Bioinformatics Pipelines and Simulation in Biological Research

Bioinformatics pipelines are structured, modular computational workflows designed to automate the processing, quality control, analysis, and interpretation of complex biological datasets arising from high-throughput experiments such as genomics, proteomics, and multi-omics. These pipelines improve reproducibility, scalability, and efficiency in data-driven biology. Simulation approaches complement pipelines by modeling biological entities and systems in silico to test hypotheses, predict behaviors, and integrate data across scales. This review elaborates on pipeline architecture, tools, construction best practices, and simulation techniques, surveying applications, challenges, and emerging trends.