Tools

The NeuroHub platform functions as a centralized toolbox integrating an ecosystem of software services and tools for seamless neuroscience research and collaboration. Components of the ecosystem include external or internally developed softwares or platforms that are interoperable with the NeuroHub platform to augment or support research activity. Whether it be multi-modal data management in LORIS, computational pipelines on high-performance computing through CBRAIN, interactive computing through Jupyter Notebooks or statistical analysis using R, NeuroHub offers a connected platform that allows users to conduct research at whatever scale is necessary to answer their questions. NeuroHub’s suite of software services supports research teams working in neuroimaging, neuroinformatics, genomics, cognitive neuroscience, machine learning and more.

CBRAIN connects to high-performance and cloud computing and allows users to run computational pipelines in an easy and reproducible manner. CBRAIN has a partnership with Compute Canada to provide millions of computing hours for the research community using the NeuroHub Portal. CBRAIN is linked directly to the NeuroHub platform, allowing users to easily move between the NeuroHub Portal and CBRAIN to launch tasks and analyze data efficiently.

Execute Pipelines on High Performance Computing

CBRAIN’s computational pipelines allow users to perform complex big data analytics. These pipelines range from simple conversion operations, to neuroimaging, to genomics to supply chain simulation modeling.

Create Your Own Pipelines

CBRAIN makes it easy for users to define, test and import their own pipelines into the system. Utilizing the easy-to-use Boutiques JSON Standard to define execution pipelines for the automatic import to CBRAIN.

Seamlessly Move Data

CBRAIN offers a number of Data Providers for storing, organizing and moving your data seamlessly throughout the NeuroHub platform. This ensures large datasets are moved efficiently and securely to perform large-scale computations.

LORIS (Longitudinal Online Research and Imaging System) is a web-based data and project management software for neuroimaging research studies. This open source framework allows for storing and processing of behavioural, clinical, neuroimaging and genetic data. LORIS also makes it easy to manage large datasets acquired over time in a longitudinal study, or at different locations in a large multi-site study.

LORIS is integrated with the NeuroHub platform, allowing curated datasets to be shared. In addition, LORIS instances are utilized to query large datasets available in NeuroHub. LORIS datasets can be exported into CBRAIN easily for pre-processing or analysis.

Multi-Modal & Multi-Site

LORIS enables you to enter, organize and validate data gathered from multiple sites. It allows multi-modal data collection and supports neuroimaging, behavioural, genetic and EEG data.

Search Large Datasets

The LORIS database handles large datasets efficiently, such as the UK Biobank, and empowers users with query building tools for generating custom curated datasets for analysis and dissemination.

Standardize Data

LORIS allows you to curate and standardize data to ensure results are FAIR principles (Findable, Accessible, Interoperable, Reusable) to facilitate publication.

NeuroHub Components

Jupyter Notebooks

JupyterHub brings the power of notebooks to groups of users by providing access to computational environments and resources without the burden of installation and maintenance. You can store Jupyter notebooks in NeuroHub projects and run them on high-performance computing resources such as the Béluga JupyterHub (if you have a Compute Canada account) or the McGill Syzygy JupyterHub (if you have a McGill username)

OSF

OSF is a free and open source project management tool that supports researchers throughout their entire project lifecycle as a collaboration tool and workflow system. NeuroHub is interoperable with OSF allowing you to move data between applications.

Boutiques

Boutiques is a tool to automatically publish, integrate and execute applications across computational platforms. Boutiques applications are summarized in a simple yet rich JSON description, and enable the simulation, validation, evaluation and application-specific monitoring of command-line tools.

CONP

The Canadian Open Neuroscience Platform (CONP) is a national Open Science network. It provides an infrastructure for the sharing of neuroscience data and ools, as well as training and data governance policies. Some cyber infrastructural elements of the CONP pPortal are also integrated within the NeuroHub Platform. As such, many CONP datasets are accessible as public projects on the NeuroHub Portal. All users are allowed access to this data to help propel a new era of commonly shared, digitally integrated, data- and algorithmic-rich neuroscience research.

Datalad

DataLad is a software tool developed to help with everything related to the evolution of digital objects. It not only keeps track of code, data, and makes sharing, retrieving and linking (meta-)data easy, but it also helps combine of all things necessary in the digital workflow of data and science. NeuroHub connects withDatalad, which allows easy publishing of objects for the scientific community.