neurondm

A data model for neuron types.

Neuron Types

For a an overview of how to use neuron-lang to describing neuron types please see this introduction. For a more in-depth look at the structures that neurons translate to in OWL and some of the modelling decisions related to which reasoner you plan to use see an Overview of OWL modelling decisions

To get started, follow the installation instructions below and then include from neurondm.lang import * in your import statements.

If you want to get started quickly, take a look at the notebook of examples of how to use neuron-lang to create new neurons

If you want to use neurondm in a jupyter notebook, see the docs for how to set up neurondm for jupyter notebooks.

Installation

You can install neurondm using the following commands.

Basics

pip install neurondm

Once installation is complete you should be able to run the following python code.

from neurondm import *
config = Config()
n = Neuron(Phenotype('TEMP:myPhenotype'))
config.write()
config.write_python()

SciGraph API

Set the API key in a separate terminal to avoid losing additional history after setting the api key.

unset HISTFILE
ontutils set scigraph-api-key <key>

Once that is done you should be able to run the following.

python -m neurondm.models.huang2017

NIF-Ontology

To work with the NIF-Ontology and build existing models you need to clone the ontology repository and set your SciGraph API key or set up a local SciGraph instance.

git clone https://github.com/SciCrunch/NIF-Ontology.git
ontutils set ontology-local-repo ./NIF-Ontology
pushd ./NIF-Ontology
git checkout neurons
popd

Further configuration

If you need more details on configuration see the pyontutils configuration section.

Use outside the NIF ontology

It is possible to use neurondm outside the NIF ontology and the pyontutils repository, however it has not been fully abstracted to support that use case. If you want to do something more complicated than the example shown in the installation section you will need to perform some additional configuration. The way to do this is to set all the relevant values via neurondm.Config. See test_neruons.test_roundtrip_py for an example.