Mouse BIRN Atlasing Toolkit (MBAT)

Overview

This document describes the Mouse BIRN Atlasing Toolkit (MBAT), which was built from the combined efforts of groups within the Mouse BIRN.

 

Short Description

The Mouse BIRN Atlasing Toolkit is a JAVA application designed to view multiple types of multiscale data, access and query databases associated with the Mouse BIRN, and process some of these data types.

 

Logo

birn logo

mousebirn logo

 

 

Figure

figure

 

Categories and Keywords

Application, tool, atlasing, viewer

 

Longer Overview

This is a collaborative effort by groups within the Mouse BIRN to create an interoperable tool that offers an intuitive way to access the functionality offered by the individual efforts.  The goal of the MBAT is to act as an intuitive, interoperable interface for viewing, accessing, processing, and analyzing multimodal data with emphasis on functionality across distributed locations and diverse databases.   

This tool allows a user to view their data and offers the ability to interface with data offered by Mouse BIRN.  Future plans include the option to incorporate and compare a variety of different data types, regardless of the user’s location or affiliation with the mouse BIRN.

This updated Beta release (1.1 beta) has changes to improve usability and have greatly expanded the Gene Expression query interface of this tool.  People interested in visualizing and querying their microarray data can load it in the BIRN Microarray Database and access it in MBAT.  The MBAT Gene Expression query tool contains a link to the data upload site, or you may link to the site directly, http://132.239.131.189/birn_uad/.  This interface also allows you to retrieve related data from other sources of Gene Expression data such as the GeneNetwork (http://www.genenetwork.org/search.html) and launch a simple query of the Allen Brain Atlas (http://www.brain-map.org/) and GNF SymAtlas (http://symatlas.gnf.org/SymAtlas/).  

To access or download this tool, visit the BIRN Portal, www.nbirn.net.  For additional information about the MBAT project, visit the MBAT wiki page, http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/MBAT.

 

User Manual

To access the user manual for this tool see the BIRN website www.nbirn.net, or the MBAT wiki page, http://www.loni.ucla.edu/twiki/bin/view/MouseBIRN/MBAT.

 

Register for Download

Much of the data offered by the BIRN group can be visualized using this tool.  You can download these datasets and get more information at the BIRN website www.nbirn.net.

 

Installation Information

  1. Make sure Java is installed on your computer, if you need to install it, download it from http://java.com/en/
  2. Create the directory, C:\mouseBIRN\MBAT and download the TAR or ZIP file
  3. Unzip the files into this directory. 
  4. If you wish to include the extra data files, download and unzip the files into the MBAT directory. 
  5. To run the program, double click the MBAT.jar file 
  6. If you wish to have the program on your desktop, create a shortcut that points to the C:\ mouseBIRN\MBAT\MBAT.jar file.

 

References for the Software

Boline JK, MacKenzie-Graham A, Shattuck D, Yuan H, Anderson S, Sforza DM, Wang J, Williams RW, Wong W, Martone ME, Zaslavsky I, Toga AW (2006)  A Digital Atlas and Neuroinformatics Framework for Query and Display of Disparate Data.  Society for Neuroscience, Abstract #100.12

 

Contributors/Authors

The Mouse BIRN Atlasing Toolkit was created from the activities of six laboratories:

  • The MRI Center in the Biological Imaging Center (BIC) at the California Institute of Technology (CIT)
  • The Center for In Vivo Microscopy (CIVM) at Duke University
  • The Laboratory of Neuro Imaging (LONI) at the University of California at Los Angeles (UCLA)
  • The National Center for Microscopy and Imaging Research (NCMIR) at the University of California at San Diego (UCSD)
  • The Informatics Center for Mouse Neurogenetics:
    • GeneNetwork (UTHSC) at University of Tennessee Health Sciences Center
    • Laboratory for Bioimaging and Anatomical Informatics (Drexel) at Drexel College of Medicine, Philadelphia, PA

Technical Contacts

Jyl Boline jyl.boline@loni.ucla.edu

 

Acknowledgements and Fundings Sciences

This project is supported by U24 RR021760 funded by the National Center for Research Resources (NCRR) at the National Institutes of Health (NIH).

 

To download the CHANGE, please go to the download form.