Rebuilding the Airway Cell Atlas from a Landmark Nature Study Using Cellxgene VIP in BxGenomics
| In the high-impact Nature study “Local and systemic responses to SARS-CoV-2 infection in children and adults (Yoshida et al.,2021)”, scientists uncovered why children often fare better than adults when infected with COVID-19. At Cellxgene VIP (Li et al., 2022), we brought this discovery to life—moving beyond reading the findings to reconstructing them through dynamic, interactive visualizations. Cellxgene VIP is an interactive frontend visualization plugin for the cellxgene framework allowing researchers to generate a comprehensive set of high resolution plots with fully customizable settings in real time. It is part of BxGenomics, an integrated online platform developed by researchers at BioInfoRx for the analysis and visualization of both single-cell and bulk RNA-seq data. |  |
Spend Less, Manage More with mLIMS
| Managing an animal colony—whether it’s a small research lab or a large biotech facility—comes with a hefty price tag. Between breeding programs, protocol tracking, cage card printing, and experiment planning, time and resources can quickly add up. That’s where mLIMS Mouse Colony Management Software comes in. Since 2006 mLIMS has been helping labs of all sizes streamline their colony management. But more than just simplifying tasks, mLIMS saves you money—often in ways you might not immediately realize. Let’s break down the cost-saving benefits built into mLIMS, with some real-world examples. |  |
Expanding Horizons: BxGenomics Adds NanoString CosMx Data Analysis to scRNA-Seq View
| In a significant advancement for single-cell and spatial transcriptomics, BxGenomics, an integrated online genomics data analysis system developed by BioInfoRx, has expanded its capabilities by incorporating NanoString CosMx Spatial Molecular Imaging (SMI) data analysis into its scRNA-Seq View application. This integration marks a pivotal step toward providing researchers with a more comprehensive and streamlined web-based platform for analyzing high-dimensional single-cell spatial transcriptomics data. |  |
ScaleSC: Supercharging Single Cell RNA-seq Analysis with GPU Power
| Single cell RNA sequencing(scRNA-seq) has transformed our understanding of cellular biology by allowing us to examine gene expression in individual cells. However, this powerful technology comes with a significant computational cost. In a revolutionary development for the single cell genomics community, Zhengyu Ouyang at BioInfoRx, along with researchers from Biogen, has introduced ScaleSC, a GPU-accelerated solution for single cell data processing (Hu et al., 2025). ScaleSC is freely available on GitHub, BioInfoRx also plans to integrate ScaleSC into the BxGenomics single-cell workflow. |  |
Unlocking the Power of Multi-Omics Data with xOmicsShiny
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In the age of high-throughput biological research, multi-omics integration is essential for unraveling complex biological processes. However, managing, analyzing, and extracting meaningful insights from vast and complex datasets remains a challenge. xOmicsShiny (Gao et al., 2025), developed by researchers from BioInfoRx and Biogen, provides a comprehensive platform for cross-omics data analysis. Unlike existing tools, xOmicsShiny offers an intuitive interface for seamless data merging and interactive visualization across transcriptomics, proteomics, metabolomics, and lipidomics datasets, allowing researchers to efficiently explore pathway-level insights. Users of BxGenomics may also enjoy some of the features from xOmicsShiny in the future. |
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BxGenomics Revolutionizes HIV Microglia Research
The persistent challenge of curing HIV lies in its ability to hide in latent reservoirs, especially in the central nervous system (CNS). In a groundbreaking study presented through a collaboration between Zhengyu Ouyang, director of Bioinformatics at BioInfoRx, Johannes Schlachetzki from UC San Diego (UCSD), and other scientists, BxGenomics played a pivotal role in unraveling the molecular dynamics of microglia in people with HIV under antiretroviral therapy (ART).
mLIMS New Feature - Split Cages
Quickly split multiple animals in a cage to new or existing cages! Find the split cage function in the cages menu.
Managing Strains in mLIMS Mouse Colony Management System
Learn about the improved workflow for managing strains in mLIMS Mouse Colony Management System.
Mouse Colony Software by BioInfoRx to improve your colony management workflow.
mLIMS Mouse Colony Management System
Mouse Colony Software in the Cloud
The leader in Animal Colony Management since 2005
New Features: mLIMS 2024
There are several improvements in mLIMS For Researchers, mLIMS For Biotech, and mLIMS Facility. Learn more here!
BioInfoRx to Attend LAMA-ATA Meeting April 15-18
BioInfoRx is an Allied Trade Association member, and will participate and present at the 40th Annual Laboratory Animal Management Association conference in Fort Walton Beach, Florida.
5 Tips for Robust and Reproducible scRNA-Seq Data Analysis
BioInfoRx and Biogen have developed scRNASequest, an open-source ecosystem for scRNA-seq analysis, visualization, and publishing. To make this powerful pipeline more accessible, our team has introduced a fully supported and user-friendly version in BxGenomics, enabling academic and small biotech researchers to leverage its capabilities without the need for extensive IT and bioinformatics expertise. Here we shared some tips we learned from developing and running the pipeline on hundreds of scRNA-Seq experiments.
RNA-Seq Case Study: Genes Regulated by p53-SET Interplay
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The oncoprotein SET can bind to p53 and inhibits p53 transcriptional activity in unstressed cells. To identify the genes regulated by SET in a p53-dependent manner, the endogenous SET was depleted by siRNA in control or p53 knockout U2OS cells. We use BxGenomics DEG and Venn Diagram tools to find genes regulated by p53-SET. Reference: Nature. 2016 Oct 6;538(7623):118-122. doi: 10.1038/nature19759. |
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RNA-Seq Case Study: iPSC Differentiation into Muscle and Neuron
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We use BxGenomics to examine RNA-Seq data from three key time points during human iPSC differentiation into mature muscle fibers with motor neurons. We can detect consistent genes changes as the cells differentiate, and myogenesis and nurogenesis genes are highly enriched in later time points. Reference: Cells. 2020 Jun 23;9(6):1531. doi: 10.3390/cells9061531. |
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Ultimate Molecular Cloning Guides
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BxSeqTools Enables Gene Sequence Anaysis and Molecular Cloning in The Cloud BxSeqTools is an integrated system allowing users to perform sequence analysis online, use your own data and resources, use public databases like GenBank, organize the results, and perform further molecular cloning work using built in bioinformatics tools. Everything is seamlessly integrated and readily available online. |
mLIMS Release Notes in December, 2021
- Improved Litter Survival and Breeding Performance Reports
- Improved Cage Usage Reports
- Create Animal Tags
- Customize the Strain Dropdown List
- Create Forms (Premium Feature)
Learn more at https://mlims.com/help/what_s_new_in_mlims_2021.htm