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The scientific motivation for this program project is to investigate the complex network of molecules and mechanisms that modulate the structure of different parts of the brain from major subdivisions such as the hippocampus, thalamus, and cerebellum, down to the level of discrete subpopulations of neurons and glial cells in single nuclei.

The bioinformatic tools and resources that we have been creating have very wide applicability, but our program project is specifically directed at exploiting a powerful new reductionist approach to explore the genetic basis of the very significant structural differences between the brains of different strains of mice. (Informatics Center for Mouse Neurogenetics).

  GeneNetwork
GeneNetwork Trait Correlation Upgrade. The most important innovation from the user's point-of-view is a fast method to compute correlations among transcripts that reduces the response latency about 20-fold--from 90 seconds to under 5 seconds using standard Affymetrix and Illumina data sets consisting of 45000 probes or probe sets. Of even greater importance, this improvement means that GN can now handle massive Affymetrix Exon 1.0 ST data sets that have over 1.1 million probe sets in about 60 seconds. The new method exploits a set of text files that are external to the database (essentially a materialized view), parallel computing technique (Parallel Python) and optimized SQL queries. more

  GenomeMixer 0.54c
Now Available GenomeMixer is a cross-platform application that allows you to simulate complex multi-generational breeding schemes. GenomeMixer will handle up to 20,000 parental strains. The number and length of chromosomes is fully editable, and you should be able to model almost any sexually reproducing diploid species. All you have to do is input the length and number of chromosomes, the names of the purbred strains, and an arbitrary breeding scheme, and GenomeMixer will output the simulated genetic results of such a cross... more

  Control a research-grade light microscope:
Gumbo 2.6 - The iScope�"internet microscope"�is a complete system for Internet microscopy. Located at the University of Tennessee in Memphis, the system uses three Zeiss Universal microscopes to provide online, realtime access to the slides which form the Mouse Brain Library. Secure user authentication and scheduling ensures reliable, responsive access to the system... more | watch movie tutorial

  Aria 3-D: for viewing focus-through movies and stereology
After using Gumbo to request that specific areas of a slide be imaged, "Aria 3-D" (Automated Remote Image Analysis) is used to browse through and view these movies. Aria 3-D doesn't directly interface with the microscopes; it downloads previously-generated movies from the iScope server, and allows you to rapidly focus through them and count cells. Since movie queuing is disabled in the current version of Gumbo you will be able to view movies from our library, but not request your own. ... more | See Movie Tutorial (require flash)

  Mouse Optic Nerve Image Database (MONID)
Sep 17th 2003 - A collection of high magnification electron micrographs of the mouse optic nerve suitable for quantitative, comparative, and genetic analysis... more

  Browse "bxdphenotypedb" Database
Aug 19th 2003 - BXD Phenotype Database (or download Excel or tab-delimited text files). Our thanks to John Belknap and the Portland group for providing an extensive file that catalyzed this BXD phenotype database. Portland-derived data in the BXD database are currently (Aug 2003) being edited and updated by John Crabbe and colleagues and many new phenotypes are being added. We will soon provide a link to this new phenome database. Queries about specific Portland-derived phenotypes can be directed to Mark Rutledge-Gorman. (By Elissa Chesler and Mary-Kathleen Sullivan; updated Aug 19, 2003 by RW) Browse | Excel File

  WEBQTL Tutorial
WebQTL Demonstration - In this demonstration, we explore one important transcript expressed in the brain: the amyloid beta precursor protein messenger RNA. The product of this mRNA, the APP protein, is associated with Alzheimer disease. Part 1: How to discover shared expression patterns (slides 2-14) Part 2. Discovering upstream modulators (15-25) Part 3. Discovering downstream targets... More

  The Mouse Brain Library
The collection now consists of images from approximately 1500 brains Search the library You can search the MBL for cases by strain, age, sex, body or brain weight.
 
Genetics
 

 
Scientists Dream of 1001 Complex Mice Geneticists want to create 1000 new lines of inbred mice to help them sort out the genes behind complex diseases such as diabetes and cancer... [Science 23/Jul/03] more
 

 
CTC Workshop
 

 
There is also a Complex Traits Consortium, whose aim is to find the genetic roots of the many important diseases that are caused by several genes acting in concert. That goal has long eluded human geneticists, and the consortium hopes to achieve the feat in the mouse.
 

 
CTC Presentation
 

 
Phenotypic Variation Among Several Common Inbred Strains: Presentation by: Molly Bogue, August 2003 .
 

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