Mating Records in Mosaic Vivarium

A mating record in Mosaic Vivarium represents a list of possible parents for a set of litters.  When you put animals together, Vivarium will inspect the list of existing mating records for the same set of parents – if the exact same set of parents exists for a mating record, Vivarium will re-use that mating record for the new mating cage.  That means new litters seen in the cage will be added to the existing mating record.

If the set of possible parents in a cage has not been seen together before, a new mating record is created.  New litters seen in the cage will be added to the new mating record.

The mating record serves at the basis of your pedigree.  To find all ancestors of an animal, Vivarium inspects the parents associated with the mating ID from which the animal came.  Then Vivarium looks at the mating IDs from which those parents came, etc., until it finds animals from the “N/A” mating ID.  Those animals are ones which were received into the system (not bred in the facility).

IMPORTANT:  The only reason to modify the parent animals associated with a mating ID is to correct an error in the identity of one or more of the parents.  When you attempt to make such a change, you will see the following message:

In rare cases, we have seen cases of people modifying a mating record and recording a descendant as a parent.  If you do this, you will see one of the following two messages:

or:

Some earlier versions of Mosaic Vivarium did not perform this check for you, and it was possible to make an error leading to an impossible pedigree (like me being my own grandfather).  We have seen one or two instances of this out of hundreds of thousands of matings.

If you do have a pedigree loop, you will see an error when you try to setup a mating indicating the loop.  The specific animal will be identified.  The easiest way to fix this is:

1. Search for the animal on the Animal Worksheet.
2. Right-click on the animal’s row, and choose Mating –> “All Matings with these Parents”.
3. Next, remove that animal from the list of parents in oldest mating record.

All your animal records will remain, but you will have incomplete pedigree information for some animals.  Of course the pedigree is already incomplete since this error likely occurred by replacing a correct parent in the mating record with a new one.

The important thing to understand is that setting up new matings is the process of putting a different set of possible parents together, resulting in a new mating ID.  Existing mating records which have litters recorded are the birth records for those animals.  Changing the parents in the offspring’s birth records (mating ID) only makes sense as an error correction if the original parents were misidentified.

ORACLE Bug Potentially Affecting Sites Hosting Mosaic Vivarium

If you are running unpatched ORACLE 11.2.0.1.0 64bit Production, you may experience incomplete query results.  The issue is described here:

http://arjudba.blogspot.com/2011/12/select-query-returns-wrong-result-after.html

If you do not apply patches, a work around is to add:

_index_join_enabled=false

to your init.ORA

If you use an spfile, you can issue the following command:

alter system set "_index_join_enabled"=false scope=spfile;

Update to Mosaic Online Help Site

We have migrated our online help site to a dedicated server to improve reliability.  To continue to use context-sensitive help (the “How Do I…” links) in Mosaic, sites that host Mosaic internally will need to take these steps:

Login as the “mosaic” user

Visit the Mosaic Settings page at Administration | Maintenance –> Mosaic Settings

In the Mosaic Application Configuration group, modify the following two settings:

The complete URLs are:

https://m1.mosaicvivarium.com/MosaicHelp/MosaicHelpHandler.aspx

https://m1.mosaicvivarium.com/MosaicHelp/SaasAlerts/alerts.aspx

NOTE:  these URLs will return a blank page if accessed directly via browser.  Content becomes available only when accessed through a Mosaic web site.

RapID Tags

When your animals enter study, you’ll often need to reliably and uniquely identify them.  Recently, we got to see how the RapID Tag technology addresses this need.  Check out RapID Lab for more information.

Cleverly, these tags combine five unique colors with a 2-D barcoded identifier.

• The colors mean you can quickly differentiate your animals visually in a cage – no scanning or animal handling needed.
• The alphanumeric identifiers provide a means of searching your Mosaic Vivarium database for specific animals.
• The 2-D barcode means you can scan the animal to unambiguously determine its identity, no matter where the animal may be.

Take a look at this view we created on the standard Mosaic Animal Worksheet:

To associate RapID Tags with animals in a cage, simply:

1. Scan the Mosaic cage barcode to search for the contained animals on the Animal Worksheet.
2. Make sure the worksheet is in Edit mode.
3. Apply a RapID Tag.
4. Click in the Code column for the appropriate animal and scan the RapID Tag using a 2-D scanner.
5. When you are done with the cage, press Save.

Each animal is now permanently and reliably identified.  Suppose an animal is separated from this cage and you wish to look up its details in Mosaic.  Use the normal Mosaic searching techniques to find the animal with the RapID identifier.  For example, you can click on the Code column header, and then use your 2-D scanner to read the animal’s RapID Tag:

When you hit enter (or your scanner may be programmed to do this automatically), the database is searched for the desired animal.  With 6.7 million unique RapID values, you will not have duplicates in your Mosaic Vivarium database!

The experienced Mosaic Vivarium user will note that we’ve co-opted the Status column to indicate an “animal in experiment with a RapID Tag color.”  This is accomplished by adding values to the Animal Status lookup list.  When registering the RapID Tag values (as shown above), we also selected the tag color.

It would be possible to determine the RapID Tag color automatically when it is scanned.  We’d be interested in hearing from our customers using RapID Tag technology with Mosaic Vivarium to learn about interest in such a capability.  Use the “feedback” link in your Mosaic Vivarium account login to contact us!

Meanwhile, head over to RapID Lab to check it out.

Extracting Results from Transnetyx for Upload to Mosaic

The following information is provided courtesy of Dr. Christian Schmedt of the Genomics Institute of the Novartis Research Foundation.

Tables with genotype data linked to specific mouse IDs can be uploaded to Mosaic via the "Genotyping" menu under "Animals":

Uploading genotypes requires a comma-separated-value (csv) file listing the animal ID in column A and genotypes in the adjacent columns (B, C, maybe D). The genotypes need to be expressed the same way as the long genotype name defined under Administration>Genotypes.

In order to derive a genotype upload file from Transnetyx results, the genotyping assay on the Transnetyx site first needs to be translated to reflect long genotype names in Mosaic:

Translation is easiest in the "full matrix" mode:

(matrix shown is incomplete)

Translation will be reflected in the way the results are displayed on the Transnetyx website:

In order to extract this information and process for Mosaic genotype upload, export the data as XML file:

Switch from "XML editor" to "Excel" to open the document:

And open as XML table in excel:

Click "OK" on the next two dialogs:

The resulting Excel document looks like this:

Column "D" contains the animal ID (this may be different for different Transnetyx users, but the animal ID will be in one of the columns). Column "M" contains the translated result.

Copy columns D and M to a new excel document.

In the new document, use the "Text to Columns" tool to separate the translated results into two columns:

Choose delimited

"Comma" (this may be Space or something else, dependent on how the translations were defined for the Transnetyx assay)

And finish

To get two columns for genotypes:

Note that each ID is represented by 4 rows (one for each Transnetyx probe-set).

Before saving the file, the duplicates need to be removed with the "Remove Duplicates" tool:

Expand the selection beyond column A, which has the animal IDs

Unselect the columns with genotypes:

Click "ok" and save the files as csv:

The saved file is ready for upload into Mosaic.

Assigning Animals to Protocols

Mosaic Vivarium very carefully tracks animal usage under Protocols (Permits).

Actually, what is tracked is the assignment of an animal to an Allocation of a Master Protocol.  Some sites do not distinguish between the Master Protocol and the Allocations.  They simply create a single Allocation for each Master Protocol.

When you assign an animal to a Protocol Allocation, a record is kept of who made the assignment and when.  If the animal is later assigned to a new Protocol Allocation, history of any previous assignments is still maintained.  This leads to a difference between the “Total Used” and the “Total (currently) Assigned” values on the Protocol worksheet.  You can read more by visiting this help topic from the Protocol worksheet “How do I…” link:

Whether to track all Protocol Allocations to which an animal has ever been assigned, or to track just the last Protocol Allocation is a matter of site animal use policy.  However, Vivarium’s history tracking tends to make life a little more difficult for sites where only the last Protocol Allocation is relevant.  It is also a little time consuming to correct errors.

To address this, we’ve added a new privilege that will allow selected users to simply replace all animal use history with the most recent assignment.  This privilege is not enabled by default, so if you do nothing, Mosaic Vivarium will behave as always.  However, if you would like to use this convenience, read the “Transfer Animals to another Protocol” online help topic available from the Animal and Protocol worksheet “How do I…” links:

Using Mosaic with Windows 8

If you are using a laptop or tablet with Windows 8, here are some tips.  By the way, you cannot use all the features of Mosaic with Windows RT, so be sure not to get a Windows RT device if you plan to use Mosaic.

Install Adobe Reader

The built-in PDF reader with Windows 8 does not work well.  (We’ve experienced crashes and an inability to manage print options conveniently.)  Installing the latest version of Adobe Reader will make cage card printing work well again.

Use the Desktop Version of Your Favorite Browser

The version of Internet Explorer you can access from the Windows 8 Start Screen does not work with Silverlight for cases we have tested.  Instead, launch the browser from the Desktop, as shown below.

March 2013:  Using Internet Explorer 10 (IE10) you will also need to click the “Compatibility View” icon.  This requirement will go away in a future release of Mosaic Vivarium.

Following these few simple steps should enable you to use all the features of Mosaic that you are familiar with.  If you have any problems, use the Feedback link on your account.