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

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.