Goal of the Collaboratory

The EBRAINS Collaboratory provides scientists an online environment to identify fellow researchers, form teams, coordinate collaborations, develop live code (in Jupyter Notebooks), document methodology and results (in Wiki and Office files), store data, and publish work in a safe environment which is entirely self-hosted. Work is organized around workspaces, known as collabs, which are created for each team or project.

The EBRAINS Collaboratory opens a portal onto the full gamut of EBRAINS services, providing you with examples of how to access services and resources, and a means of applying this quickly with little effort to your research. Visit some of the highlighted collabs here.

What is a collab?

A collab is a workspace inside the Collaboratory. A collab extends across multiple services to share its content with a team of users who have set permissions within that collab. The most intuitive entry point for a collab is its wiki home page. From this page, users can:

• browse, edit, and manage wiki pages
• browse, edit, and manage files in the collab’s Drive
• view and manage the members of the Team of the collab, and their respective permissions
• browse, run, and create Jupyter Notebooks in the Lab

Create your own collab today. Click the Collabs menu at the top of this page and then the Create a collab button. Choose a significant name and description with all the right keywords to help authorized people locate your collab quickly.

The settings of the collab can be updated at any time from the wiki home page with the Settings button.

You can find a collab by clicking the Collabs menu at the top of the page.

Wiki pages

Wiki pages are a convenient way of publishing content on the web, either addressing the Team of the collab, or making the content completely public, i.e. also accessible to visitors without an account. The wiki home page of the collab is created for you. You can edit this page and add sub-pages. The wiki page hierarchy appears in the left margin.

More advanced users can use the XWiki macros which can be inserted when in edit mode by clicking the cog icon in the formatting toolbox at the top of the page.

New wiki sub-pages offer more diversity: plain blank wiki pages, article pages with an automatic table of content in the right margin, or 3rd party content: an external web page (iframe) or a community app.

Curious about how a wiki page was written? You can always see the source for it from the kebab menu (upper right).

You can run a search on all the wiki pages you have access to from the search widget at https://wiki.ebrains.eu or from the magnifying glass icon at the top of this page. This will find words in the page names and in their content, with advanced filters available from the first result page.

Drive

The drive of a collab stores files for its users. The drive is perfect for files and documents that need to be worked on collaboratively, such as Office documents or Notebooks, but is not meant to be used for larger files and datasets. File sizes in the Drive have a maximum limit of 1 GB.

All files are version controlled and can be shared via smart links with the Team members or public (read-only) links with anybody (see the FAQ). See the history of a specific file from its triangle icon menu: date and modifier (username) for each version.

The interface offers drag-and-drop functionality for easy upload of files.

Put an end to exchanging files by email which stuff your Inbox, where you never know who has the latest version, and require manual merging. Work online collaboratively. The version control on files is also an easy way to check who edited your file and rollback to a prior version.

You can also install the Seadrive application on your computer to access the storage directly.

Bucket

The bucket of a collab stores larger files for its users. Although it does not offer exactly the same functionality as the Drive, it offers better and faster storage for larger files, videos and datasets. You can still access these files programmatically via Jupyter Notebooks by using the bucket API

Office

Accessible directly from the Drive, users can edit Office documents collaboratively online. The OnlyOffice application supports Word, PowerPoint and simple Excel modern file formats.

Use it for collaboratively taking minutes of your meetings without the need to share screens.

Hint: contrary to other files in the Drive, collaborative edition of a common file implies that the edits of a group session are saved under the name of a single user. Don’t be surprised if you don’t find in the history a specific username.

Lab / Notebooks

The Collaboratory.lab is the place to find and run Jupyter Notebooks. Access JupyterLab from the Lab menu at the top of this page. You will be taken to the Lab with this collabs Drive loaded. You can now navigate around the Lab using the left hand navigation pain to all collabs you have access to (See permissions below).

You can also link directly to a particular Notebook in the Lab from a collab by following the instructions as laid out in our tutorial.

Permissions / Team

Collabs are private or public. The wiki pages of public collabs are viewable by anyone on the internet. For files in the Drive of a public collab to be readable by anyone, the files (or folders) must be referenced via a public link in a wiki page.

The Team app is one of the few non-wiki pages that appears in the collab’s navigation panel in the left margin. The admins of the collab can add/remove users from the Admin, Editor and Viewer roles of that collab. A user has one of these 3 roles throughout that whole collab; there are no finer-grain permissions per folder in the Drive or per wiki page.

Roles in a collab’s Team can also be attributed to all the users in a Unit or in a Group. Units are managed by more formal policies than Groups, e.g. to indicate HBP user accreditation or to indicate the institution a user belongs to. Groups are more flexible in nature.

How To, FAQ and tips

Browse through the navigation of this collab. You will find a How To section and a FAQ & Tips section. Did you not find an answer to a question you have? Try the wiki search (see the wiki section above) or contact support from the Support menu at the top of the page. Is the wording of the documentation not clear? Let us know too.

Extensions / Community apps

As a service provider, you can develop an app and share it with Collaboratory users to be added to any collab’s navigation panel. Find out more here.

Two Collaboratory versions

The EBRAINS Collaboratory is developed in the HBP project. A major modernization of the Collaboratory was initiated in 2019. Collaboratory 1 has been shutdown in Sep 2021; users can no longer access Collaboratory 1.

Key collabs from Collaboratory 1 are still accessible via the https://collab.humanbrainproject.eu URLs which now redirect the user to content in Collaboratory 2.

Collaboratory 2 is accessible at https://wiki.ebrains.eu

The new Collaboratory offers a more modern user interface and more functionality: wiki pages, collaborative edition of Office documents, running multiple Jupyter Notebooks in a common environment, simplified access to file IO from notebooks, integration of notebooks to wiki pages, version tracking on files in the Drive, storage for larger datasets, ...