Command Line Interface¶

There are 2 entry points in the command line interface:

A command: Can be written in a command line prompt such as the Terminal on Linux or CMD on Windows.
The shell: Can be opened by giving typing bsb into a command line prompt.

Scaffold shell¶

The scaffold shell is an interactive environment where commands can be given. Unlike with the command line your state is maintained in between commands.

Opening the shell¶

Open your favorite command line prompt and if the scaffold package is succesfully installed the bsb command should be available.

You can close the shell by typing exit.

The base state¶

After opening the shell it will be in the base (default) state. In this state you have access to several commands like opening morphology repositories or hdf5 files.

List of base commands¶

open mr <filename>: Open a morphology repository. See List of mr commands
open hdf5 <filename>: Open an HDF5 file. See List of hdf5 commands:

The morphology repository state¶

In this state you can modify the morphology repository. After you’ve opened a repository the shell will display a prefix:

repo <filename>:

List of mr commands¶

list all: Show a list of all morphologies available in the repository.
list voxelized: Show a list of all morphologies with voxel cloud information available.
import repo <filename>: Import all morphologies from another repository. -f/--overwrite: Overwrite existing morphologies.
import swc <file> <name>: Import an SWC morphology and store it under the given name.
arborize <class> <name>: Import an Arborize model.
remove <name>: Remove a morphology from the repository.
voxelize <name> [<n=130>]: Generate a voxel cloud of n (optional, default=130) voxels for the morphology.
plot <name>: Plot the morphology.
close: Exit the mr state.

The HDF5 state¶

In this state you can view the structure of HDF5 files.

List of hdf5 commands:¶

view: Create a hierarchical print of the HDF5 file, groups, datasets, and attributes.
plot: Display a plot of the HDF5 network.

List of command line commands¶

Note

Parameters included between square brackets are optional, the brackets need not be included in the actual command.

compile¶

bsb [-v=1 -c=mouse_cerebellum] compile [-p -o]

Compiles a network architecture: Places cells in a simulated volume and connects them to eachother. All this information is then stored in a single HDF5 file.

-v, --verbosity: Sets the verbosity of the scaffold. The higher the verbosity the more console output will be generated.
-c, --configuration: Sets the configuration file that will be used.
-p: Plot the created network.
-o=<file>, --output=<file>: Output the result to a specific file.

simulate¶

bsb [-v=1] simulate <name> [-rc=<config>] --hdf5=<file>

Run a simulation from a compiled network architecture.

-v, --verbosity: Sets the verbosity of the scaffold. The higher the verbosity the more console output will be generated.
-c, --configuration: Sets the configuration file that will be used.
name: Name of the simulation.
--hdf5: Path to the compiled network architecture.
-rc, --reconfigure: The path to a new configuration file for the HDF5 file.

run¶

bsb [-v=1 -c=mouse_cerebellum] run <name> [-p]

Run a simulation creating a new network architecture.

-v, --verbosity: Sets the verbosity of the scaffold. The higher the verbosity the more console output will be generated.
-c, --configuration: Sets the configuration file that will be used.
-p: Plot the created network.

plot¶

bsb plot <file>

Create a plot of the network in an HDF5 file.