administration area Mutrack suggest change Biotutos Tennessee Mouse Genome Consortium
Mouse and State of Tennessee Tennessee Mouse Genome Consortium

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Bioinformatics Core

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Project Summary

Goals

  1. Acquire primary screen, secondary screen, and other data.
  2. Automate and support the screening procedures and mouse tracking.
  3. Support end-user access to data and promote dissemination of mutant mice.
  4. Statistically find phenotypic variants among the screened mice.
  5. Provide a common system, application, and data infrastructure that supports the previous aims.
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Approach

The current database has been implemented in ORACLE 8i. Most front end user interfaces were programmed in PHP. We are also using PERL and the GD image library to visualize statistical summaries of the data. System and user analyses were done to create the core data model of this database. User requirements and beta release prototypes were used to refine that data model and improve the user interfaces to the database. This database version and its user interfaces are primarily designed to track the major processes required for primary screening and to acquire the data electronically. This electronic data is then used in searching for meaningful patterns, esp. in finding mouse pedigrees that have phenotypically deviant mice.

Progress

To date we have finished MuTrack vers. 1.0 (http://www2.tnmouse.org/mutrack). There are currently over 20 tables in this database. More importantly, the database system is currently acquiring primary screen data from the different screens and tracking the movement of the mice. The data that we are now entering from different labs and institutions is now used to track the mouse through routine operations and, also, provide a shared electronic archive of the data. By working closely together, the TMGC project members have successfully co-engineered the experimental screening processes and the database processes so that both can begin to work very well together.

The required data entry can now be done either via a web site or from uploaded comma-separated values (CSVs) files. The latter form of entry is particularly relevant for screening results that are automatically produced by machines; this does not require researchers to type in data into a web form. We have also acquired an understanding of what additional functions are needed that can further assist the consortium members in carrying out this project; these new functions can be constructed on top of the current information foundation of MuTrack vers. 1.0. In summary, the current system can (1) Acquire primary screen phenotype data from cores and domains in this project. (2) Automate and support the most basic screening procedures and mouse tracking. (3) Support end-user access to data for the TMGC researcher and provide the underlying database for later user interfaces (to be developed in the second year) that can better disseminate information about the mutant mice. (4) Provides the core information infrastructure that can support additional analysis and collaborative work in this project and support all of the project's aims.