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.
- Django (1.11.7).
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 (TODO)
Animation reading files and make some plots goes here
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 (TODO)
Explain how to run the automated tests for this system
Built With
- Django - The web framework used
- Geppetto - Used to build a web-based applications to visualize and simulate the NWB 2.0 files.
Contributing (TODO)
Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.
Authors
See also the list of contributors who participated in this project.