NWB Explorer

NWB Explorer is an application that can be used by scientists to read, visualize and explore the content of NWB 2 files.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

Below you will find the software you need to install to use nwb explorer (and the versions we used)

• Git (2.17.0).
• Node (9.11.1) and npm (6.0.0).
• Redis-Server (4.0.9).
• Python 3 (3.6.5), pip (10.0.1) and Python3-tk.

Python Dependencies

pip install -r requirements.txt

or

• Django (1.9). pip install django
• Pygeppeto_server. git clone https://github.com/MetaCell/pygeppetto-django.git && cd pygeppetto-django && git checkout development && pip install -e .
• Pygeppeto_model.git clone https://github.com/openworm/pygeppetto.git && cd pygeppetto && git checkout manager && pip install -e .
• Pyecore (0.8.1). pip install pyecore
• Pynwb. git clone https://github.com/NeurodataWithoutBorders/pynwb.git && cd pynwb && git checkout dev && pip install -e .
• Seaborn (0.8.1). pip install seaborn

Installing

A step by step instructions to get a development env running

git clone https://github.com/tarelli/nwb-explorer
cd nwb-explorer
mkdir static
cd static
git clone https://github.com/openworm/org.geppetto.frontend
cd org.geppetto.frontend/src/main/webapp/extensions
git clone https://github.com/tarelli/geppetto-nwbexplorer
cd ..
/bin/cp -rf ../../../../../GeppettoConfiguration.json .
npm install
npm run build-dev-noTest

Deployment

Run the redis-server manually:

OSX

nohup redis-server &

Linux

redis-server &

Then, on the nwb-explorer folder, run :

python manage.py runserver

How to use

How to develop

Any change you make in the python code will be automatically redeployed by the Django server.

JS/HTML code can be found inside static/org.geppetto.frontend/src/main/webapp/. The code needs to be rebuilt with webpack everytime there is a change. The recommended way is to run in /static/org.geppetto.frontend/src/main/webapp/ this command:

npm run build-dev-noTest:watch

Running the tests

python manage.py test

Built With

• Django - The web framework used
• Geppetto - Used to build a web-based application to visualize and simulate the NWB 2.0 files.

Authors

• Matteo Cantarelli (MetaCell)
• Giovanni Idili (MetaCell)

See also the list of contributors who participated in this project.