bmtool 0.1.6

BMTools

bmtools

A collection of scripts to make developing networks in BMTK easier.

Getting Started

Installation

pip install bmtool

For developers who will be pulling down additional updates to this repository regularly use the following instead.

git clone https://github.com/tjbanks/bmtools
cd bmtools
python setup.py develop

Then download updates (from this directory) with

git pull

Example Use

> cd your_bmtk_model_directory
> bmtools
Usage: bmtools [OPTIONS] COMMAND [ARGS]...

Options:
  --verbose  Verbose printing
  --help     Show this message and exit.

Commands:
  debug
  plot
  util

>  
> bmtools plot 
Usage: bmtools plot [OPTIONS] COMMAND [ARGS]...

Options:
  --config PATH  Configuration file to use, default: "simulation_config.json"
  --no-display   When set there will be no plot displayed, useful for saving
                 plots
  --help         Show this message and exit.

Commands:
  connection  Display information related to neuron connections
  positions   Plot cell positions for a given set of populations
  raster      Plot the spike raster for a given population
  report      Plot the specified report using BMTK's default report plotter
>
> bmtools plot positions

Single Cell Tuning

From a BMTK Model directory containing a simulation_config.json file:

bmtools util cell tune --builder

For non-BMTK cell tuning:

bmtools util cell --template TemplateFile.hoc --mod-folder ./ tune --builder

FIR Curve plotting

> bmtools util cell fir --help
Usage: bmtools util cell fir [OPTIONS]

  Creates a NEURON GUI window with FI curve and passive properties

Options:
  --title TEXT
  --min-pa INTEGER   Min pA for injection
  --max-pa INTEGER   Max pA for injection
  --increment FLOAT  Increment the injection by [i] pA
  --tstart INTEGER   Injection start time
  --tdur INTEGER     Duration of injection default:1000ms
  --advanced         Interactive dialog to select injection and recording
                     points
  --help             Show this message and exit.

> bmtools util cell fir
? Select a cell:  (Use arrow keys)
 » CA3PyramidalCell
   DGCell
   IzhiCell
   IzhiCell_BC
   IzhiCell_EC
   IzhiCell_EC2
   IzhiCell_EC_BIO
   IzhiCell_EmoExcitatory
   IzhiCell_EmoInhibitory
   IzhiCell_OLM
   IzhiCell_int

VHalf Segregation Module

Based on the Alturki et al. (2016) paper.

Segregate your channel activation for an easier time tuning your cells.

> bmtools util cell vhseg --help

Usage: bmtools util cell vhseg [OPTIONS]

  Alturki et al. (2016) V1/2 Automated Segregation Interface, simplify
  tuning by separating channel activation

Options:
  --title TEXT
  --tstop INTEGER
  --outhoc TEXT         Specify the file you want the modified cell template
                        written to
  --outfolder TEXT      Specify the directory you want the modified cell
                        template and mod files written to (default: _seg)
  --outappend           Append out instead of overwriting (default: False)
  --debug               Print all debug statements
  --fminpa INTEGER      Starting FIR Curve amps (default: 0)
  --fmaxpa INTEGER      Ending FIR Curve amps (default: 1000)
  --fincrement INTEGER  Increment the FIR Curve amps by supplied pA (default:
                        100)
  --infvars TEXT        Specify the inf variables to plot, skips the wizard.
                        (Comma separated, eg: inf_mech,minf_mech2,ninf_mech2)
  --segvars TEXT        Specify the segregation variables to globally set,
                        skips the wizard. (Comma separated, eg:
                        mseg_mech,nseg_mech2)
  --eleak TEXT          Specify the eleak var manually
  --gleak TEXT          Specify the gleak var manually
  --othersec TEXT       Specify other sections that a window should be
                        generated for (Comma separated, eg: dend[0],dend[1])
  --help                Show this message and exit.

Examples

Wizard Mode (Interactive)

> bmtool util cell vhseg

? Select a cell:  CA3PyramidalCell
Using section dend[0]
? Show other sections? (default: No)  Yes
? Select other sections (space bar to select):  done (2 selections)
? Select inf variables to plot (space bar to select):   done (5 selections)
? Select segregation variables [OR VARIABLES YOU WANT TO CHANGE ON ALL SEGMENTS at the same time] (space bar to select):  done (2 selections)

Command Mode (Non-interactive)

bmtool util cell --template CA3PyramidalCell vhseg --othersec dend[0],dend[1] --infvars inf_im --segvars gbar_im --gleak gl_ichan2CA3 --eleak el_ichan2CA3

Example:

Simple models can utilize

bmtool util cell --hoc cell_template.hoc vhsegbuild --build
bmtool util cell --hoc segmented_template.hoc vhsegbuild

ex: https://github.com/tjbanks/two-cell-hco

Planned future features

bmtools build
    Create a starting point network
    Download sample networks

bmtools plot
    Plot variable traces
    Plot spike rasters
    X Plot cell positions
    X Plot connection matricies

bmtools debug 
    X list cell types available for single debug
    X Run a single cell in the network
    Isolate a single cell in the network