Si elegans Web-based GUI Tools

Web-based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioural Experiment Definition and Experiment Results Visualisation

This repository contains the open source code of the web-based GUI tools developed within the [FP7 Si-elegans project].

Our goal is to open the developed web-tools to the community.

The web-based GUI tools running instance is available at: [Si-elegans platform online]

Local setup instructions (Tested with python 2.7 in both Windows 10 and Ubuntu 14.04)

1.- Clone repository

2.- Create & activate virtualenv

3.- Run the following commands:

pip install -r requirements_local.txt

python manage.py migrate --settings=mysite.local_settings

python manage.py loaddata sielegans-fixture.json --settings=mysite.local_settings

python manage.py loaddata cenet-fixture.json --settings=mysite.local_settings

python manage.py loaddata lems_ui-fixture.json --settings=mysite.local_settings

python manage.py createcachetable spirit_cache --settings=mysite.local_settings

python manage.py runsslserver --addrport 0.0.0.0:8000 --settings=mysite.local_settings

4.- Open https://127.0.0.1:8000 in your browser. (https!!)(user: demo password: demo)

Notes:

• Admin user creation: python manage.py createsuperuser --settings=mysite.local_settings
• Source code includes examples for Neuron models, Network configuration, Behavioural experiments and results. (See fixtures loaded in local setup instructions).
• Some external modules had to be fixed / modified during integration within the Web-GUI tools, therefore they are included as folders in the source code. (i.e. django_notify, django_nyt, registration, spirit and wiki)
• This development uses [Spirit forum] user extension of the strandard Django user.
• Emulation logic is not included. The Si elegans project includes a FPGA-based emulation, but web-based GUI tools could be integrated with software-based simulation frameworks.
• Emulation dependent GUI's functionality might have limitations in the provided repository setup.
• Configuration keys for certain services have been deleted from code, so some services will not directly work (e.g. mailing (for account registration, for error reporting, ...), Google account-based login, Amazon Web Services)
• Amazon Web Services deployment configuration files are included (i.e. requirements.txt and mysite.settings.py) - This configuration requires filling some account info - Will not directly work as provided.

Contact: [email protected]