基于个人计算机的进化生物学分析新时代：以eGPS为例新时代多功能软件探讨
收稿日期: 2024-09-03
修回日期: 2024-11-08
网络出版日期: 2024-11-27
基金资助
国家自然科学基金青年基金项目(32400511)
A new era of evolutionary analysis based on a personal computer: the future of multifunctional software such as eGPS
Received date: 2024-09-03
Revised date: 2024-11-08
Online published: 2024-11-27
Supported by
Youth Fund of the National Natural Science Foundation of China(32400511)
各种多组学技术所产生的大规模数据，提出了如何快速、准确地分析这些数据的重要科学问题。如何在发展创新性新理论和数学模型的基础上，基于软件工程开发出能够让用户高效且精确地处理大规模生物学数据的便捷工具，是生物信息学和计算生物学的重要研究方向。本文主要介绍了生物信息学相关软件的发展历史、基于进化生物学的应用场景和进化与组学多功能分析软件平台eGPS、计算机使用的3种方式和软件编程的3个范式，以及如何基于Conda、R语言生态与eGPS软件平台分析单基因、通路和基因组水平的数据。针对不同科学目标的用户群体，提出了软件开发、使用、维护的新思路，并对进化生物学软件应用领域的未来发展进行了展望。最后，本文提出使用个人计算机进行进化与多组学分析不仅是时代所需也是未来发展的趋势，在生物信息学分析中扮演越来越重要的角色。
虞达浪, 杨佳宁, 张建威, 张皖豫, 李海鹏 . 基于个人计算机的进化生物学分析新时代：以eGPS为例新时代多功能软件探讨[J]. 遗传, 2025 , 47(2) : 271 -285 . DOI: 10.16288/j.yczz.24-254
The large-scale data generated by various omics technologies pose significant scientific challenges about how to rapidly and accurately analyze these data. It is essential to develop convenient tools that allow users to efficiently and precisely handle massive biological data. Based on new theories and mathematical models, as well as software engineering, this field is becoming an important research direction in bioinformatics and computational biology. In this review, we briefly review the development history of bioinformatics-related software. We also summarize the recent progress, focus on their application on evolutionary biology, and discuss three major ways of computer running mode and three paradigms of software programming. We also introduce the eGPS, a self-developed multi-functional evolutionary and omics analysis software platform, including the application of eGPS along with Conda and R for data analysis on individual genes, pathways, or genomes. We then propose new ideas for software development, use, and maintenance tailored to different users with varying scientific objectives. It posits that using a personal computer for evolutionary and multi-omics analysis is not only a necessity but also playing an important role.
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