High-performance Integrated Virtual Environment
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  • High-performance Integrated Virtual Environment (HIVE) platform

    HIVE is a cloud-based environment optimized for the storage and analysis of extra-large data, such as biomedical data, clinical data, next-generation sequencing (NGS) data, mass spectrometry files, confocal microscopy images, post-market surveillance data, medical recall data, and many others. HIVE provides secure web access for authorized users to deposit, retrieve, annotate and compute on Big Data, and analyze the outcomes using web user interfaces.

  • High-throughput Sequencing Computational Standards for Regulatory Sciences (HTS-CSRS)

    For this FDA funded project, we are developing a framework for community-based development of standards for harmonization of High-throughput Sequencing (HTS), standardization of data formats, promotion of interoperability, and bioinformatics verification protocols. The HTS Computational Standards for Regulatory Sciences (HTS-CSRS) web portal will serve as a collaborative ground to encourage a dialogue which will ensure future interoperability between different bioinformatic pipelines, industries, and developers. We are extending HIVE capabilities to support the development of HTS standards. The HTS standards will be versatile and adaptable to other common HTS analysis platforms.

  • Glycoproteomics Characterization Workflow and Data-Analysis Pipeline for Vaccines and Biosimilars

    In this FDA funded project we are extending High-performance Integrated Virtual Environment (HIVE) capabilities through the development and integration of software tools and datasets for comparative analysis of glycoproteins. Glycomic analysis has many angles and has been extensively reviewed in recent literature. We propose to rely on the independent development of the glycomics field and incorporate these approaches in the HIVE pipeline as they mature while we develop a standardized glycoinformatics pipeline that will benefit investigators and regulators at the FDA.

  • GutFeeling: Gut Microbiome Analytic System

    The HIVE team received NSF funding to develop a Gut Microbiome Monitoring System (GutFeeling) as a tool which when used over time will allow users to rectify their dietary (such as consumption of probiotics and prebiotics) and other lifestyle habits and to help restore their normal microbiome. Rapid analysis of the large amount of metagenomic data, a major bottleneck, has been resolved by our group through the development of a novel algorithm and accompanying software called CensuScope. Through analysis of healthy gut microbiome data, we are actively developing a KnowledgeBase (GutFeelingKB) to provide a clearer picture of not only an ideal personalized microbiome but also establish baseline characteristics for each customer. The Mazumder Lab is collaborating with the Milken School of Public Health and Kamtek Sequencing Facility to investigate the relationship between bacterial species commonly present in the digestive tract, diet, physical activity, lifestyle habits, and metabolic risk factors.

  • Rapid and accurate virus detection from NGS data

    The main goal supported by this collaboration is to develop and optimize a pipeline for virus detection through the analysis of Next-Generation Sequence (NGS) data on HIVE. This pipeline supports the characterization of vaccine samples and cultures used to make biological medicines. The approach will involve optimizing virus detection workflows, data visualization, and an end-to-end pipeline to facilitate viral metagenomics analyses.

  • HIVE-EQAPOL Project on HIVE NGS Data Processing and Analysis

    For this project, our group works closely with the External Quality Assurance Program Oversight Laboratory (EQAPOL) team to conduct HIV NGS data analysis and collaborate in terms of analyzing, storing, and tracking HIV NGS Data. Reliable identification of strains is critical for developing new assays, validating assay platforms, assisting regulators to evaluate test kits, monitoring HIV drug resistance, and informing vaccine development. The HIVE tools and platform are used for virus identification, recombination analysis, and clone discovery.