TCP LIMS - Introduction Objectives provide TCP users with an understanding of how to use TCP’s Laboratory Information Management System (LIMS)

Browser Support We recommend using Firefox or Chrome when accessing LIMS. Other browsers (especially Internet Explorer) will work 'most of the time' but they are not supported.

Log In The Tour LIMS link can be used to go to the Online Help pages.

Home Page 1 - Menu 2 - Link to User's Preferences and Details 3 - Logout 4 - Breadcrumb 2 3 5 - Quick Search 1 6 - Bookmarks 5 6 4 7 - Link to the Online Help 7 8 - Notifications 9 - Quick Stats 10 - News 11 - Updates 8 9 12 - Calendar 13 - Health Concerns 11 14 - My Lab Groups 12 10 13 15 - Cages by Room 14 15

User Preferences and Details Click on your user name to navigate to the page containing the contact information, preferences, courses, and building access information. You can also change your LIMS account password. Keep your contact information up-to-date on the LIMS production system, especially the email address and phone number. This information is used by the animal care attendants to contact you about your mice.

User Preferences and Details The User page also allows you to set certain account preferences. Try It Log in to the LIMS system (https://lims.phenogenomics.ca) and verify your account’s details and preferences.

Breadcrumb The breadcrumb bar is the lighter-coloured bar just below the navigation bar which shows you where you are in the site. It shows the real path that you've followed through the site to get to the current page. That means that even if you take an unusual route to the page, you can always get back to any page along that path, either using the breadcrumb directly, or using the Close button. Navigating the site using the breadcrumb will cancel any unsaved changes.

Quick Search The Quick Search option, found in the top right corner of the screen, is an easy way to search for something. Enter the information (i.e. AUP #, contact name, mouseline, etc) into the search field and press enter. If you've entered something with only one result, for example a cage card number, you'll be taken directly to that result's view page. If you've entered something with multiple results, like a common first name or a partial mouseline name, you'll go to a page with all the results listed by object type (ie. allele, mouseline, person, etc).

Bookmarks Click on the small bookmark icon on the breadcrumb bar on any page which you'd like to bookmark. Clicking on the dropdown icon will show you all your bookmarks. Delete a bookmark by hovering over the link and clicking the small 'x' beside the bookmark.

Online Help Click on the LIMS Tutorial link to access the LIMS on-line help.

The Notifications feature allow facility and lab members to communicate important messages regarding their cages. Notifications Click on the Notification title and scroll to the bottom of the page to see the details. The Home page’s Notification panel shows the most recent active notifications that have been sent to the user. Once you have seen a notification, dismiss it to remove it from the Active list and your Home Page.

Notifications To create a new notification, click the New Notification button at the top of the page

The Quick Stats area on the Home page provides a summary of important cage details. Active Cages indicates the number of active cages on the lab’s AUP(s) regardless of the cage's contact person. Cages Unscanned are likely those whose mice have been euthanized, but the cage not terminated in LIMS. Per diems will continue to be charged to the PI until the cage record is terminated. Empty Active Cages are those with no mice associated with them. This can happen when: Cages are removed from the racks and need to be terminated on LIMS; or Cages are improperly terminated on LIMS and found by TCP staff during a census scan. Once it has been verified that the cage is no longer in the facility, click on the Cages Unscanned link and Terminate the cage. You need to find the cages in the facility and update LIMS accordingly to ensure cage information is accurate.

News The News sections displays information of general interest such as Changes to room and equipment availability Upcoming service outages Courses or presentations that could be of interest to some users

Updates The Updates section displays information of interest to the logged in user, including: Reservations the user have made Courses the user has enrolled in Upcoming weanings in the user’s cages Received mouse orders New mouse log entries for mice in the user’s cages

Health Alerts The Health Alerts panel provides a list of cages with mouse/litter welfare issues TCP staff are monitoring or treating for and your cages with mice/litters that have reached an endpoint. Click on the Health Alert Cage link to navigate to the affected cage. For more information, please review the Cage Cards II course.

These images are from the Mouseline Search screen. Most search pages allow the user to enter detailed search criteria. Searching To access detailed search fields, click the Change link or the + sign at the right side of the search panel. Results can be sorted by clicking on the column heading. To customize the columns you want to see when using any search page, click on the Column Options link and select or deselect the preferred fields. Only the columns selected for display will be scanned for the text entered in the Search field.

Bug Reports The Bug Report link at the bottom of the page can be used to notify the LIMS development team of any issues encountered or to provide suggestions that would improve the functionality of LIMS. Remember: If you don't tell us about an issue, we can't fix it.

Navigation Links are available to navigate to related objects. Links are denoted as blue text or a link icon.

Editing Fields Click the link, edit the information, and click the green check mark to save or the red X to cancel. Any field that is grey with a dotted underline is editable. Required fields are denoted by a red asterisk.

TCP LIMS The live site is available at https://lims.phenogenomics.ca. Questions Contact the LIMS Team at tcpwebteam@phenogenomcs.ca