We are happy to announce OmicsBox Web, a new browser-based companion to BioBam’s OmicsBox platform. OmicsBox Web is available at https://omicsbox.biobam.com and uses the same OmicsBox account credentials, so analysis jobs launched via OmicsBox, input data and results as well as account settings are now reachable from any device with a web browser. OmicsBox Web is designed to complement the
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
Introduction Driven by advances in long-read sequencing technologies, high-quality phased (haplotype-resolved) reference genomes are becoming increasingly available for complex polyploid organisms, including agronomically important crops. In this blog post, we will explain what phased reference genomes are and how they can be combined with long-read RNA-seq to unlock the secrets of allele- and haplotype-specific gene expression in complex polyploid organisms.
Introduction Differential gene expression analysis is a fundamental step in the interpretation of RNA-seq data. It aims to identify genes whose expression levels change significantly between experimental conditions, such as treated versus control samples or different biological states. These changes provide insight into the molecular mechanisms underlying phenotypic differences, enabling the discovery of biomarkers, regulatory pathways, and functional responses to
Establishing a high-quality de novo transcriptome is the first step for quantifying transcript abundance and mapping the biological pathways active in non-model species. For researchers working with non-model plants like Rorippa indica, a wild mustard known for its tolerance to the mustard aphid (Lipaphis erysimi), the challenge lies in turning millions of raw Illumina short reads into a biological insight
Introduction Differential Expression vs Gene Co-Expression Analyses In transcriptomics, differential expression analysis (DEA) is a standard step to identify genes whose expression levels significantly differ between conditions. This approach highlights candidate genes associated with a phenotype but focuses only on changes in expression magnitude and typically evaluates a limited number of factors or pairwise comparisons. As a result, it does
At PAG33, we had the opportunity to participate once again in one of the most important international meetings for Plant and Animal Genomics. In addition to our exhibition booth, this year we were pleased to organize an industry workshop focused on practical non-code bioinformatics workflows using OmicsBox. The session brought together both methodological overviews and real research applications, and
BioBam returns to San Diegeo for another year. After many editions participating in The Plant & Animal Genome Conference (PAG), we are excited to host our own Industry Workshop for the first time. This special session will bring together our team and invited experts will walk through end-to-end workflows for functional analysis, transcriptomics, genetic variation, and long-read data, all without
Long-read sequencing technologies, led by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), have transformed transcriptomics research1. They enable scientists to study alternative splicing and isoform diversity in unprecedented detail. Unlike short-read sequencing, which requires computational assembly of millions of fragments into transcript models, long reads can capture entire RNA molecules in a single read. However, due to various
