BlueNaaS-Subcellular

BlueNaaS-Subcllular was developed as a software environment for simulation of brain molecular networks. It was designed to reach several objectives related to major restrictions of currently available software tools, such as the lack of integration with existing biological data relevant for modeling and low compatibility of different types of models.

System design

See System design document

Dev env run

There are targets in makefile to start development environment for all parts of the app. Backend dev setup needs docker image to be present in the system when starting, which can be build with make docker_build_latest from ./backend directory.

Backend dev environment requires docker engine to be installed and consists of:

• mongoDB instance
• backend server
• sim worker replica with minimum one instance

Check the ./backend/docker-compose.yml for more information.

To start:

make run_dev_backend

Dev frontend env is powered by Webpack and can be started with:

make run_dev_frontend

To start both dev envs in a single session use:

make run_dev

Usage

See Guidebook

Deployment

Makefile has a create_oo_deployment target that will deploy current version of the app to an OpenShift instance. This target will create OpenShift deployment configs, services and external routes needed by the app to function. See makefile for configuration and options; requires OpenShift CLI.

Citation

When you use this software, we kindly ask you to cite the following DOI (under "Cite as"):

Funding & Acknowledgment

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.

This project/research received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA).

Copyright (c) 2022-2024 Blue Brain Project/EPFL