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Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource.

Julia M Kelliher1, Yan Xu1, Mark C Flynn1

  • 1Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.

Computational and Structural Biotechnology Journal
|February 18, 2025
PubMed
Summary

The National Microbiome Data Collaborative developed NMDC EDGE, a user-friendly web application for standardized microbiome bioinformatics workflows. This resource enhances data accessibility and interoperability for multi-omics research.

Keywords:
Bioinformatics workflowsMicrobiomeMulti-omicsOpen-sourceSoftwareStandardization

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Area of Science:

  • Microbiome Research
  • Bioinformatics
  • Computational Biology

Background:

  • Standardized bioinformatics workflows are crucial for advancing microbiome research from observational studies to large-scale, data-driven approaches.
  • Standardized multi-omics data facilitates comparative studies, data reuse, and machine learning applications for modeling biological processes.

Purpose of the Study:

  • To introduce the Empowering the Development of Genomics Expertise (NMDC EDGE) resource, an open-source web application designed to improve the accessibility of standardized multi-omics bioinformatics workflows.
  • To describe the design and functionality of NMDC EDGE for processing diverse microbiome data types.

Main Methods:

  • Developed a user-friendly, open-source web application (NMDC EDGE) with a three-layer architecture (web application, orchestration, execution).
  • Leveraged software containers and accommodated high-performance and cloud computing services for flexibility and expansion.
  • Employed a robust user research process for continuous feedback and improvement.

Main Results:

  • NMDC EDGE provides an accessible interface for researchers to process metagenome, metatranscriptome, natural organic matter, and metaproteome data.
  • The architecture ensures flexibility and scalability for future workflow integration.
  • Production-quality workflows are integrated to enhance data standardization and interoperability.

Conclusions:

  • NMDC EDGE significantly lowers the barrier for researchers to utilize standardized multi-omics bioinformatics workflows.
  • The resource promotes data standardization and interoperability, accelerating microbiome research and data-driven discoveries.