MetaboAnalyst is an easy-to-use, comprehensive web server for metabolomics data analysis, visualization and interpretation. It currently receives over 3 million data analysis jobs yearly. Some major milestones include:

• 2020 - MetaboAnalystR (v3.0)
• 2019 - MetaboAnalystR (v2.0)
• 2018 - MetaboAnalystR (v1.0)
• 2018 - MetaboAnalyst (v4.0)
• 2015 - MetaboAnalyst (v3.0)
• 2012 - MetaboAnalyst (v2.0)
• 2011 - Nature Protocol on MetaboAnalyst
• 2009 - MetaboAnalyst (v1.0)

NetworkAnalyst is a powerful web-based visual analytics platform for comprehensive gene expression profiling, meta-analysis and systems interpretation. It currently supports transcriptomics data (gene lists, gene expression tables or raw RNAseq data) for 17 species. The public server receives around 20,000 jobs monthly. Some major milestones include:

• 2019 - NetworkAnalyst (v3.0)
• 2015 - Nature Protocol on NetworkAnalyst (v2.0)
• 2014 - NetworkAnalyst (v1.0)

MicrobiomeAnalyst is a comprehensive web application for microbiome data analysis. It contains four modules - Marker Data Profiling module offers various options for community profiling, comparative analysis and functional prediction of 16S rRNA data; Shotgun Data Profiling module supports exploratory data analysis, functional profiling and metabolic network visualization of shotgun metagenomics data; Taxon Set Enrichment Analysis module helps interpret taxonomic signatures; and Projection with Public Data module allows users to visually explore their data with a public reference data.

• 2020 - Nature Protocol on MicrobiomeAnalyst
• 2017 - MicrobiomeAnalyst (v1.0)

miRNet is a comprehensive web application for microRNA-target functional analysis and visualization. miRNet offers a wide array of networks connecting miRNAs to genes, metabolites, lncRNAs, epigenetic modifiers, as well as diseases. The system allows users to intuitively explore miRNAs and targets for functional interpretation and hypothesis generation. Since 2018, it also contains a comprehensive list of xeno-miRNAs collected from diverse hosts. The potential target genes of those xeno-miRNAs are also predicted using two popular algorithms.

• 2020 - miRNet (v2.0)
• 2016 - miRNet (v1.0)

OmicsNet is a novel network visual analytics system for creating and exploring relationships among genes, proteins, miRNAs, metabolites or transcription factors in 3D space. OmicsNet has been developed to address three needs: 1) systems analysis of a single list of molecules; 2) integrative analysis of multiple lists of different types of molecules; and 3) web-based 3D visualization. OmicsNet leverages four types of molecular interactions (PPI, TF-gene, miRNA-gene and metabolite-protein). The 3D network visualization was implemented based on the innovative WebGL technology. Users can perform various style customization, functional enrichment analysis, targeted interactor search, and several network topology analyses to gain systems-level insights

• 2018 - OmicsNet (v1.0)

Tools developed in the past have become modules to be maintained and updated together with our current tools. Locations of these tools are given below:

• Xeno-miRNet now part of miRNet
• INMEX now part of NetworkAnalyst
• INVEX now part of NetworkAnalyst
• ROCCET now part of MetaboAnalyst
• MetPA now part of MetaboAnalyst
• MSEA now part of MetaboAnalyst
• MetATT now part of MetaboAnalyst
• MetaboMiner stand alone tool (project home)