We are happy to announce OmicsBox 4.0, a major update to BioBam’s OmicsBox platform. The release extends transcriptomics and functional analysis, deepens the integration with cloud execution, and introduces AI-powered analysis summaries. This major release, OmicsBox 4.0, is a significant milestone for BioBam. It brings together several new concepts: Cloud Sync, full visibility and logging for cloud execution, AI features and new methods for differential and co-expression analysis.
One of the most important additions is CloudSync, together with the surrounding improvements in cloud usage, logging, and file handling. CloudSync moves more than thirty data-intensive tools off the desktop and into the cloud, where they run independently and are tied to Cloud Files. Analyses can be started in OmicsBox and continue even after the application is closed; results become available once they complete. The Cloud Usage viewer lists task details, including parameters and the size of input and output data. A new Log Viewer adds real-time log streaming to follow long runs as they progress. On the last page of each wizard, cloud file handling now allows outputs to be stored in the cloud, downloaded locally, or both, so that results land where they are needed for the next step.
On the analytical side, OmicsBox 4.0 extends transcriptomics and functional interpretation. Gene Co-expression Network analysis integrates WGCNA-style workflows, including module detection, gene network charts, and module-trait correlation, for studies where groups of co-regulated genes are of interest rather than a single ranked list. Finally, AI-powered analysis summaries provide a concise textual overview of enrichment results, taxonomic classifications, and sequence annotation outputs. The summaries are shown alongside the existing tables and plots and are intended to support, not replace, the interpretation of the underlying data.
OmicsBox 4.0 Release Notes:
New features
- New Cloud Sync system: 30+ data-intensive tools now run independently from OmicsBox in the cloud with Cloud Files integration
- New Cloud Usage viewer with task details such as parameters, input and output data size, and a Log Viewer with real-time log streaming
- New cloud file handling on the last wizard page: save outputs to the cloud, download locally, or both
- New AI-powered analysis summaries for enrichments, taxonomic classifications, and sequence annotation
- New Gene Co-expression Network analysis with WGCNA: module detection, gene network charts, module-trait correlation, and more
- New Differential Expression analysis with DESeq2: interactive volcano plots, and more
- New Fasta Splitter tool
Transcriptomics
- Improved interactive volcano plots with tooltip for regulated genes
- Improved time course analysis with FET side-panel action and expression profile tooltips
- Improved SingleR with annotation by group, quantile, and aggregate reference parameters
Functional analysis
- Improved Pathway search
- Improved functional enrichment plots with GO category filters
- Improved GSEA bubble plot with GO category selection and top/bottom filtering
- Improved FET enriched GO graph with over/under regulation selection
- Improved word cloud with a filter wizard for top/bottom tags
- GFF as default output in InterProScan
- GSEA downstream analysis option for differential expression results
- New combine Blast2GO project files option
General
- New interface improvements (report styles, icons, toolbar)
- New tab renaming feature
- New email notification for Cloud Sync jobs
- Enhanced Cloud Files with drag-and-drop, copy/paste, last modified column, and multi-part upload and download with progress tracking
- New combine/merge tool in the General tools menu for .box files
- Removed forced device scale on high-DPI screens to fix blurriness
- Enhanced charts with more options for nodes and edges (size, color, label)
- Multiple minor bug fixes
Step-by-step instructions for each tool are available in the OmicsBox user manual.
About OmicsBox
OmicsBox is BioBam’s bioinformatics software for the analysis of omics data. It provides out-of-the-box workflows for genomics datasets, organised in five modules: Genome analysis, Transcriptomics, Genetic Variation, Functional analysis, and Metagenomics. The Functional analysis module is based on the Blast2GO annotation methodology, with more than 10k citations in the scientific literature, and is widely used in non-model organism research. Computationally demanding steps, such as genome assemblies and other CPU- or memory-intensive pipelines, are executed in the cloud. OmicsBox itself runs on a standard PC or laptop under Windows, Linux, or macOS. Licensing is subscription-based, with flexible options.
Feedback, questions, and feature requests are welcome at support@biobam.com or through the BioBam account. Further information, documentation, and contact options are available at biobam.com/omicsbox and in the user manual. Trade names: BioBam, OmicsBox, and Blast2GO as used by BioBam.
About the Author
Stefan Götz
Stefan started his career in computer science and developed a keen interest in biomedical applications. He transitioned from biomedical informatics to computational biology, specializing in functional genomics and sequence analysis. After completing a Ph.D. in bioinformatics, Stefan chose to pursue a non-academic path and became an entrepreneur. In 2011, he founded BioBam, a bioinformatics company aimed at advancing genomics research to enhance human health, food safety, and environmental quality.
As the CEO of BioBam, Stefan is responsible for various aspects of the company's growth, such as business strategy, product management, team leadership, and research and innovation.
