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Data dependencies

This document lists the static data dependencies required by the notebooks.

Feature extraction dependencies

  1. Voltage traces The traces required for these 6 cells
    • C060109A1-SR-C1
    • C060109A3-SR-C1
    • C080501A5-SR-C1
    • C060109A2-SR-C1
    • C070109A4-C1
    • C080501B2-SR-C1

The data is available at feature_extraction/input-traces

Model management dependencies

  1. The following morphologies
    • C060110A2.asc
    • rat_20160316_E2_LH3_cell1.asc
    • C060114A5.asc
    • rp110616_C1_idB.asc
    • rat_20140925_RH1_Exp1_cell2.asc
    • rp110630_P1_idC.asc

They are located at model_management/mm_run_minimal/morphologies

  1. An emodel directory located at model_management/mm_run_minimal/emodels_dir.

The emodel directory contains a list of mechanisms and parameter files.

The mechanisms are:

  • CaDynamics_DC0.mod
  • Ca_HVA.mod
  • Ca_HVA2.mod
  • Ca_LVAst.mod
  • Ih.mod
  • K_Pst.mod
  • K_Tst.mod
  • KdShu2007.mod
  • NaTg.mod
  • NaTg2.mod
  • Nap_Et2.mod
  • SK_E2.mod
  • SKv3_1.mod
  • StochKv2.mod
  • StochKv3.mod

The parameters include other etypes that we are not showing in this notebook. Suggestion: we may delete them.

optimization dependencies

  1. cADpyr_L5TPC_1.pkl file from the optimization results.

The file is located at optimization/opt_module/checkpoints/run.a6e707a/cADpyr_L5TPC_1.pkl.

  1. The emodel directory as well as the mechanisms below.
  • CaDynamics_DC0.mod
  • Ca_HVA.mod
  • Ca_HVA2.mod
  • Ca_LVAst.mod
  • Ih.mod
  • K_Pst.mod
  • K_Tst.mod
  • KdShu2007.mod
  • NaTg.mod
  • NaTg2.mod
  • Nap_Et2.mod
  • SK_E2.mod
  • SKv3_1.mod
  • StochKv2.mod
  • StochKv3.mod
  1. The morphology file used in the optimization is the following. optimization/opt_module/morphologies/C060114A5.asc

Validation dependencies

  1. The experimental data acquired from the literature
  • Berger2001_Fig3.csv
  • Berger2001_Fig3.dig
  • Berger2001_Fig3.png
  • Berger2001_Fig3_2.csv
  • Larkum2001_Fig8.csv
  • Larkum2001_Fig8.dig
  • Larkum2001_Fig8.png
  • Larkum2001_Fig8E.csv
  • Larkum2001_Fig8E.dig
  • Larkum2001_Fig8_2.csv
  • Nevian2007_Fig1.csv
  • Nevian2007_Fig1.dig
  • Nevian2007_Fig1.png
  • Nevian2007_Fig1_2.csv
  • Nevian2007_Fig1h.csv
  • Nevian2007_Fig1h.dig
  • Nevian2007_Fig2.csv
  • Nevian2007_Fig2.dig
  • Nevian2007_Fig2.png
  • Nevian2007_Fig2_2.csv
  • Nevian2007_Fig2_email.csv
  • Nevian2007_Fig4.csv
  • Nevian2007_Fig4.dig
  • Nevian2007_Fig4.png
  • Nevian2007_Fig4_2.csv
  • Nevian2007_SupFig3.png
  • Schiller1995.png
  • StuartSakmann1994_Fig1.csv
  • StuartSakmann1994_Fig1.dig
  • StuartSakmann1994_Fig1.png
  • StuartSakmann1994_Fig1_2.csv

Some of these data are not used in the plots. Suggestion: Perhaps we can remove those.

  1. 1000 morphologies to be validated are located at validation/input/morphologies

  2. the mecombo_emodel.tsv file

This file contains ~200.000 lines Suggestion: perhaps we can remove the lines irrelevant to this notebook.

  1. the following mechanisms
  • CaDynamics_DC0.mod
  • Ca_HVA.mod
  • Ca_HVA2.mod
  • Ca_LVAst.mod
  • Ih.mod
  • K_Pst.mod
  • K_Tst.mod
  • KdShu2007.mod
  • NaTg.mod
  • NaTg2.mod
  • Nap_Et2.mod
  • ProbAMPANMDA_EMS.mod
  • SK_E2.mod
  • SKv3_1.mod
  • StochKv2.mod
  • StochKv3.mod

Licences dependencies

  1. Certain files in the singlecell-optimization setup directories contain the following license information.

""" This file is part of BluePyOpt https://github.com/BlueBrain/BluePyOpt

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License version 3.0 as published by the Free Software Foundation. """

  1. Licences of the mechanisms (MOD files) should be checked