Bioinformatics software development: Principles and future directions

Xu-Kai Ma; Yan Yu; Tao Huang; Dake Zhang; Caihuan Tian; Wenli Tang; Ming Luo; Pufeng Du; Guangchuang Yu; Li Yang

doi:10.59717/j.xinn-life.2024.100083

The Innovation Life > Accepted

REVIEW Open Access

Bioinformatics software development: Principles and future directions

1.
Center for Molecular Medicine, Children’s Hospital of Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
2.
College of Life Sciences, Sichuan University, Chengdu 610065, China
3.
CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
4.
Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing 100083, China
5.
Center of Peony, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
6.
Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
7.
South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
8.
College of Intelligence and Computing, Tianjin University, Tianjin 300350, China
9.
These authors contributed equally

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Corresponding authors: liyang_fudan@fudan.edu.cn (L.Y.); gcyu1@smu.edu.cn (G.Y.); pdu@tju.edu.cn (P.D.);
Received Date: 09 May 2024

Accepted Date: 21 July 2024

Published Online: 13 August 2024

The Innovation Life https://doi.org/10.59717/j.xinn-life.2024.100083 | Cite this article

GRAPHICAL ABSTRACT

GRAPHICAL ABSTRACT

PUBLIC SUMMARY

PUBLIC SUMMARY
1. The growing volume of biomedical big data is driving a tremendous demand for advanced bioinformatics software.
  
  Artificial intelligence (AI) is expected to accelerate and enhance the development process of bioinformatics software.
  
  AI-augmented cloud computing is paving the way for the future of autonomous research.

ABSTRACT

ABSTRACT

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.

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Ma X.-K., Yu Y., Huang T., et al., (2024). Bioinformatics software development: Principles and future directions. The Innovation Life 2(3): 100083. https://doi.org/10.59717/j.xinn-life.2024.100083

Ma X.-K., Yu Y., Huang T., et al., (2024). Bioinformatics software development: Principles and future directions. The Innovation Life 2(3): 100083. https://doi.org/10.59717/j.xinn-life.2024.100083

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