MouseTRACS is a web-based Laboratory Information Management System (LIMS) for tracking large numbers of animals in a centralized breeding facility.


The mouse N-ethyl-N-nitrosourea (ENU) mutagenesis program at the Genomics Institute of the Novartis Research Foundation (GNF) uses MouseTRACS to analyze phenotype screens and manage animal husbandry. MouseTRACS is a web based laboratory informatics system that electronically records and organizes mouse colony operations, prints cage cards, tracks inventory, manages requests, and reports Institutional Animal Care and Use Committee ( IACUC) protocol usage. For efficient phenotype screening, MouseTRACS identifies mutants, visualizes data, and maps mutations. It displays and integrates phenotype and genotype data using likelihood odds ratio (LOD) plots of genetic linkage between genotype and phenotype. More detailed mapping intervals show individual Single Nucleotide Polymorphism (SNP) markers in the context of phenotype. Additionally, dynamically generated pedigree diagrams and inventory reports linked to screening results summarize the inheritance pattern and the degree of penetrance. MouseTRACS displays screening data in tables and uses standard charts such as box plots, histograms, scatter plots, and customized charts looking at clustered mice or cross pedigree comparisons. In summary, MouseTRACS enables the efficient screening, analysis, and management of thousands of animals to find mutant mice and identify novel gene functions. MouseTRACS is available under an Open Source license at

Web Browser IE or Mozilla, Safari for MacOSX
Web Server Apache
Database MySQL
Java 1.4+ Browser Plugin
Platform Linux, MacOSX
Scripts go into the cgi-bin directory. Library paths, server name, database login info needs to be updated in the config files. If symbolic link following is enabled on Apache, you can just make links to the distribution folders. Otherwise, you have to copy the folders to the expected locations.

Madeline Pedigree Rendering
ghostscript postscript to pdf conversion
JPost Applet Database updating
R Statistics, Graphing, QTL plots
R - qtl R package
R- cluster R package
Data::Table Perl package
CGI Perl package
Statistics::Descriptive Perl package

Mamm Genome. 2006 Apr;17(4):288-97. Epub 2006 Apr 4. Data and animal management software for large-scale phenotype screening. Ching KA, Cooke MP, Tarantino LM, Lapp H. Pubmed

CreditsKeith Ching - Design and implementation.
Mike Cooke - Screening requirements functionality
Lisa Tarantino - Colony requirements functionality
Hilmar Lapp - Project oversight and contribution to schema design