Bioinformatics Workflows With NoSQL Database in Cloud Computing

Area of Science:

• Bioinformatics
• Computational Biology
• Molecular Biology

Background:

• Scientific workflows are crucial in Bioinformatics for molecular biology and sequence analyses.
• Reproducibility and computational environment management are key challenges in Bioinformatics research.
• Cloud computing offers an accessible and configurable environment for computational tasks.

Purpose of the Study:

• To propose a solution for improving the reproducibility of Bioinformatics workflows in a cloud environment.
• To explore the use of Infrastructure as a Service (IaaS) and NoSQL databases for managing provenance data.
• To provide a guide for deploying cloud environments for Bioinformatics research.

Main Methods:

• Developed and executed three typical Bioinformatics workflows on private and public clouds.
• Utilized Infrastructure as a Service (IaaS) for the computational environment.
• Employed various NoSQL database systems to store provenance data following the PROV-DM standard.

Main Results:

• Demonstrated improved reproducibility of Bioinformatics workflows in a cloud setting.
• Evaluated the performance of different NoSQL databases for persisting provenance data.
• Identified characteristics of NoSQL systems suitable for Bioinformatics provenance tracking.

Conclusions:

• Cloud computing combined with NoSQL databases effectively enhances Bioinformatics workflow reproducibility.
• The PROV-DM standard is applicable for managing provenance data in cloud-based Bioinformatics workflows.
• The findings offer practical guidance for researchers establishing reproducible computational environments.