frogs_biom_to_tsv

frogs_biom_to_tsv converts BIOM files to TSV format to enable interoperability and downstream analysis of microbiome and metagenomics data.

Key Features:

• Format Conversion: Converts BIOM (Biological Observation Matrix) files into TSV (Tab-Separated Values) format.
• Galaxy Integration: Operates within the Galaxy platform (Galaxy@Pasteur, Institut Pasteur) and leverages cluster resources for execution (Afgan et al., 2016).
• Galaxy API and Bioblend Integration: Communicates with Galaxy via its API or the Bioblend library (Sloggett et al., 2013) for job submission and execution.
• Web Service Utilization: Utilizes custom web services developed around the Galaxy@Pasteur instance.
• Reproducibility and Transparency: Execution within Galaxy supports reproducible and transparent conversion workflows.

Scientific Applications:

• Metagenomic Data Analysis: Facilitates integration of BIOM-derived microbiome data into TSV-based analytical workflows and databases.
• Reproducible Computational Research: Supports reproducible and transparent data conversion when incorporated into Galaxy workflows.

Methodology:

Communicates with Galaxy via its API or the Bioblend library (Sloggett et al., 2013) to execute conversions on the Institut Pasteur cluster and manages conversions through a centralized server coordinating Institut Pasteur storage and computing resources.