Data sharing collaborations

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ZENBU provides for fine level control of who can have access to uploaded data through the concept of a Collaboration.

While other genome browsers like UCSC and Ensembl provide for user upload of private data, and they may provide a limited amount of data security, they do not provide any means of sharing that data with a limited group of other scientists in a secured manner. Since Science is a collaboration process involving many people from PIs, to research scientists, to technicians, to bioinformaticians, it makes sense to extend that collaboration process into the genome browser. But of course prior to publication the data and any discoveries in it, must be kept secured.

With the concept of the Collaboration, users of ZENBU can select who they want to have access to which data. In addition a user can create or be a member of more than one collaboration which reflects the how scientists often are working on more than one project at the same time.

Creating Collaborations

All users of the system are allowed to create new collaborative projects. Collaborative projects can be useful not only for sharing data and views with other users in the system, but also for managing your own data and projects like folders on a desktop.

The process of creating a new collaboration is simple. In the User Profile system, make sure the collaborative projects sub-menu is selected. At the top of the page one will see a button for creating a new collaboration.


Once pushed, the user is presented with a form to describe the collaboration. In addition the user can select if the new collaboration will be publicly announced to all users of the system. Publicly announcing a collaboration simply means that any user of the system can request to join the collaboration. The owner of the collaboration still has the control to decide who can and who can not join the collaboration. Publicly announcing a collaboration does not mean the data will be shared with the public.


After creation the new collaboration will appear in the user's list of available collaborations. They can now share data into this collaboration, save view/track/script configurations into this collaboration, and invite other users to join.


Joining Collaborations / Inviting Users

Depending on if the collaboration was publicly announced or not the process of adding users to a collaboration is different.

For publicly announced collaborations, all users of the system will see the collaboration in their list of collaborative projects but they are not members which means they can not see the data in the collaboration nor can they share things with the collaboration. To join a publicly announced collaboration the user clicks the request to join button. The owner of the collaboration will then see this new user it the list of pending requests for the collaboration and then decide if they wish to accept or reject that users. The user also has the option of ignoring the collaboration so that it no longer appears in their collaborative projects list.

For private collaborations, the owner of the collaboration must explicitly invite users to join the collaboration. This is done by entering the user OpenID (not their email). If a correct OpenID has been entered, the invited user will appear in a list of outstanding invitations. The user who was invited, when they visit their collaborative projects page, will see the invitation and then decide if they will accept or decline it.

Overall the process is similar to other social networking sites like the facebook 'friend request' system.

Sharing data

After data has been uploaded it can be shared with specific collaboration projects. This provides a secured means for only members of that collaboration to see the data. By focusing data sharing at a Collaboration level, it makes it easier for many people to work together on a particular set of pre-publication data.

Sharing data is provided through the my data interface section. Prior to sharing data, the user must upload it into the system. After uploading the new data sources will appear in the my data table and become available for sharing.


Select the data source you want to share and click the share button. This will then popup a panel where the user can select which collaboration(s) they wish to share the data with.


After a data source has been shared with a collaboration, the panel will show the sharing


Public sharing

In addition to all user created collaborations, the ZENBU system provides a special collaboration called public sharing which all users are automatically members. This collaboration is used for sharing configurations or data with all users of the system, there by making the data public to the world. The public sharing collaboration is useful for

  • creating new views/tracks/scripts based on already published data
  • loading publicly available data from other systems and databases
  • sharing your newly published data with the world on the ZENBU system.