Biocompute Objects-A Step towards Evaluation and Validation of Biomedical Scientific Computations.

Area of Science:

• Computational Biology
• Bioinformatics
• Scientific Reproducibility

Background:

• Physical, chemical, and biological experiments are known for their unpredictability due to environmental and procedural variables.
• Computational biology algorithms also exhibit volatility, influenced by a multitude of parameters, yet this is often overlooked.
• A lack of standardized metadata schemas for computational objects hinders the reporting and reproducibility of bioinformatics analyses.

Purpose of the Study:

• To address the challenge of reproducibility in computational biology by introducing a standardized method for reporting computational parameters and results.
• To develop a concept for 'biocompute objects' and their generalized versions, 'biocompute templates', to meet regulatory research needs for bioinformatics pipelines.
• To propose a cross-platform implementation for biocompute templates and discuss their broader usability within the scientific community.

Main Methods:

• Description of the 'biocompute object' concept, designed to capture parameters, dependencies, usage, and other critical information for computational instances.
• Envisioning 'biocompute templates' as adaptable generalized versions supporting specific analysis classes.
• Outlining a simple, powerful cross-platform implementation strategy for biocompute templates.

Main Results:

• The proposed biocompute objects provide a standardized way to record computational parameters and results, essential for evaluation, validation, and verification.
• Biocompute templates offer flexibility for adaptation to unique analytical needs while maintaining standardization.
• A biocompute object database, starting with records relevant to the U.S. Food and Drug Administration, is proposed to foster collaboration and interoperability.

Conclusions:

• Biocompute objects and templates are crucial for enhancing the reproducibility and reliability of computational biology research.
• Standardized reporting through biocompute objects will facilitate regulatory compliance and scientific rigor.
• The proposed database mechanism will serve as a collaborative platform, ensuring interoperability across diverse stakeholders in biocomputing.