This version update is mostly about bug fixes, but there are several important changes.
Collaborations can now be "published". This allows for projects to be more neatly packaged into a collaboration group. A published collaboration means that all the views/tracks/scripts and data which was shared with the collaboration, will now be visible to all users. Publishing is currently done by the system administrator but I will add a user interface in the future. "Publishing" should only be done after a project has been made public since everything will be visible by the world. After publishing, the collaboration can see be edited by it's selected members, while the public has read-only access. Of course secured collaborations are the norm. On the http://fantom.gsc.riken.jp/zenbu server one can see two "published" collaboration at this time "FANTOM5 Promoterome" and "FANTOM5 Time Course".
Please note for people upgrading from a previous version: this feature required a change in the mysql schema for collaborations. Please apply the 2.9.1_patch file in the zenbu/sql directory if you are upgrading.
Adding users to a collaboration now allows for directly adding new people to the system. When a collaboration manager adds a person to a collaboration, it will now create new accounts if the person has not previously made a ZENBU account. The person is sent an email inviting them to confirm their account. This dramatically simplifies the process of adding many people to a collaboration, and for people to join ZENBU and a collaboration.
Refinements in the zenbu_upload command line program. This is a client tool to allow upload and metadata editing from any remote machine to a zenbu server. It is most useful for bulk loading of data from a computation-node server (aka bioinformatics processing pipeline).
A more robust remote-data access system. There is now a direct-stream-process system to send track data to a remote server even if the track has not been processed into a cache. This is the first step in toward a more powerful cache and data-sharing system which is planed for the future 3.0 release.
Last edit: Jessica Severin 2015-03-19
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Please note for people upgrading from a previous version of zenbu to 2.9.1. The collaboration publishing feature required a change in the mysql schema. Please apply the 2.9.1_patch file in the zenbu/sql directory if you are upgrading.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
This version update is mostly about bug fixes, but there are several important changes.
Collaborations can now be "published". This allows for projects to be more neatly packaged into a collaboration group. A published collaboration means that all the views/tracks/scripts and data which was shared with the collaboration, will now be visible to all users. Publishing is currently done by the system administrator but I will add a user interface in the future. "Publishing" should only be done after a project has been made public since everything will be visible by the world. After publishing, the collaboration can see be edited by it's selected members, while the public has read-only access. Of course secured collaborations are the norm. On the http://fantom.gsc.riken.jp/zenbu server one can see two "published" collaboration at this time "FANTOM5 Promoterome" and "FANTOM5 Time Course".
Please note for people upgrading from a previous version: this feature required a change in the mysql schema for collaborations. Please apply the 2.9.1_patch file in the zenbu/sql directory if you are upgrading.
Adding users to a collaboration now allows for directly adding new people to the system. When a collaboration manager adds a person to a collaboration, it will now create new accounts if the person has not previously made a ZENBU account. The person is sent an email inviting them to confirm their account. This dramatically simplifies the process of adding many people to a collaboration, and for people to join ZENBU and a collaboration.
Refinements in the zenbu_upload command line program. This is a client tool to allow upload and metadata editing from any remote machine to a zenbu server. It is most useful for bulk loading of data from a computation-node server (aka bioinformatics processing pipeline).
A more robust remote-data access system. There is now a direct-stream-process system to send track data to a remote server even if the track has not been processed into a cache. This is the first step in toward a more powerful cache and data-sharing system which is planed for the future 3.0 release.
Last edit: Jessica Severin 2015-03-19
Please note for people upgrading from a previous version of zenbu to 2.9.1. The collaboration publishing feature required a change in the mysql schema. Please apply the 2.9.1_patch file in the zenbu/sql directory if you are upgrading.