Known Issue: Magic Scrolling in Chrome 37.0

If you are using Chrome around version 37, such as this version:

you may find that wide worksheets in Mosaic (those with a horizontal scrollbar at the bottom of the grid) will slowly scroll themselves back to the left.  This has just started with the introduction of recent versions of Chrome.  We are working on a fix.

Meanwhile, we’ve also identified that this behavior does not occur if the browser is set at 100% zoom.  You can check your zoom using the menu in the upper right:

Adjusting back to 100% seems to eliminate the unwanted scrolling.

Heartbleed Vulnerability

Mosaic Vivarium does not use the open source “OpenSSL” package and is therefore not vulnerable to the Heartbleed exploit.  Mosaic Vivarium servers (either hosted by us or at our customers’ facilities) use Microsoft web servers with Microsoft’s implementation of SSL.

Known Issue: Intermittent Error Messages, Especially with Chrome version 33+

You may sometimes see an error dialog:

If you click on Details you then see “breeze error: Error: Illegal construction – use ‘or’ to combine checks”:

This happens mostly when you first login and seems especially prevalent with the latest version of Chrome, version 33.

The message is a nuisance that poses no problems for your data:  simply refresh the web page.  We apologize for the inconvenience.

We are working hard to find the cause and fix it.

Cage Card Printing with Chrome version 33+

During a recent update to Chrome, Google introduced a built-in PDF viewer.  Unfortunately, this does not have the control needed to properly print cage cards.  There is a simple procedure to restore the previous behavior using Adobe Reader:

In the Chrome address bar, type chrome://plugins

Find a section that looks like this:

Disable the Chrome PDF Viewer and Enable the Adobe Reader so the settings look like this:

Done.

Note – there are always security considerations with browser plugins.  Adobe Reader is widely used and from a trusted author.  Nevertheless, you should take care to install recommended security updates for Adobe Reader as they become available.

Updating MosaicService

For customers with Mosaic installed on your own servers with a current software maintenance contract, you will occasionally receive updates to the MosaicService.  This component is responsible for scheduled Notifications, and other services.  Here are the steps:

• Stop the Mosaic Service
• COPY your MosaicService directory as a precaution
• Extract the new MosaicService.zip contents over your existing MosaicService directory
• Start the Mosaic Service

Additional notes (before re-starting the service):

Make sure to retain a copy of your original vci.config.xml file which resides in your MosaicService directory.  This file is overwritten when you extract the .zip file.  You will need to re-introduce any local modifications made to this file, usually those settings which start with Vci.Mosaic.Email.* which configure email.  Pro tip:  enter XML comments in your version of vci.config.xml that remind you which settings you have modified for your local install.

You do not need to retain contents of the Vci.Mosaic.MosaicSchedulerService.Clients node because you will re-register the web with the service later.

If your Mosaic sandbox does not reside at D:\MosaicSandbox, you will need to modify:
<add key="Vci.Mosaic.Sandbox" value="D:\MosaicSandbox\Service" />
in your MosaicService.exe.config file.  This file is overwritten with new updates, so you’ll need to inspect your original MosaicService.exe.config for the proper value of Vci.Mosaic.Sandbox on your server.

Finally, re-register your Mosaic web with the service:

• Login as mosaic
• Visit Administration | Maintenance -> Mosaic Maintenance
• "Cache and Miscellaneous"tab
• Press "Register With Scheduler"
• Visit Administration | Reports -> Event Log to confirm

Uploading Genotypes to Mosaic Vivarium

Background

Genotype results frequently are provided in Excel format. Here we describe how to prepare your data for direct upload to Mosaic Vivarium.

Procedure

An example results download from Transnetyx looks like this:

First, eliminate all information except the animal identifier and genotype calls until the spreadsheet looks like this:

If you have fewer than 100,000 animals in Vivarium, you’ll need to format the numbers to include leading zeros. Drag the following formula down:

To get this:

If your Transnetyx download includes hyperlinks, right-click the column header and choose “Remove Hyperlinks”:

Select your formatted values and click Control-C to copy them:

Right-click in cell A1 and choose Paste Values:

Then right-click the column header of the column you created and choose delete:

You are left with the animal identifier column and one or more genotype call columns. Save this as a CSV file:

If you open the saved file with Notepad, you should see:

Now visit Animals | Genotyping:

Press the “Upload Genotypes” button and follow the prompts. Make sure the order of the columns shown matches the order of columns in your CSV file:

Press the Upload button at the top of the grid, follow the prompts.

If you get errors such as the following:

it means that the nomenclature used by your genotyping service does not match the nomenclature you have used in Mosaic Vivarium. Vivarium uses the long name of the genotype call to perform the match. You can either modify the import file, or modify Mosaic Vivarium. Genotype nomenclature must match for the import to work.

If you wish to modify Mosaic Vivarium, visit Administration | Lists -> Lookup Lists and select the Genotypes list. You can edit the long or short names of any genotype in the system. Note: if modifying the central genotype lookup modifies the genotype label for ALL EXISTING animals in the system that use that genotype. Be sure you understand what you are doing before performing this edit.

Once your genotype data file matches your Vivarium genotype nomenclature, the import will work:

For more details specific to Transnetyx, see also Extracting Results from Transnetyx for Upload to Mosaic