Assemblies, synapse clustering and network topology interact with plasticity to explain structure-function relationships of the cortical connectome

Dataset linked to the article with the same title

The model itself is very similar to its non-plastic counterpart under the following DOI: 10.5281/zenodo.7930275, i.e. a 1.5 mm diameter  cortical tissue comprising 211,712 neurons and their connectivity in the front limb and jaw subregions and the dysgranular zone of the Paxinos & Watson rat brain atlas. It's formatted in the open SONATA standard and contains neuron locations and their properties (such as morphological types, cortical layer, etc.), their detailed morphologies, and synaptic connectivity (with all their anatomical and physiological parameters). The main difference from the non-plastic version is the addition of plasticity related parameters to O1/S1nonbarrel_neurons__S1nonbarrel_neurons__chemical/edges.h5. Extrinsic synaptic connections from the thalamus are included in this release, but for inputs from neurons in the remainder of non-barrel somatosensory cortex please see the non-plastic version of the circuit.

Analyzing the model

The model can be analyzed in terms of its anatomy, physiology and connectivity using the packages NeuroM, BlueBrain SNAP and ConnectomeUtilities. (see first Jupyter notebook)

Simulating the model

To simulate the model we'd recommend using out using our open-source simulator Neurodamus. The reference version is the branch nbS1-2023, which is archived under the following DOI: 10.5281/zenodo.8075202. Instructions on how to use the simulator are provided on the GitHub page linked above. Briefly, you'll first have to install Neurodamus. Next, build a "special" executable that include compiled versions of ion channel and synapse models. To do that, follow these instructions, where mod-files-from-released-circuit is replaced by the location of O1/mods on your system. Finally, run a simulation. The specific simulation conditions and stimuli are specified in simulation configuration files. An exemplary simulation configuration is included in this release (simulation_config.zip).

Analyzing simulation results

Simulation results can be analyzed with BlueBrain SNAP, ConnectomeUtilities, and assemblyfire. Notebooks 2-5 go though these analysis and recreate some of the panels from our article. In most cases the notebooks can be run with the shared HDF5 files and don't require running any simulations.

Version 2

Bug fix in simulation_config.json and therefore new version of results (and corresponding notebooks). The underlying circuit model (O1.xz) did not change from v1.

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The development of this dataset 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.