Welcome to ZENBU
ZENBU ( fantom.gsc.riken.jp/zenbu ) is a data integration, data processing, and visualization system based around three main web interfaces : an expression data enhanced genome browser interface, a secured user system for data upload and secured data sharing, and a data explorer interface to find and manipulate data across the many supported experimental data types and to find shared user configurations.
With version 3 of the system, an entirely new paradigm for user configurable data presentation and integration has been created: ZENBU-Reports. ZENBU Reports is a flexible data portal and interactive website builder. It is based around a page-layout graphical interface with various Elements such as Tables, Charts, Plots, Heatmaps, Network graphs, Genomewide visualizations and integrated ZENBU Genome Browsers. ZENBU Reports uses the same ZENBU user data upload and secured sharing system. Users can create interactive websites which mirror the figures of their papers, but where the paper might have to show only one example from their data, ZENBU Reports will allow you to build a query-able database for all possible examples.
One of the key differences is that ZENBU allows for novel data exploration through data integration and "on-demand" data processing within the system. This means that more raw or unprocessed data (like BAM files) can be loaded into the ZENBU system, and then ZENBU can perform many of the basic data manipulations that previously required bioinformatics experts with knowledge of the unix command line and a collection of bioinformatics tools. In ZENBU, the data is not a static picture, but instead it is a living melting pot where scientists and can explore and discover. Have a look at our case studies to see powerful examples of the ZENBU data processing and visualization capabilities.
Another key concept in ZENBU is that of data-pooling from multiple data sources into a single merged Track. It is becoming much easier to do many experiments within a study. For example in the FANTOM5 project we used the ZENBU Genome Browser to merge all 1885 CAGE BAM and CTSS files into a single track to allow easy comparison of expression at various loci FANTOM5_promoterome_hg38. The simple process of managing different experimental combinations into different visualization tracks is becoming unmanagable. Data-pooling allows one to easily compare experimental expression within a series of related experiments that would previously require bioinformaticians to externally process each group analysis and upload each as different precalculated visualization tracks. With ZENBU, the data can be loaded independently and the system can perform the pooling and group analysis. Because the system performs the pooling/group operations, the data can be interactively explored via region selection within a pooled track or through filtering of experiments within the pool. These realtime interactions within a pooled data track are immediately reflected in both the expression profile visualization and in the "experimental expression bar graph".
ZENBU also provides a platform for scientific data social-networking through a secured user environment for data upload and controlled data sharing within user managed collaborations. Collaborations and data sharing are managed in a facebook style of "friend requests" providing users with the flexibility to create and manage their own collaborations without needing central adminstrators. ZENBU also provides guest access to view published, public data and without any data upload functions. User profiles are available to anyone and are managed through a simple email and password login system.
- ZENBU Genome Browser interface : a highly user configurable and expression data enhanced genome browser with built in "on demand data processing". It is built on the concept of Tracks which consist of pooled data source, Data Processing, and visualization. It allows for various on-demand data manipulation and visualization of both raw mapping data or analyzed annotations uploaded from BAM, BED, GFF, GTF, and OSCtable files. It also provides interfaces for data downloading and interfaces for sharing through a flexible user defined configurations system for Tracks, Views and Scripts.
- Data Explorer interface to search the data which have been loaded into data sources of the system. This interface also allows for searching the user configurations of Tracks, Views and data processing scripts and to launch Views into the genome browser.
- User system for secure and controlled data sharing of user uploaded data with collaborations of other users.
Please have a look at the table of contents to see an overview of this documentation.
The entire wiki is also available in the form of PDF guides.
In addition various PowerPoint presentations for ZENBU are available via | google drive
ZENBU is also available for distribution and local installation
ZENBU is funded by a research grant for RIKEN Omics Science Center from the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT) to Yoshihide Hayashizaki and a grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT to Yoshihide Hayshizaki.