Blue Brain data

There is a newer version of the record available.

Published June 18, 2024 | Version v1
Dataset Open

Dataset related to "A connectome manipulation framework for the systematic and reproducible study of structure-function relationships through simulations"

Creators

  • 1. Blue Brain Project, EPFL, Switzerland

Description

This is an accompanying dataset to the article with the title "A connectome manipulation framework for the systematic and reproducible study of structure-function relationships through simulations" (DOI: 10.1101/2024.05.24.593860). It contains the resulting data of the manipulated SSCx network model, such as fitted stochastic models, manipulated connectomes, structural validations, as well as simulation data and analysis results.

The corresponding repository with code, configuration files, and detailed instructions for reproducing the results in this dataset as well as generating the results figures in the accompanying article is available here: https://github.com/BlueBrain/sscx-connectome-manipulations

The underlying Connectome-Manipulator software is available here: https://github.com/BlueBrain/connectome-manipulator

Additional requirement: Original SSCx network model (DOI: 10.5281/zenodo.8026353)

ℹ️ Disclaimer: Some results may have been produced with an older version of Connectome-Manipulator, so slight differences might be possible when re-running with the latest version.

Funding

Funding provided by the Swiss government’s ETH Board to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL).

Table of contents

  • interneuron_rewiring.xz … Data/results related to the interneuron rewiring experiment
    • connectivity_matrices/ … Input ConnectivityMatrix object
    • circuits/ … New SONATA circuit with rewired connectome
    • model_building/ … Results from model fitting
    • structural_comparator/ … Results from structural comparison
    • simulations/ … Results from simulation campaigns
    • analysis/ … Analysis results from CortexETL
  • simplified_connectomes.xz … Data/results related to the simplified connectomes experiment
    • circuits/ … Readme pointing to separate datasets containing the five SONATA circuits with rewired (simplified) connectomes:
    • model_building/ … Results from model fitting
    • model_validation/ … Results from model order validation
    • structural_comparator/ … Results from structural comparison
    • missing_synapses/ … Results from missing synapses estimation
    • simulations/ … Results from calibration simulation campaigns
    • analysis/ … Calibration analysis results from CortexETL
    • calibration/ … Calibration data frames as .parquet files (order0 = original)

Notes

Uncompress: tar -xf <filename>.xz

For rewired circuits under circuits/:

  • Download and uncompress the original network model (DOI: 10.5281/zenodo.8026353)
  • EITHER: Replace edges.h5 from the original SSCx network model by extracted edges.h5 file
  • OR: Adjust the path references in circuit_config<_tc>.json from the extracted circuit pointing to the folder location of the original SSCx network model

For simulation data under simulations/:

  • Adjust path references in simulation_config.json according to the respective circuit location
  • For re-running simulations, follow simulation instruction of the original network model (DOI: 10.5281/zenodo.8026353)

Files

Files (40.8 GB)

Name Size Download all
md5:7461b0b061eb93cfc2a5ec5ae6c3a934
37.0 GB Download
md5:90e40f8d97b092eb8e813e2aac7098cd
3.8 GB Download

Additional details

Has part
Dataset: 10.5281/zenodo.12071006 (DOI)
Dataset: 10.5281/zenodo.12077952 (DOI)
Dataset: 10.5281/zenodo.12078722 (DOI)
Dataset: 10.5281/zenodo.12080631 (DOI)
Dataset: 10.5281/zenodo.12082177 (DOI)
Is derived from
Dataset: 10.5281/zenodo.8026353 (DOI)
Is published in
Preprint: 10.1101/2024.05.24.593860 (DOI)
Is referenced by
Software: https://github.com/BlueBrain/connectome-manipulator (URL)
Is required by
Software: https://github.com/BlueBrain/sscx-connectome-manipulations (URL)