From 1c02c120168d4e2fa7c42ef4f85c0665a1c105b0 Mon Sep 17 00:00:00 2001 From: ilkilic <10600022+ilkilic@users.noreply.github.com> Date: Wed, 14 Feb 2024 16:15:35 +0100 Subject: [PATCH] Add Sonata example (#361) --- .compile_mod.sh | 12 + examples/sonata-network/O1/POm/nodes.h5 | Bin 0 -> 38056 bytes .../edges.h5 | Bin 0 -> 221832 bytes .../O1/S1nonbarrel_neurons/nodes.h5 | Bin 0 -> 26032 bytes examples/sonata-network/O1/VPM/nodes.h5 | Bin 0 -> 41660 bytes .../edges.h5 | Bin 0 -> 225320 bytes .../sonata-network/O1/circuit_config.json | 75 + .../O1/emodels_hoc/dSTUT_L23BP.hoc | 541 + .../O1/emodels_hoc/dSTUT_L2SBC.hoc | 541 + .../O1/emodels_hoc/dSTUT_L4BP.hoc | 541 + .../O1/emodels_hoc/dSTUT_L5BP.hoc | 541 + .../ascii/C230998A-I3_-_Clone_9.asc | 678 + ...-_Scale_x1.000_y1.050_z1.000_-_Clone_9.asc | 678 + ...-_Scale_x1.000_y0.975_z1.000_-_Clone_0.asc | 10301 +++++ ...0301C_idA_-_Scale_x1.000_y1.050_z1.000.asc | 16383 ++++++++ ...-_Scale_x1.000_y1.025_z1.000_-_Clone_0.asc | 12128 ++++++ .../ascii/mtC291001C_idA_-_Clone_2.asc | 14212 +++++++ .../ascii/rp110120_L5-2_idH_-_Clone_3.asc | 33556 ++++++++++++++++ ...-_Scale_x1.000_y1.025_z1.000_-_Clone_1.asc | 33556 ++++++++++++++++ .../ascii/rp110127_L5-3_idI_-_Clone_1.asc | 25987 ++++++++++++ ...-_Scale_x1.000_y0.950_z1.000_-_Clone_0.asc | 25987 ++++++++++++ ...-_Scale_x1.000_y1.050_z1.000_-_Clone_1.asc | 25987 ++++++++++++ ...-_Scale_x1.000_y1.050_z1.000_-_Clone_1.asc | 12702 ++++++ ...-_Scale_x1.000_y0.950_z1.000_-_Clone_4.asc | 14498 +++++++ ...-_Scale_x1.000_y0.975_z1.000_-_Clone_4.asc | 14498 +++++++ examples/sonata-network/O1/node_sets.json | 510 + examples/sonata-network/mechanisms/Ca.mod | 72 + .../mechanisms/CaDynamics_DC0.mod | 57 + .../mechanisms/CaDynamics_E2.mod | 36 + examples/sonata-network/mechanisms/Ca_HVA.mod | 73 + .../sonata-network/mechanisms/Ca_HVA2.mod | 77 + .../sonata-network/mechanisms/Ca_LVAst.mod | 69 + .../sonata-network/mechanisms/DetAMPANMDA.mod | 342 + .../sonata-network/mechanisms/DetGABAAB.mod | 340 + .../sonata-network/mechanisms/GluSynapse.mod | 699 + examples/sonata-network/mechanisms/Ih.mod | 62 + examples/sonata-network/mechanisms/Im.mod | 61 + examples/sonata-network/mechanisms/K_Pst.mod | 72 + examples/sonata-network/mechanisms/K_Tst.mod | 69 + .../sonata-network/mechanisms/KdShu2007.mod | 68 + examples/sonata-network/mechanisms/NaTa_t.mod | 98 + examples/sonata-network/mechanisms/NaTg.mod | 104 + .../sonata-network/mechanisms/NaTs2_t.mod | 98 + .../sonata-network/mechanisms/Nap_Et2.mod | 108 + .../mechanisms/ProbAMPANMDA_EMS.mod | 620 + .../mechanisms/ProbGABAAB_EMS.mod | 624 + examples/sonata-network/mechanisms/README.md | 7 + examples/sonata-network/mechanisms/SK_E2.mod | 57 + examples/sonata-network/mechanisms/SKv3_1.mod | 56 + .../sonata-network/mechanisms/StochKv.mod | 550 + .../sonata-network/mechanisms/StochKv3.mod | 545 + .../mechanisms/TTXDynamicsSwitch.mod | 49 + .../sonata-network/mechanisms/VecStim.mod | 182 + examples/sonata-network/mechanisms/gap.mod | 18 + .../mechanisms/netstim_inhpoisson.mod | 583 + .../sonata-network/simulation_config.json | 43 + examples/sonata-network/sonata-network.ipynb | 479 + tox.ini | 12 +- 58 files changed, 250241 insertions(+), 1 deletion(-) create mode 100755 .compile_mod.sh create mode 100644 examples/sonata-network/O1/POm/nodes.h5 create mode 100644 examples/sonata-network/O1/POm__S1nonbarrel_neurons__chemical/edges.h5 create mode 100644 examples/sonata-network/O1/S1nonbarrel_neurons/nodes.h5 create mode 100644 examples/sonata-network/O1/VPM/nodes.h5 create mode 100644 examples/sonata-network/O1/VPM__S1nonbarrel_neurons__chemical/edges.h5 create mode 100644 examples/sonata-network/O1/circuit_config.json create mode 100644 examples/sonata-network/O1/emodels_hoc/dSTUT_L23BP.hoc create mode 100644 examples/sonata-network/O1/emodels_hoc/dSTUT_L2SBC.hoc create mode 100644 examples/sonata-network/O1/emodels_hoc/dSTUT_L4BP.hoc create mode 100644 examples/sonata-network/O1/emodels_hoc/dSTUT_L5BP.hoc create mode 100644 examples/sonata-network/O1/morphologies/ascii/C230998A-I3_-_Clone_9.asc create mode 100644 examples/sonata-network/O1/morphologies/ascii/C230998A-I3_-_Scale_x1.000_y1.050_z1.000_-_Clone_9.asc create mode 100644 examples/sonata-network/O1/morphologies/ascii/mtC050301A_idC_-_Scale_x1.000_y0.975_z1.000_-_Clone_0.asc create mode 100644 examples/sonata-network/O1/morphologies/ascii/mtC070301C_idA_-_Scale_x1.000_y1.050_z1.000.asc create mode 100644 examples/sonata-network/O1/morphologies/ascii/mtC151200D_idA_-_Scale_x1.000_y1.025_z1.000_-_Clone_0.asc create mode 100644 examples/sonata-network/O1/morphologies/ascii/mtC291001C_idA_-_Clone_2.asc create mode 100644 examples/sonata-network/O1/morphologies/ascii/rp110120_L5-2_idH_-_Clone_3.asc create mode 100644 examples/sonata-network/O1/morphologies/ascii/rp110120_L5-2_idH_-_Scale_x1.000_y1.025_z1.000_-_Clone_1.asc create mode 100644 examples/sonata-network/O1/morphologies/ascii/rp110127_L5-3_idI_-_Clone_1.asc create mode 100644 examples/sonata-network/O1/morphologies/ascii/rp110127_L5-3_idI_-_Scale_x1.000_y0.950_z1.000_-_Clone_0.asc create mode 100644 examples/sonata-network/O1/morphologies/ascii/rp110127_L5-3_idI_-_Scale_x1.000_y1.050_z1.000_-_Clone_1.asc create mode 100644 examples/sonata-network/O1/morphologies/ascii/rp110201_L5-2_idA_-_Scale_x1.000_y1.050_z1.000_-_Clone_1.asc create mode 100644 examples/sonata-network/O1/morphologies/ascii/rp110710_C3_idA_-_Scale_x1.000_y0.950_z1.000_-_Clone_4.asc create mode 100644 examples/sonata-network/O1/morphologies/ascii/rp110710_C3_idA_-_Scale_x1.000_y0.975_z1.000_-_Clone_4.asc create mode 100644 examples/sonata-network/O1/node_sets.json create mode 100644 examples/sonata-network/mechanisms/Ca.mod create mode 100644 examples/sonata-network/mechanisms/CaDynamics_DC0.mod create mode 100644 examples/sonata-network/mechanisms/CaDynamics_E2.mod create mode 100644 examples/sonata-network/mechanisms/Ca_HVA.mod create mode 100644 examples/sonata-network/mechanisms/Ca_HVA2.mod create mode 100644 examples/sonata-network/mechanisms/Ca_LVAst.mod create mode 100644 examples/sonata-network/mechanisms/DetAMPANMDA.mod create mode 100644 examples/sonata-network/mechanisms/DetGABAAB.mod create mode 100644 examples/sonata-network/mechanisms/GluSynapse.mod create mode 100644 examples/sonata-network/mechanisms/Ih.mod create mode 100644 examples/sonata-network/mechanisms/Im.mod create mode 100644 examples/sonata-network/mechanisms/K_Pst.mod create mode 100644 examples/sonata-network/mechanisms/K_Tst.mod create mode 100644 examples/sonata-network/mechanisms/KdShu2007.mod create mode 100644 examples/sonata-network/mechanisms/NaTa_t.mod create mode 100644 examples/sonata-network/mechanisms/NaTg.mod create mode 100644 examples/sonata-network/mechanisms/NaTs2_t.mod create mode 100644 examples/sonata-network/mechanisms/Nap_Et2.mod create mode 100644 examples/sonata-network/mechanisms/ProbAMPANMDA_EMS.mod create mode 100644 examples/sonata-network/mechanisms/ProbGABAAB_EMS.mod create mode 100644 examples/sonata-network/mechanisms/README.md create mode 100644 examples/sonata-network/mechanisms/SK_E2.mod create mode 100644 examples/sonata-network/mechanisms/SKv3_1.mod create mode 100644 examples/sonata-network/mechanisms/StochKv.mod create mode 100644 examples/sonata-network/mechanisms/StochKv3.mod create mode 100644 examples/sonata-network/mechanisms/TTXDynamicsSwitch.mod create mode 100644 examples/sonata-network/mechanisms/VecStim.mod create mode 100644 examples/sonata-network/mechanisms/gap.mod create mode 100644 examples/sonata-network/mechanisms/netstim_inhpoisson.mod create mode 100644 examples/sonata-network/simulation_config.json create mode 100644 examples/sonata-network/sonata-network.ipynb diff --git a/.compile_mod.sh b/.compile_mod.sh new file mode 100755 index 00000000..45fb24bf --- /dev/null +++ b/.compile_mod.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +set -e + +INSTALL_DIR=$1 +MOD_DIR=$2 + +cd ${INSTALL_DIR} + +echo "Building mod files" +rm -rf x86_64 +nrnivmodl ${MOD_DIR} >nrnivmodl.log 2>&1 diff --git a/examples/sonata-network/O1/POm/nodes.h5 b/examples/sonata-network/O1/POm/nodes.h5 new file mode 100644 index 0000000000000000000000000000000000000000..cf08550b07ea3202c4efad9045b78b44bfb62ff7 GIT binary patch literal 38056 zcmeHv30#fc+IJ%&N<7LCNr*@&iP*Qfkc@>yNGe4_#-u@$hP@k
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