DOI: 10.5281/zenodo.11402578
title: Dataset related to "A connectome manipulation framework for the systematic and reproducible study of structure-function relationships through simulations"

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: 10.1162/netn_a_00429). It contains the resulting data of the manipulated SSCx network model, such as benchmarks, 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.

Update 25/09/2024 (v2): Added benchmark results for assessing strong and weak scaling behavior of connectome rewiring.



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).
description: 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:



1st order - DOI: 10.5281/zenodo.12071006

2nd order - DOI: 10.5281/zenodo.12077952

3rd order - DOI: 10.5281/zenodo.12078722

4th order - DOI: 10.5281/zenodo.12080631

5th order - DOI: 10.5281/zenodo.12082177



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)



benchmarks.xz … Benchmark results related to strong/weak scaling behavior



runtimes_strong_scaling.csv ... Runtimes from strong scaling tests

runtimes_weak_scaling.csv ... Runtimes from weak scaling tests

nodesets_weak_scaling.json ... Node set definitions used in weak scaling tests
description: 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)