We are pleased to announce a new OmicsBox release focused on improving your experience. You provided valuable feedback, and we listened carefully. This update introduces thoughtful improvements across the platform, making it smoother, faster, and more reliable to support your daily research.
Here are a few highlights. Find the complete release notes here:
General Improvements:
- The Table Export feature has been enhanced, allowing columns to be adjusted before export.
- File dialogs now remember the last selected location
- Job Messages have a clearer layout.
- All tables now support horizontal scrolling for wide results.
- The FASTA extraction feature runs faster
- Sorting in large tables is more stable.
- The Flye assembler has been updated for improved performance.
- FASTA file inputs are now automatically checked before indexing.
Functional Analysis:
- Pathway diagrams can now be exported in batch, and linked sequences can be extracted directly from the pathway table.
- Enrichment analysis messages and summaries have been refined for better clarity, and plots now include new parameters to filter by tag and Gene Ontology category.
- All BLAST binaries have been updated to the latest version, and results are simplified by removing redundant identifiers.
- EggNOG-mapper has been updated to latest version, which enhances speed, adds new options. OmicsBox now splits datasets into batches for parallel execution.
- InterProScan now saves GFF output by default.
- The Compare GO Annotations tool has been improved.
Transcriptomics and Single-cell Analysis
- For Single-Cell RNA-Seq, violin plots per group are now available, and PCA, UMAP, and t-SNE coordinates can be exported with annotated cells. A new clustering assessment feature provides additional quality metrics and Cell-type annotation with SingleR can now be performed by groups.
- New FLAIR re-quantification option has been added.
- Count tables and differential expression subsets can be extracted more easily for downstream analysis.
- Issues in sample renaming have been resolved.
Metagenomics:
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New taxa-level columns have been added to the results table, providing more informative views of community composition.
About OmicsBox:
BioBam’s bioinformatics solution offers a user-friendly data analysis platform that allows getting from next-generation sequencing reads to biological insights with ease.
OmicsBox offers “out-of-the-box” data analysis and functional interpretation of genome, transcriptome, and metagenome datasets for industry, academic, and governmental research biologists. Our Bioinformatics Software, OmicsBox, is used by top private and public research institutions worldwide.
OmicsBox is structured in the following modules and can be configured as required: Genome Analysis, Transcriptomics, Functional Analysis, and Metagenomics. The Functional Analysis module includes the Blast2GO functional annotation methodology and makes Omicsbox especially popular in non-model organism research with over 10.000 scientific citations.
OmicsBox relies on cloud computation for all resource-consuming tasks like genome assemblies or any other CPU or memory-consuming algorithms. All these computationally challenging bioinformatics pipelines can be run transparently with OmicsBox from any standard PC or laptop on Windows, Linux, or Mac. OmicsBox is based on a subscription model with very flexible licensing options. Please contact us for more information.
How to update?
- OmicsBox will update automatically. If you are working with OmicsBox 2.0 or higher you don’t have to do anything to update to the latest version.
- If you are still using Blast2GO PRO we highly recommend upgrading to OmicsBox. You can download the latest version here
Feedback, questions, and feature requests are most welcome. Please write to support@biobam.com or log in to your BioBam Account.
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.
