About MausDB

About MausDB

MausDB is a laboratory mouse information and Mangement system (LMIMS). MausDB has been custom develeoped for the needs and requirements of the German Mouse Clinic. It has been publish and made available to the scientific community:


Its purpose is to facilitate all aspects of handling laboratory mice in a mouse facility - ranging from just one rack with few cages up to tens of thousands of mice:

  • by storing all relevant data of a mouse facilityincluding animal data in one central database.
  • by providing this data to all users simultaneously on a multi-user access platform.
  • by ensuring that information is up-to-date and all users have access to the same information (in contrast to working with distributed spredsheet files).
  • by providing useful overviews and search functions.

 

 

Publication:
Maier, H., Lengger, C., Simic, B., Fuchs, H., Gailus-Durner, V., Hrabé de Angelis, M. (2008) MausDB: an open source application for phenotype data and mouse colony management in large-scale mouse phenotyping projectsBMC Bioinformatics 2008, 9: 169

 

 

Explicite Features

MausDB covers most aspects of handling laboratory mice for scientific purposes, including:

  • importing mice from external sources
  • mouse breeding
    • mating
    • embryo transfer
  • weaning
  • moving mice (cage and/or rack transfers)
  • cage card printing
  • locating mice, full rack and cage overview
  • virtually collecting and grouping mice in a so called cart
  • genotyping mice (multiple genotypes possible)
  • culling mice
  • manage experiment assignment
  • manage cost center assignment (multiple cost centers possible)
  • mouse phenotyping
    • definition of structured phenotyping workflows
    • definition of phenotyping parameters
    • schedule phenotyping tasks for single mice or groups of mice on a weekly basis
    • query and manage status of phenotyping tasks
    • upload phenotyping results to database from spreadsheet files
    • extract and export phenotyping results from database to spreadsheet format
    • statistical analysis and visualisation of phenotype data using pre-defined R scripts via the MausDB web user interface
  • export mouse breeding data to spreadsheet files
  • uploading and attaching custom files to single mice or groups of mice, e.g. image files or spreadsheet files

Technical Issues

MausDB is a web-based CGI application built on Linux, Apache, MySQL and Perl (LAMP).

As MausDB heavily works with database transactions, it makes use of the InnoDB storage engine provided by MySQL. MausDB should also work with any other transactional storage engine or transactional database management system (e.g. PostgreSQL) in principle. Though this has not been tested at all, it might be neccessary to adapt SQL statements in order to fully comply with SQL standards or RDBMS-specific SQL dialects.

In order to avoid dependency of a single database management system, the whole business logic has been implemented on application level rather than on database level, i.e. stored procedures.

Requirements and recommendations

  • Hardware: Although MausDB has shown to run on standalone Desktop and notebook computers and even on virtual machines, we recommend a dedicated 24/7 server with at least redundant hard disks in a RAID setup. We do not recommend running MausDB on Desktop or notebook computers for other than testing purposes.
  • Security: we recommend running a MausDB on the smallest internal subnet possible. Although there are basic security mechanism implemented that prevent i.e. SQL injections, MausDB has not been designed to be exposed to the internet.
  • IT expertise needed for installation: MausDB is not a Desktop application that can be installed by anyone. A certain level of Linux, MySQL, Apache and Perl skills is needed in order to install MausDB successfully.
  • IT expertise needed for operation: Every now and then - depending on users - database entries have to be corrected, which not always can be done on the web user interface. In these cases, database tables have to be manipulated directly. Even when using the provided scripts for frequent situations, this has to be done by someone familiar with SQL and who exactly understands what the script is doing. If you are not familiar with SQL and don't have access to someone who is, you should not consider MausDB as a solution for your colony management.

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