 60 | UNITSOFF 61 | v = v + 10 62 | mInf = (1/(1 + exp(-(v+1)/12))) 63 | if(v<-50){ 64 | mTau = (1.25+175.03*exp(-v * -0.026))/qt 65 | }else{ 66 | mTau = ((1.25+13*exp(-v*0.026)))/qt 67 | } 68 | hInf = 1/(1 + exp(-(v+54)/-11)) 69 | hTau = (360+(1010+24*(v+55))*exp(-((v+75)/48)^2))/qt 70 | v = v - 10 71 | UNITSON 72 | } 73 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/mechanisms/K_Tst.mod: -------------------------------------------------------------------------------- 1 | :Comment : The transient component of the K current 2 | :Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000 3 | :Comment : shifted -10 mv to correct for junction potential 4 | :Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21 5 | 6 | NEURON { 7 | SUFFIX K_Tst 8 | USEION k READ ek WRITE ik 9 | RANGE gK_Tstbar, gK_Tst, ik 10 | } 11 | 12 | UNITS { 13 | (S) = (siemens) 14 | (mV) = (millivolt) 15 | (mA) = (milliamp) 16 | } 17 | 18 | PARAMETER { 19 | gK_Tstbar = 0.00001 (S/cm2) 20 | } 21 | 22 | ASSIGNED { 23 | v (mV) 24 | ek (mV) 25 | ik (mA/cm2) 26 | gK_Tst (S/cm2) 27 | mInf 28 | mTau 29 | hInf 30 | hTau 31 | } 32 | 33 | STATE { 34 | m 35 | h 36 | } 37 | 38 | BREAKPOINT { 39 | SOLVE states METHOD cnexp 40 | gK_Tst = gK_Tstbar*(m^4)*h 41 | ik = gK_Tst*(v-ek) 42 | } 43 | 44 | DERIVATIVE states { 45 | rates() 46 | m' = (mInf-m)/mTau 47 | h' = (hInf-h)/hTau 48 | } 49 | 50 | INITIAL{ 51 | rates() 52 | m = mInf 53 | h = hInf 54 | } 55 | 56 | PROCEDURE rates(){ 57 | LOCAL qt 58 | qt = 2.3^((34-21)/10) 59 | 60 | UNITSOFF 61 | v = v + 10 62 | mInf = 1/(1 + exp(-(v+0)/19)) 63 | mTau = (0.34+0.92*exp(-((v+71)/59)^2))/qt 64 | hInf = 1/(1 + exp(-(v+66)/-10)) 65 | hTau = (8+49*exp(-((v+73)/23)^2))/qt 66 | v = v - 10 67 | UNITSON 68 | } 69 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/mechanisms/NaTa_t.mod: -------------------------------------------------------------------------------- 1 | :Reference :Colbert and Pan 2002 2 | 3 | NEURON { 4 | SUFFIX NaTa_t 5 | USEION na READ ena WRITE ina 6 | RANGE gNaTa_tbar, gNaTa_t, ina 7 | } 8 | 9 | UNITS { 10 | (S) = (siemens) 11 | (mV) = (millivolt) 12 | (mA) = (milliamp) 13 | } 14 | 15 | PARAMETER { 16 | gNaTa_tbar = 0.00001 (S/cm2) 17 | } 18 | 19 | ASSIGNED { 20 | v (mV) 21 | ena (mV) 22 | ina (mA/cm2) 23 | gNaTa_t (S/cm2) 24 | mInf 25 | mTau 26 | mAlpha 27 | mBeta 28 | hInf 29 | hTau 30 | hAlpha 31 | hBeta 32 | } 33 | 34 | STATE { 35 | m 36 | h 37 | } 38 | 39 | BREAKPOINT { 40 | SOLVE states METHOD cnexp 41 | gNaTa_t = gNaTa_tbar*m*m*m*h 42 | ina = gNaTa_t*(v-ena) 43 | } 44 | 45 | DERIVATIVE states { 46 | rates() 47 | m' = (mInf-m)/mTau 48 | h' = (hInf-h)/hTau 49 | } 50 | 51 | INITIAL{ 52 | rates() 53 | m = mInf 54 | h = hInf 55 | } 56 | 57 | PROCEDURE rates(){ 58 | LOCAL qt 59 | qt = 2.3^((34-21)/10) 60 | 61 | UNITSOFF 62 | if(v == -38){ 63 | v = v+0.0001 64 | } 65 | mAlpha = (0.182 * (v- -38))/(1-(exp(-(v- -38)/6))) 66 | mBeta = (0.124 * (-v -38))/(1-(exp(-(-v -38)/6))) 67 | mTau = (1/(mAlpha + mBeta))/qt 68 | mInf = mAlpha/(mAlpha + mBeta) 69 | 70 | if(v == -66){ 71 | v = v + 0.0001 72 | } 73 | 74 | hAlpha = (-0.015 * (v- -66))/(1-(exp((v- -66)/6))) 75 | hBeta = (-0.015 * (-v -66))/(1-(exp((-v -66)/6))) 76 | hTau = (1/(hAlpha + hBeta))/qt 77 | hInf = hAlpha/(hAlpha + hBeta) 78 | UNITSON 79 | } -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/mechanisms/NaTs2_t.mod: -------------------------------------------------------------------------------- 1 | :Reference :Colbert and Pan 2002 2 | :comment: took the NaTa and shifted both activation/inactivation by 6 mv 3 | 4 | NEURON { 5 | SUFFIX NaTs2_t 6 | USEION na READ ena WRITE ina 7 | RANGE gNaTs2_tbar, gNaTs2_t, ina 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gNaTs2_tbar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ena (mV) 23 | ina (mA/cm2) 24 | gNaTs2_t (S/cm2) 25 | mInf 26 | mTau 27 | mAlpha 28 | mBeta 29 | hInf 30 | hTau 31 | hAlpha 32 | hBeta 33 | } 34 | 35 | STATE { 36 | m 37 | h 38 | } 39 | 40 | BREAKPOINT { 41 | SOLVE states METHOD cnexp 42 | gNaTs2_t = gNaTs2_tbar*m*m*m*h 43 | ina = gNaTs2_t*(v-ena) 44 | } 45 | 46 | DERIVATIVE states { 47 | rates() 48 | m' = (mInf-m)/mTau 49 | h' = (hInf-h)/hTau 50 | } 51 | 52 | INITIAL{ 53 | rates() 54 | m = mInf 55 | h = hInf 56 | } 57 | 58 | PROCEDURE rates(){ 59 | LOCAL qt 60 | qt = 2.3^((34-21)/10) 61 | 62 | UNITSOFF 63 | if(v == -32){ 64 | v = v+0.0001 65 | } 66 | mAlpha = (0.182 * (v- -32))/(1-(exp(-(v- -32)/6))) 67 | mBeta = (0.124 * (-v -32))/(1-(exp(-(-v -32)/6))) 68 | mInf = mAlpha/(mAlpha + mBeta) 69 | mTau = (1/(mAlpha + mBeta))/qt 70 | 71 | if(v == -60){ 72 | v = v + 0.0001 73 | } 74 | hAlpha = (-0.015 * (v- -60))/(1-(exp((v- -60)/6))) 75 | hBeta = (-0.015 * (-v -60))/(1-(exp((-v -60)/6))) 76 | hInf = hAlpha/(hAlpha + hBeta) 77 | hTau = (1/(hAlpha + hBeta))/qt 78 | UNITSON 79 | } -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/mechanisms/SK_E2.mod: -------------------------------------------------------------------------------- 1 | : SK-type calcium-activated potassium current 2 | : Reference : Kohler et al. 1996 3 | 4 | NEURON { 5 | SUFFIX SK_E2 6 | USEION k READ ek WRITE ik 7 | USEION ca READ cai 8 | RANGE gSK_E2bar, gSK_E2, ik 9 | } 10 | 11 | UNITS { 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | (mM) = (milli/liter) 15 | } 16 | 17 | PARAMETER { 18 | v (mV) 19 | gSK_E2bar = .000001 (mho/cm2) 20 | zTau = 1 (ms) 21 | ek (mV) 22 | cai (mM) 23 | } 24 | 25 | ASSIGNED { 26 | zInf 27 | ik (mA/cm2) 28 | gSK_E2 (S/cm2) 29 | } 30 | 31 | STATE { 32 | z FROM 0 TO 1 33 | } 34 | 35 | BREAKPOINT { 36 | SOLVE states METHOD cnexp 37 | gSK_E2 = gSK_E2bar * z 38 | ik = gSK_E2 * (v - ek) 39 | } 40 | 41 | DERIVATIVE states { 42 | rates(cai) 43 | z' = (zInf - z) / zTau 44 | } 45 | 46 | PROCEDURE rates(ca(mM)) { 47 | if(ca < 1e-7){ 48 | ca = ca + 1e-07 49 | } 50 | zInf = 1/(1 + (0.00043 / ca)^4.8) 51 | } 52 | 53 | INITIAL { 54 | rates(cai) 55 | z = zInf 56 | } 57 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/mechanisms/SKv3_1.mod: -------------------------------------------------------------------------------- 1 | :Comment : 2 | :Reference : : Characterization of a Shaw-related potassium channel family in rat brain, The EMBO Journal, vol.11, no.7,2473-2486 (1992) 3 | 4 | NEURON { 5 | SUFFIX SKv3_1 6 | USEION k READ ek WRITE ik 7 | RANGE gSKv3_1bar, gSKv3_1, ik 8 | } 9 | 10 | UNITS { 11 | (S) = (siemens) 12 | (mV) = (millivolt) 13 | (mA) = (milliamp) 14 | } 15 | 16 | PARAMETER { 17 | gSKv3_1bar = 0.00001 (S/cm2) 18 | } 19 | 20 | ASSIGNED { 21 | v (mV) 22 | ek (mV) 23 | ik (mA/cm2) 24 | gSKv3_1 (S/cm2) 25 | mInf 26 | mTau 27 | } 28 | 29 | STATE { 30 | m 31 | } 32 | 33 | BREAKPOINT { 34 | SOLVE states METHOD cnexp 35 | gSKv3_1 = gSKv3_1bar*m 36 | ik = gSKv3_1*(v-ek) 37 | } 38 | 39 | DERIVATIVE states { 40 | rates() 41 | m' = (mInf-m)/mTau 42 | } 43 | 44 | INITIAL{ 45 | rates() 46 | m = mInf 47 | } 48 | 49 | PROCEDURE rates(){ 50 | UNITSOFF 51 | mInf = 1/(1+exp(((v -(18.700))/(-9.700)))) 52 | mTau = 0.2*20.000/(1+exp(((v -(-46.560))/(-44.140)))) 53 | UNITSON 54 | } 55 | 56 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/run_RmpRiTau_py.sh: -------------------------------------------------------------------------------- 1 | nrnivmodl ./mechanisms 2 | ./run_RmpRiTau.py "$@" 3 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/run_hoc.sh: -------------------------------------------------------------------------------- 1 | nrnivmodl ./mechanisms 2 | nrngui mosinit.hoc 3 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/run_py.sh: -------------------------------------------------------------------------------- 1 | nrnivmodl ./mechanisms 2 | 3 | # Use for python 2.6+ 4 | python ./run.py "$@" 5 | 6 | # Use for python 3.4+ 7 | # python3 ./run.py "$@" 8 | -------------------------------------------------------------------------------- /YRE2016/NMC/L5_TTPC2_cADpyr232_1/synapses/mtype_map.tsv: -------------------------------------------------------------------------------- 1 | 0 L1_DAC 2 | 1 L1_NGC-DA 3 | 2 L1_NGC-SA 4 | 3 L1_HAC 5 | 4 L1_DLAC 6 | 5 L1_SLAC 7 | 6 L23_PC 8 | 7 L23_MC 9 | 8 L23_BTC 10 | 9 L23_DBC 11 | 10 L23_BP 12 | 11 L23_NGC 13 | 12 L23_LBC 14 | 13 L23_NBC 15 | 14 L23_SBC 16 | 15 L23_ChC 17 | 16 L4_PC 18 | 17 L4_SP 19 | 18 L4_SS 20 | 19 L4_MC 21 | 20 L4_BTC 22 | 21 L4_DBC 23 | 22 L4_BP 24 | 23 L4_NGC 25 | 24 L4_LBC 26 | 25 L4_NBC 27 | 26 L4_SBC 28 | 27 L4_ChC 29 | 28 L5_TTPC1 30 | 29 L5_TTPC2 31 | 30 L5_UTPC 32 | 31 L5_STPC 33 | 32 L5_MC 34 | 33 L5_BTC 35 | 34 L5_DBC 36 | 35 L5_BP 37 | 36 L5_NGC 38 | 37 L5_LBC 39 | 38 L5_NBC 40 | 39 L5_SBC 41 | 40 L5_ChC 42 | 41 L6_TPC_L1 43 | 42 L6_TPC_L4 44 | 43 L6_UTPC 45 | 44 L6_IPC 46 | 45 L6_BPC 47 | 46 L6_MC 48 | 47 L6_BTC 49 | 48 L6_DBC 50 | 49 L6_BP 51 | 50 L6_NGC 52 | 51 L6_LBC 53 | 52 L6_NBC 54 | 53 L6_SBC 55 | 54 L6_ChC 56 | -------------------------------------------------------------------------------- /YRE2016/NMC/README.md: -------------------------------------------------------------------------------- 1 | ## Neocortical Microcircuit Collaboration Portal (NMC Portal) 2 | 3 | This portal provides an online public resource of the Blue Brain Project's first release of a **digital reconstruction of the microcircuitry** of juvenile Rat somatosensory cortex, access to experimental data sets used in the reconstruction, and the resulting models. 4 | 5 | URL: https://bbp.epfl.ch/nmc-portal/welcome 6 | 7 | From the NMC portal we can download e.g. a model of a Layer 5 Thick Tufted Pyramidal cell: 8 | https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L5_TTPC2_cADpyr/details 9 | 10 | This model is also available in this repository [here](L5\_TTPC2\_cADpyr232\_1) 11 | 12 | When you run this model according to these instructions: 13 | 14 | https://bbp.epfl.ch/nmc-portal/tools 15 | 16 | You get the following to see the following GUI: 17 | 18 | ![NMC model package GUI](nmc_package_gui.png) 19 | -------------------------------------------------------------------------------- /YRE2016/NMC/nmc_package_gui.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BlueBrain/SimulationTutorials/44fa01c22bc83fbbe8a01d3580de75ffadf92ea4/YRE2016/NMC/nmc_package_gui.png -------------------------------------------------------------------------------- /YRE2016/Neuron/README.md: -------------------------------------------------------------------------------- 1 | ## Neuron simulator tutorial 2 | 3 | The first part of the tutorial consists an introduction to the **Neuron simulator** itself. 4 | 5 | The tutorial is explained in the following notebook: [Neuron simulator tutorial.ipynb](Neuron%20simulator%20tutorial.ipynb) 6 | 7 | This notebook can be run from a browser: [binder instance](http://mybinder.org/repo/BlueBrain/SimulationTutorials/YRE2016/Neuron/Neuron%20simulator%20tutorial.ipynb) 8 | -------------------------------------------------------------------------------- /YRE2016/README.md: -------------------------------------------------------------------------------- 1 | # Neuron modeling demo @ HBP Young Research Event 2016 2 | 3 | This demo consists of four parts: 4 | * [**Neuron simulator**](Neuron/) 5 | * [**NMC portal**](NMC/) 6 | * [**eFEL**](eFEL/) 7 | * [**BluePyOpt**](BluePyOpt/) 8 | 9 | Click on the links above to jump to the respective tutorial pages. 10 | 11 | ## Binder instances 12 | 13 | Most examples in this demo can be run from a web browser, thanks to Binder (http://mybinder.org/, supported by The Freeman Lab @ HHMI Janelia Research Campus). 14 | 15 | To access the Binder instance set up for this demo, visit: 16 | http://mybinder.org/repo/BlueBrain/SimulationTutorials/YRE2016 17 | 18 | ## Extra material 19 | 20 | A **Google drive** was created with **extra material** 21 | 22 | https://drive.google.com/open?id=0B5FLVTgErnMSc200LWFBQVMwOVU 23 | 24 | This drive contains the **slides**, and a **Virtual Machine** that can be used to run the demoed software. 25 | -------------------------------------------------------------------------------- /YRE2016/eFEL/README.md: -------------------------------------------------------------------------------- 1 | ## eFEL 2 | 3 | The **Electrophys Feature Extraction Library** (eFEL) allows neuroscientists to automatically extract features from time series data recorded from neurons (both in vitro and in silico). Examples are the action potential width and amplitude in voltage traces recorded during whole-cell patch clamp experiments. The user of the library provides a set of traces and selects the features to be calculated. The library will then extract the requested features and return the values to the user. 4 | 5 | https://github.com/BlueBrain/eFEL 6 | 7 | The tutorial is explained in the following notebook: [efel.ipynb](efel.ipynb) 8 | 9 | This notebook can be run from a browser: [binder instance](http://mybinder.org/repo/BlueBrain/SimulationTutorials/YRE2016/eFEL/efel.ipynb) 10 | --------------------------------------------------------------------------------