Mouse colony management - Here's how I do it. How about you?


Anybody who works with transgenic mice will encounter the problem of dealing with all the information that is needed to maintain the colony. Crosses, litters, weaning, mouse IDs, etc. It can be overwhelming. If the colony is small and you’re just one person, an Excel spreadsheet can work. But as the colony grows and as you try to associate additional information (tissue, samples, litters, downstream experiments), spreadsheets become less useful.

I tried some of the commercial colony management solutions, and databases like the one from Jax. But I found them too clunky and complex.

In the end, I settled on something in between a spreadsheet and an all out SQL database.

I’m using something called Airtable, which is a cloud-based database, akin to Microsoft access but more user friendly and flexible.

It looks just like a spreadsheet, but the main difference is that you can easily link entities across different tables. So for example, you can see I have tabs for Mice, Cages, Tissues, Microscopy Slides and so on. The beauty is, through linking, you can keep track of relationships without having to copy-paste redundant info. So for example, if I’m making some slides from tissue from a certain mouse, I can back track all the way back to the mouse tab, seeing the original cage, the litter, the tissue section, etc.

This works for me now, and it’s collaborative. There is also a legit nice mobile app.

What do you do?

@esypek @tberta @liz


I swear by SoftMouse for colony management:

It’s free, which is nice, and also cloud-based with a decent mobile website (no app yet though). There are some handy features, such as color-coding a good mechanism for genotype info. It doesn’t have much functionality when it comes to tracking the animals in downstream experiments, but you can assign each animal an ID so when I use an animal in an experiment I make a note of the ID. That way I can still trace it back in the SoftMouse software. There is a comment section where you can make notes about a given animal, cage, or litter - so I guess this could also be a good way to document how each animal is used.

SoftMouse has a pedigree/family tree feature in the paid version of the program but not the free version. Therefore I use an Excel spreadsheet to keep track of pedigree and breeding records in conjunction with SoftMouse. There’s some redundancy of info between these two programs but there have been times when that has come in handy so I’m still happy with the system I’ve worked out.