JAX Colony Management System (JCMS): an extensible colony and phenotype data management system

Abstract

The Jackson Laboratory Colony Management System (JCMS) is a software application for managing data and information related to research mouse colonies, associated biospecimens, and experimental protocols. JCMS runs directly on computers that run one of the PC Windows operating systems, but can be accessed via web browser interfaces from any computer running a Windows, Macintosh, or Linux operating system. JCMS can be configured for a single user or multiple users in small- to medium-size work groups. The target audience for JCMS includes laboratory technicians, animal colony managers, and principal investigators. The application provides operational support for colony management and experimental workflows, sample and data tracking through transaction-based data entry forms, and date-driven work reports. Flexible query forms allow researchers to retrieve database records based on user-defined criteria. Recent advances in handheld computers with integrated barcode readers, middleware technologies, web browsers, and wireless networks add to the utility of JCMS by allowing real-time access to the database from any networked computer.

Fig. 1

Illustration of the three primary installation configurations for the JCMS application. (1) JCMS can be used as a stand-alone application for a single user, or (2) in a multi-user networked configuration. The most flexible configuration, (3) shows JCMS accessible via the web and accessed from multiple operating system platforms (LINUX™, Windows™ or Macintosh™). In the multi-user configuration examples, the black dots indicate that there may be any number of users, not just three users as depicted in the illustration

Fig. 2

Screen shots of the JCMS welcome page (a), main function bar (b) and forms for adding (c) and editing (d) information about mice. Function buttons are designed to support numerous workflows and are organized by task on the function bar

Fig. 3

Typical animal husbandry workflow supported by JCMS. Optional database entry tasks (Design Mating, and Record Litters) and reports (Check Mating, Wean Work) are shown with dashed outline. Wean work reports can only be generated if the JCMS user records litters when they are observed in the mouse room. Regardless of which JCMS functions used, the mouse room activities (illustrated as trapezoids) are the same in each workflow. Some database entry steps (illustrated as rectangles with solid boarders) are required in the workflow to ensure the colony data are stored in the JCMS database

Fig. 4

An example cage card for a cage holding three mice. Cage cards can be custom formatted in any size or layout orientation that is supported by the printer

Fig. 5

The JCMS sample storage browser. The browser allows users to quickly search a storage facility to locate samples. The left panel is the navigation tree; in the right panel is a list of all samples stored in the selected node. If the “Recurse” checkbox is selected, all samples in the selected node and all sub-nodes are displayed (as in the above diagram, where all samples in ISLE-1 are displayed

Fig. 6

Ad-hoc mouse query form and an example output table. In this example query we have selected live mice with IDs that have EX in the name and are in the STOCK Igf1/ImJ strain. The report output fields are selected by check-box selection on the right side of the form. The remaining fields on the form are query filters which allow the user to apply highly specific criteria for the report output. This query form also allows the user to press a button and associate groups of mice with experiments

Fig. 7

JPT ancestor tree for mouse BW-L160-6. From right to left, each generation is represented by columns. Thus, mouse BW_1W0001 and BW_1W0006 are parents of mouse BW-L160-6 and BR_WR002 and HH-W0004 are grandparents. BR_WR0002 has three parent mouse records (trio mating): HH-W0002, HH-W0003, and HH-W0004. Genotype, sex, and strain information are also displayed for each mouse in the tree. The bottom panel shows details for selected mouse