Human-L2-3-Cortical-Microcircuit/NeuroML2/Readme.md

This folder contains versions of model components standardised in NeuroML2 format.

Learn more about NeuroML here: https://docs.neuroml.org

Files/folders and their descriptions

• tests: tests with original Neuron cell model descriptions
• channels: all channel definitions
• synapses: all synapse definitions
• rotated_cells: folder storing all rotated cells with tonic inhibition (not tracked in Git, so you may have to re-run the network creation script to regenerate these files)
• cell_plots: plots of NeuroML cell morphologies and channel properties

• mod: original Neuron mod files and plots of their properties

• cellmorph2nml.py: exports the Neuron cell morphology to NeuroML format

• postprocess_cells.py: post process the NeuroML morphology files to add biophysics to the cells

• convert_cells_to_neuroml.sh: script to run the above two python scripts

• getinfoneuroml.py: gets information about NeuroML cell models

• create_test_network.py: creates a test network to test for validation

• create_omv_tests.py: script to create OMV test templates

• nml_main.py: main script for creation of network and simulation

These files are created for different network scales:

• lems_component*.xml: files including LEMS definitions for inclusion into the LEMS simulation files
• LEMS*xml: LEMS simulation scripts
• HL23Net*.net.nml: Network description files

NeuroML files are stored in a git-annex repository

Because of the large number of files and large sizes of the NeuroML files, not all files can be stored on GitHub, which limits files to 100Mb. These large files are are stored on g-node which supports large files using git-annex. If you want to obtain these, please follow these steps.

https://gin.g-node.org/ankursinha/Human-L2-3-Cortical-Microcircuit

Install git-annex

It is a tool that allows for version control of large files, and is used by other tools like datalad. Installation instructions can be found at:

https://git-annex.branchable.com/install/

Clone the G-node repository:

git clone https://gin.g-node.org/ankursinha/Human-L2-3-Cortical-Microcircuit
git annex init

You can also use the gin client if you wish. Instructions are provided on g-node.

The files that are managed by git-annex will only be shown as links. This way, they don't take up space on your local machine until you fetch them. You can fetch individual files:

git annex get <path to file>

or get all of them:

git annex sync --content

If you don't need a file, you can "drop" it from your local hard disk:

git annex drop <path to file>