Brainlife is a free and open source platform for neuroscience data management. The project promotes engagement and education in FAIR and reproducible neuroscience.
Brainlife is a single integrative interface to manage, visualize, preprocess and analyze data (fMRI, dMRI, anatomical MRI, EEG and MEG). THe platform also allows to publish all research assets associated with a scientific project (data, preprocessing services and data analysis notebooks) in a single record addressed by a digital-object-identifier (DOI). The platform is unique because of its focus on supporting scientific reproducibility beyond open code and open data, by providing fundamental smart mechanisms for what we refer to as “Open Services.”
Currently the installation supports Linux and Mac OS You will need to have an environment with the following software packages
- docker / docker-compose
- git
- Node.js 16
apt install docker-compose golang-docker-credential-helpers
Not all novnc vis apps require GPU, but if you have nvidia gpu on your local machine, you should be able to launch it by having these tools installed
- vglserver (run vglserver_config and allow all access)
- nvidia-docker2 (required to run vis app with
--gpus alloption. See https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html#installing-on-ubuntu-and-debian
The vis/Dockerfile installs specific version of libnvidia drivers. I believe the version must match with the version of the driver installed on your host or vglrun won't work.
Please make sure that you have the correct docker-compose version installed
docker-compose version
docker-compose version 1.29.2, build 5becea4c
docker-py version: 5.0.0
CPython version: 3.9.0
OpenSSL version: OpenSSL 1.1.1h 22 Sep 2020
Then git clone this repo and all of its submodules.
git clone https://github.com/brainlife/brainlife --recursive Then launch the dev stack (with auto-reload on code changes) by
./dev.shOnce all services starts up, you can open your browser to access the warehouse UI at https://localhost:8080. If this is the first time you are running the dev instance, you can insert some database records by running ./scripts/populate_db.sh. This inserts the following collections.
- auth - user/group
- warehouse - datatypes/uis/apps
The default data contain two users: admin and guest.
They come with no password, so make sure to set-up a password for them by using:
./scripts/passwd.sh <user>The following functionalities are not yet implemented by this local dev instance
- Group Analysis (jupyter notebook)
- Dataset/Datalad import
- Pipeline rules are not yet fully tested
- Publication / datacite integration
This research was supported by NSF OAC-1916518, NSF IIS-1912270, NSF, IIS-1636893, NSF BCS-1734853, NIH 1R01EB029272-01, a Microsoft Research Award, A Microsoft Investigator Fellowship to Franco Pestilli