Frequently Asked Questions

From Whole Brain Catalog

Please browse our frequently asked questions and if you can not find your answer, contact our team at: contact@wholebraincatalog.org

[edit] General FAQs

[edit] What issues does the Whole Brain Catalog address?

A grand goal in neuroscience research is to understand how the interplay of structural, chemical and electrical signals in nervous tissue gives rise to behavior. Neuroscientists are making use of an increasingly powerful arsenal of instruments and tools for obtaining data, from the level of molecules to nervous systems. At the same time, researchers are also engaged in the arduous and challenging process of adapting and assembling neuroscience data at all scales of resolution and across disciplines into computerized databases, ensuring that they are accessible to the wider community.

A challenge in developing databases for diverse neuroscience data is to provides the means to inter-relate the data acquired by different techniques, across vastly different scales and by geographically-distributed researchers. A consolidated strategy for integrating neuroscience data is to provide a multi-scale structural or spatial framework in which elements of neuroscience knowledge can be located and relationships explored among them from any network-linked computer. Efforts to integrate multi-scale data from different methods using a common spatial framework are hampered by incomplete descriptions of the microanatomy of nervous systems. In this project, we will apply advanced imaging methods and develop the software tools required to build representations of complete braincells and their microenvironments, targeting gaps in spatial and temporal domains, so as to enable the construction of a continuous framework onto which one may "hang" or associate information accruing from the diversity of brain research activities, from molecular to systems neuroscience. This open and accessible software environment is intended to broadly and rapidly facilitate the integration of knowledge pertaining to brain structure and function across spatial and temporal scales. It is also intended to provide multi-scale structural frameworks for construction of models allowing users to test hypotheses not amenable to direct experimental analysis using software tools for computational simulation of microphysiological properties of cellular microdomains, cells and their assemblies in nervous systems.

[edit] What makes the Whole Brain Catalog unique?

The Whole Brain Catalog is open source. Development and success of the Whole Brain Catalog is driven by a community of both developers who contribute code and users who contribute their data. The structure and engineering of the Whole Brain Catalog allows you to integrate most types of data and your own data analysis and modeling tools.
The Whole Brain Catalog is multiscale. Whole Brain Catalog allows users to integrate data across multiple scales in a common spatial framework including both Allen Brain Atlas and INCF’s international standard mouse brain atlas coordinate system for spatial brain mapping known as the “Waxholm Space”. Scales include: http://wiki.wholebraincatalog.org/wiki/Data_Summary
The Whole Brain Catalog is a catalog. Whole Brain Catalog is community-based repository for data that uses the Cell Centered Database (CCDB) as a host for data in the environment.
The Whole Brain Catalog is a virtual catalog. Whole Brain Catalog situates data within brain anatomy, analogous to how Google Earth has allowed the world to cross borders and have access through a single source to a wide variety of information and tools via the internet.

[edit] Who is going to use this?

Everyone! Scientists, students, educators and anyone interested in learning about and contributing to the research of the neuroscience community.

[edit] Where can I go to learn about the development of the Whole Brain Catalog?

Brain Catalog development

[edit] What is the technology behind the Whole Brain Catalog?

The catalog is built using many open source libraries. jMonkey Engine is being used as the 3D game engine to display the graphics. Protege is being used behind the scenes as an API to interface with OWL ontologies. NeuroML is being used as a standard for representing neuronal morphologies. We are writing other libraries to interface with our database for cellular data, the Cell Centered Database, CCDB. In addition, the catalog will leverage ongoing efforts in many national and international research projects focused on reconstructing and understanding morphology and function of mammalian brain and assembling related multimedia resources such as BlueBrain, NIF, digital brain atlasing efforts of the International Neuroinformatics Coordinating Facility, INCF. Our development and support teams are powered by a psychoactive stimulant known as caffeine.

Take a look at a more complete list of projects we are incorporating.