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Neuron Lang setup

Prerequisites
- NIF-Ontology
- The notebook environment for neuron lang support
Running the notebook
If you want to run this on an existing dedicated notebook server

Prerequisites

NIF-Ontology

Neuron Lang depends on a set of core ontology files that define the predicates and complex neuronal phenotypes that are the building blocks for neurons. At the moment these files live in the neurons branch ofthe NIF-Ontology repository. As such, Neuron Lang requires a local copy of the NIF-Ontology repository which has the neurons branch checked out. To accomplish this run the following.

git clone https://github.com/SciCrunch/NIF-Ontology.git`
cd NIF-Ontology
git checkout neurons

The notebook environment for neuron lang support

Install neurondm following the installation and configuration instructions.
If you encounter any issues the most detailed instructions can be found in the setup documentation for bootstrapping a full pyontutils/NIF-Ontology/protc development environment.

Running the notebook

From the outer neurondm folder (../ from the folder of this README) run the following commands.

export SCICRUNCH_API_KEY=$(cat path/to/my/apikey)
cd docs/
jupyter-notebook

At this point your browser should open up with a view of this folder and you should be able to select NeuronLangExample.ipynb and run it.

If you want to run this on an existing dedicated notebook server

Create an issue and I will help you figure out how to get all the dependencies installed.