HiOmics 2.0: An All-in-One Intelligent Cloud Platform for Multi-Omics Analysis in Biomedical Research

Abstract

Rapid advances in high-throughput sequencing and mass spectrometry have introduced substantial challenges for multi-omics data analysis, including fragmented workflows, slow interactive responsiveness, and limited reproducibility of results. To address these issues, we present HiOmics 2.0 (https://henbio.com), a substantially upgraded cloud platform. The core innovation is a hierarchical task-scheduling system that decouples lightweight interactive tasks from compute-intensive analytical pipelines and enables real-time responses via a dedicated API cluster. This redesign reduces the generation time of common analytical plots from over 30 seconds to below 5 seconds (an improvement exceeding 80%), delivering responsiveness comparable to local desktop software. Building on this foundation, the platform adds modules for single-cell transcriptomics, proteomics, metabolomics, pathogen detection, and Mendelian randomization. Accordingly, HiOmics has evolved from a collection of discrete tools into an integrated infrastructure that supports systematic life science research. The unified platform enables users to complete an end-to-end research workflow—from data preprocessing and multi-omics mining to model development and visualization. As of November 2025, HiOmics 2.0 integrates 453 analytical tools, has recorded 112,957 visits from users worldwide, and has completed 36,726 analytical tasks. Representative case studies demonstrate its utility in both basic research and clinical translation. Overall, through architectural innovation and functional integration, HiOmics 2.0 provides an efficient, user-friendly, and reproducible all-in-one solution for life science research.