Introducing Projects

Working on the standard coordinate space,
creating and sharing hardware, data-sets, methods and tools for analyses:
and activate brain science !

Using Transcriptome Tomography,
Make invisible  gene expression visible and share the information !  

                                                                               (cc) Song and Okamura-Oho 2011

BReNt- starts with activating ViBrism ( gene expression atlas DB) for the open science


A recent progress in genome biology has had a huge impact on our view of life and now enables us to use these biological information for improving quality of life.
The number of  hereditary diseases, caused by a tiny change occurring somewhere in 30 million base-pairs of the human genome for each disease, is now comes up to 2,000 or more, although each disease is  rare in the population. Moreover, susceptibility of common diseases is expected to be statistically understood as a combination of multiple (sometimes a large number of ) tiny changes in the genome, certainly environmental factors need to be seriously considered.

In order to increase practical availability of knowledge of genome biology for the purpose of managing these diseases and improving quality of life, information of bio-molecules, in particular genes, which are copies of parts of the genome as functional units,  needs to be analysed how they are produced and functioning in the cells, tissues, and organs along with the anatomical information. And the information needs to be shared among researchers to activate innovation.

The brain, especially, has a complex anatomical structure and highly differentiated and organized functions. Therefore, successfully understanding of the brain requires sophisticated technology of computation for the integration of neuroscience with information sciences: neuroinformatics. To rise to this integration, OECD launched International Neuroinformatics Coordinating Facility (INCF)."INCF develops and maintains database and computational infrastructure for neuroscientists. Software tools and standards for the international neuroinformatics community are being developed through the INCF Programs. The INCF Digital Brain Atlasing Program is now integrating atlases of the rodent brain at different biological levels, from gene activity to large-scale structure, using a standard coordinate space (Waxholm space: Supporting this aim is the associated Digital Atlasing Infrastructure, which facilitates access to a large range of spatially disparate data and tools.

Using the latest computation technology, you can do research in the virtual web space.
Presence of genes is invisible, however they carry important information of the basic brain function.
Making invisible gene expression visible and discover something new on the web.

Principle Idea

BReNt- Brain Research Network is participated in
Creation of Digital Atlases for expression of bio-molecules, working with RIKEN, and
Data and Tools Sharing in the standard coordinate Waxholm Space (WHS) on the web organized by INCF.

That is our proposing
1. Creation of Data
Discuss on the web about what and how data is to be open
Organize groups of fundraising for the data creation
Create bio-molecullar data-sets for brain atlasing using Transcriptome Tomography.
2. Sharing Data and Tools
Develop tools for data sharing
Develop tools for data analysis
Open analysed data on the web
Raise fund for sustain the open science

Waxholm space (WHS): the 3D-coordinate space for digital brain atlases is named after the island of Waxholm, where the first meeting to create the virtual space was held. (referred from the Current Biology featured article seen in the Cabinet. photo: Waxholm Fortress, Wikimedia Commons)


1. Creation of Data using Transcriptome Tomography for
#1 Expression databases of fine resolution 
creating 100 times more precise data than existing data-sets in ViBrism for gene expression atlas of the adult mouse brain.
#2 Cross-ages comparative research
analyzing developmental stages through embryos to the adult using underlying  transcriptome (whole coding and non-coding genes) features of the mouse brain.
#3 Cross-species comparative research
eliciting differences and similarities of anatomical structure, function and underlying  transcriptome features among the brains of human and other species.
#4 multiple bio-molecular expression databases
creating databases for proteins, sugars and lipids expression atlases.
2. Sharing Data and Tools
mapping quantified data for sharing onto the virtual 3D-coordinate space Waxholm Space: WHS
developing software for analyzing mapped data and other data (MRI etc.) in WHS
Based on anatomy ontology and gene ontology, statistically analyze expression data.
Time and Space (4D) Visualization
Developing interface for the visualization and making resources easy to manipulate and understand for many people.