[!WARNING] The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization. Future development will take place at: https://github.com/openbraininstitute/synthdb

SynthDB

Small database to host synthesis-related files.

The synthesis inputs stored in SynthDB are usually created by the synthesis-workflows package and are usually meant to be used by the region-grower package.

Installation

Use pip to install this package:

bash pip install synthdb

For some operations (e.g. create, update or delete operations), this package should be installed in editable mode: bash git clone https://github.com/BlueBrain/synthdb.git cd synthdb pip install -e .

Usage

This package contains a set of configuration files for the synthesis codes and a small database that maps a given set of brain region, mtype and luigi configuration. It also provides several commands to manage the database and to create new sets of configuration files.

The commands are listed in the Command Line Interface page of the documentation.

If you use commands that modify the internal state you will probably want to commit the changes afterwards.

Example

Here is an example of a variety of commands

Prepare environment

bash mkvirtualenv demo_synthdb mkdir /tmp/synthdb_demo cd /tmp/synthdb_demo git clone https://github.com/BlueBrain/synthdb.git pip install -e ./synthdb

Show usage

bash synthdb --help synthdb morphology-release --help synthdb synthesis-inputs --help

Morphology release command

Show list of morphology releases

bash synthdb morphology-release list

Create a new morphology release

bash synthdb morphology-release create a_new_rat_release --gpfs-path rat_release

Check the new entry

bash synthdb morphology-release list

Check the auto-generated pip list of the new entry

bash synthdb morphology-release list --with-pip-list

Remove a morphology release

bash synthdb morphology-release remove a_new_rat_release

Check that the entry was removed

bash synthdb morphology-release list

Synthesis inputs command

Show list of synthesis-inputs

bash synthdb synthesis-inputs list

Show filtered list

bash synthdb synthesis-inputs list --mtype L6_TPC:A

Check that all entries are valid according to the current environment

bash synthdb synthesis-inputs validate

Pull params and distrs for a given entry (one can also pull several or all entries at once)

bash synthdb synthesis-inputs pull --species rat --brain-region sscx --mtype L6_TPC:A --luigi-config luigi_sscx --output-path synth_inputs It is possible to refine the filter using any combination of the --brain-region, --mtype and --luigi-config parameters.

Pull params and distrs for several entries into one file

bash synthdb synthesis-inputs pull --species rat --brain-region sscx --output-path synth_inputs_sscx --concatenate Here all the distributions and parameters of the SSCx brain region are pulled in the tmd_parameters.json and tmd_distributions.json files. It is possible to refine the filter using any combination of the species, --brain-region, --mtype and --luigi-config parameters.

Create a new entry

bash synthdb synthesis-inputs create new_species new_region L6_TPC:A luigi_sscx --parameters-path tmd_parameters_luigi_sscx_sscx_L6_TPC:A.json --distributions-path tmd_distributions_luigi_sscx_sscx_L6_TPC:A.json

Check the new entry

bash synthdb synthesis-inputs list --brain-region new_region

Remove the new entry

bash synthdb synthesis-inputs remove new_species new_region L6_TPC:A luigi_sscx

Rebuild an entry using the morphology release given in the luigi config file

bash synthdb synthesis-inputs rebuild --species rat --brain-region sscx --mtype L6_TPC:A --luigi-config luigi_sscx

Funding & Acknowledgment

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.

For license and authors, see LICENSE.txt and AUTHORS.md respectively.

Copyright © 2022-2024 Blue Brain Project/EPFL