eduomics

eduomics automates the simulation of genomic and transcriptomic next-generation sequencing data within realistic clinical scenarios to support storyline-based bioinformatics education.

Key Features:

• Automated simulation workflow: The pipeline removes dependencies and requirements typically needed by data simulation tools, requiring users only to select which chromosome datasets to simulate and which data type to generate.
• Multi-omics data generation: eduomics simulates both genomic and transcriptomic next-generation sequencing data.
• Clinical scenario generation: The Gemini API generates plausible clinical scenarios consistent with genes containing simulated pathological mutations or differential expression.
• Scalable dataset production: The pipeline enables generation of multiple datasets with identical characteristics for tutoring or assessment in higher education.

Scientific Applications:

• Bioinformatics education: eduomics supports teaching students to interpret results within realistic biological and biomedical contexts rather than learning only algorithms and code.
• Storyline-based learning: The pipeline provides students with clues and biomedical narratives necessary for interpreting their bioinformatics results.
• Assessment and tutoring: eduomics facilitates generation of consistent datasets for evaluation purposes in higher education settings.

Methodology:

eduomics is implemented as a Nextflow pipeline that automates data simulation workflows.