Managing a mouse colony effectively is a critical but often underestimated aspect of laboratory research. Whether you’re creating a new mouse model tailored to your study or purchasing an existing line from a company or repository, the real challenge begins when the mice arrive: efficient and accurate colony management.

If your lab relies on spreadsheets or basic tools like Microsoft Access, you may already be familiar with the frustrations of static data tracking. These tools can quickly become cumbersome, leading to disorganization and potentially costly errors in your research data. Without the right tools, staying on top of breeding, genotyping, and cage organization as your colony expands can feel overwhelming.

This is where investing in dedicated colony management software can make all the difference. With the right solution, your lab can:

• Streamline animal tracking: Consolidate all data into an intuitive, centralized platform.

• Improve organization: Easily monitor cage details, breeding schedules, and lineage tracking.

• Ensure compliance: Stay ahead of animal welfare laws and regulatory requirements.

• Save time and resources: Reduce administrative overhead, allowing researchers to focus on science.

As your lab’s needs evolve, colony management software provides the scalability and flexibility required to maintain order, accuracy, and compliance. Adopting these tools enhances operational efficiency and frees up critical resources to advance research goals.

As of January 2025, mouse colony management systems have evolved to offer comprehensive, web-based solutions that streamline the complexities of managing laboratory mouse colonies. These platforms enhance efficiency, accuracy, and compliance in research settings.

Here Are The Top 5 Lab Mouse Colony Management Software Options We Found, As Recommended By real users and scientists on ResearchGate, X, and other platforms:

1) SoftMouse.NET by Iseehear Inc.: A widely adopted solution

SoftMouse.NET is still the most widely adopted colony management software among academic institutions. It is known for its user-friendly interface and cost-effective solutions. It offers a "FOREVER FREE" plan tailored for individual users and smaller labs, enabling efficient tracking of relational data between mice and supplies without the need for advanced features.

For laboratories requiring more comprehensive functionalities, SoftMouse.NET provides a "PREMIUM" option, which includes:

Breeding Schemas: Streamline complex and simple breeding setups, including male rotations, trio breeding, and timed matings.
Email Alerts: Stay informed with automated reminders for critical events such as weaning dates, breeder replacements, and custom events.
Family Tree Visualization: Access a dynamic pedigree chart to track up to 10 generations of ancestors and progeny, facilitating comprehensive lineage analysis.
File Uploads: For centralized data management, attach relevant documents, such as genotype gel images, directly to animal records.
Statistics and Reports: Generate real-time colony counts, productivity metrics, and detailed reports with ease.
Experiment Planning: Design and manage study timelines, methodologies, and protocols within the platform.

Both plans include free, unlimited technical support, ensuring users receive assistance as needed.

SoftMouse.NET is accessible on desktop and mobile devices, including iPad and Android tablets, allowing researchers to manage their colonies remotely.

Users have reported significant improvements in efficiency and usability over the years, as commented on Researchgate. One researcher noted a 75% increase in speed compared to previous methods, while another praised the intuitive interface that facilitated quick adaptation among colleagues.

2) mLIMS by BioInfoRx, Inc.: Another widely adopted contender

mLIMS has offered efficient mouse breeding colony management solutions for almost two decades. This user-friendly, web-based software stores real-time data in the cloud and is optimized for mobile devices, enabling researchers to manage their colonies anywhere. By consolidating multiple processes into a single workflow, mLIMS aims to streamline laboratory operations, ultimately saving time and resources.

The software is available in various versions to cater to different user needs:

• mLIMS for Researchers: Designed for individual research labs, providing essential tools for managing animals, cages, breeding, and experiments.

• mLIMS for Biotech: This version is tailored to biotech and pharmaceutical companies and includes features from both the Researchers and Facility versions.

• mLIMS Enterprise: Suited for departments or organizations, allowing management of multiple labs under one system with administrative controls.

• mLIMS Facility: Developed for core animal facilities or vivariums, offering additional features like census reporting, cage and rack management, task management, medical records, and billing capabilities.

• mLIMS Complete combines all the features from the Standard, Enterprise, and Facility versions to meet the comprehensive needs of an entire organization.

All versions include animal and cage management tools, breeding, protocol tracking, and features such as email notifications and built-in reporting.

Academic researchers can access a free trial to evaluate the software’s capabilities. Scientists in biotech, commercial labs, organizations, and core facilities should schedule a demo to experience mLIMS firsthand.

3) PyRAT Animal Facility Software by Scionics

PyRAT, a web-based mouse colony management system, aims to help labs simplify their processes and save money. It features billing, invoicing, visualizing data, and complying with legislation easily. Other features support mouse breeding charts, mouse genotyping services, ordering services and supplies, and more. This animal facility software is available to users globally and offers English, French, German, Italian, Portuguese, and Spanish language support.

Not only is PyRAT user-friendly, but it also stores all of its data in a central database for added security. This allows users to access their data from anywhere conveniently. You can try PyRAT out for yourself by requesting a free private demo.

4) Climb™ By RockStep Solutions

Climb™ 2.0’s software was developed to help labs in biotech, pharma, CRO, and academic spaces manage their overall studies. Colony management and veterinary care are just some of the main features, alongside biological sample management, analysis, and protocol management. Others include animal welfare compliance, data delivery, and remote study planning and scheduling. Climb™ has also partnered with Scientist.com to allow users to order scientific materials remotely.

Because biotech and academic labs have unique needs, it’s crucial to evaluate precisely what features are needed to manage mice. RockStep Solutions has prepared a special “Climb-A™” introductory package for research and development labs, offering the most optimized features specifically for mouse colony management.

To find out if Climb-A™, or Climb™’s full suite of features, would be a good fit for your lab, you can schedule a demo with their experts.

5) Mouse J: an entirely free system developed by and for academics

Mouse J was developed by an academic scientist for the benefit of the scientific community and thus is distributed fully for free. MouseJ is a lightweight and interactive mouse colony management software designed specifically for research laboratories. It emphasizes simplicity and usability, allowing users to view all essential information on a single screen. Features include a refined main interface with icons and images, a calendar function for essential dates like weaning and timed pregnancies, and the ability to import and export data to Excel. These functionalities have contributed to its growing popularity among small research labs seeking an efficient, straightforward solution for managing mouse colonies.

Other popular options include mausoleum, myVivarium, and the most recently launched and free MouseJ. The latter gets the least mentions, suggesting it might be more niche or less known. The table below provides an overview of various mouse colony management software options, highlighting their distinctive features, cost, supported platforms, release and update history, and estimated user base.

Mouse Colony Management Software Comparison

Mouse Colony Management Software Comparison

Comprehensive overview of leading laboratory mouse colony management solutions for 2025

SoftMouse.NET

Easy-to-use interface
Breeding schemas
Family trees
Email alerts

Cost:

Free version available
Premium: ~$600/year for 5 users

Platforms:

Web-based Mobile

Last Updated:

2024

First Released:

2007

Estimated Users:

High

mLIMS

Cloud-based real-time data storage
Multiple versions
Protocol tracking

Cost:

Varies by version
(Contact for pricing)

Platforms:

Web-based Mobile

Last Updated:

2024

First Released:

2006

Estimated Users:

High

PyRAT

Billing and invoicing
Data visualization
Multi-language support

Cost:

Contact for pricing

Platforms:

Web-based

Last Updated:

2024

First Released:

Not specified

Estimated Users:

Medium

Climb™

Customizable options
Optimized for R&D labs

Cost:

Contact for pricing

Platforms:

Not specified

Last Updated:

2024

First Released:

Not specified

Estimated Users:

Medium

Other options with very low or niche users

MyVivarium

QR code-enhanced cage cards
Task assignments and reminders
IoT-based ambient sensing

Cost:

Contact for pricing

Platforms:

Web-based Mobile

Last Updated:

2024

First Released:

Not specified

Estimated Users:

Very Low

Mausoleum

Drag-and-drop functionality
Automatic cage detection for breeding

Cost:

One-time server license fee + additional client licenses

Platforms:

Windows OSX Linux

Last Updated:

2024

First Released:

Not specified

Estimated Users:

Very Low

TopoDB

Individual animal tracking
Genetic and phenotypic data storage
Preliminary data analysis

Cost:

Not specified

Platforms:

Web-based

Last Updated:

2020

First Released:

2020

Estimated Users:

Very Low

MouseJ

Free and open-source
Easy data sharing
Simple colony management

Cost:

Free

Platforms:

Windows

Last Updated:

Not specified

First Released:

2019

Estimated Users:

Very Low

Bonus: Mouse Breeding Planner By ingenious targeting laboratory

Before trying out any software options discussed here, you can get a headstart on your mouse colony with our exclusive Breeding Planner. This free software allows you to create a fully customized breeding plan before your mice arrive at your facility. Our guided software will help you predict the time and cost of your project based on your strain’s breeding performance and your facility’s operating costs. You can also quickly compare different breeding options with the graphical output feature.

We hope you’ve found this article helpful and that you can choose the ideal lab animal management software for your lab!

Top 5 Lab Mouse Colony Management Software Options For 2025

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