Open Source Brain v2#

OSBv2 is under active development

The beta release of OSBv2 is available at https://www.v2.opensourcebrain.org. Please do get in touch if you have any queries or would like to help with user testing.

Open Source Brain (OSB) v2 is a new integrated research platform that builds on the features of OSBv1. It is currently under active development, and a beta release of the platform is available for users to try out.

OSBv2 is structured around 3 key concepts: Repositories, Workspaces and Applications.

OSBv2 Overview

Fig. 1 Relationship between Repositories, Workspaces and Applications on OSBv2.#

Repositories#

Repositories are views of files and data in public resources like GitHub, Figshare and DANDI.

  • A repository on OSBv2 lists the current contents of the remote resource

  • Repositories are public: all users can browse repositories that have been added to OSBv2

  • Private repositories, and interfaces to other neuroinformatics resources are also planned

More details on repositories can be found here.

Workspaces#

Workspaces are persistent spaces for users to carry out their work in.

  • Empty workspaces can be created, or they can be seeded from OSBv2 repositories using some or all of the files in the repository at that point in time

  • Each workspace is saved on a persistent cloud volume, allowing users to save their work and resume it at a later time

  • Any files which are generated (e.g. analysis outputs, simulation results) are also stored in the workspace, and other files can be uploaded

  • Users can keep their workspaces private or make them public to share them with the community

More details on workspaces can be found here.

Applications#

OSBv2 integrates a number of applications for use by researchers, and workspaces can be opened in any of the supported OSBv2 applications:

  • NWB Explorer: for the interactive exploration/visualisation of the contents of Neurodata Without Borders files

  • NetPyNE: a graphical user interface for the construction and simulation of neuroscience models

  • JupyterLab: a complete development environment for the Python programming language

Both NWB Explorer and NetPyNE also include inbuilt Python consoles for ad-hoc scripting and analysis, and a number of Python libraries are pre-loaded into the JupyterLab application for convenience.

More details on OSBv2 applications can be found here.