Bioinformatics software development: Principles and future directions

The bioinformatics software for analyzing biomedical data is essential for converting raw data into meaningful biological insights. In this review, we outline the key stages and considerations in the development of bioinformatics software, using clusterProfiler and CIRCexplorer2 as illustrative examples. Furthermore, we examine some established large-scale life sciences platforms and summarize the design principles in the era of big data and Artificial Intelligence (AI) for open science. Future large-scale platforms are expected to offer graphical programming languages and transition from the sharing of data and codes to that of physical resources. The AI revolution will alter the landscape of bioinformatics software development and redefine the research paradigm of life sciences.