帕维2.0:在乳头瘤病毒流行病的幕后
Jennifer Dommer1, Koenraad Van Doorslaer2, Cyrus Afrasiabi1
1Bioinformatics and Computational Biosciences Branch (BCBB), National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.
Journal of molecular biology
|December 28, 2024
概括
乳头瘤病毒表观 (PaVE) 数据库已大幅升级为PaVE 2.0,增强其功能和用户可访问性,用于乳头瘤病毒研究. 这一更新确保了对科学界的持续支持,提供了改进的工具和现代化的基础设施.
科学领域:
- 病毒学 病毒学
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 乳头瘤病毒表观 (PaVE) 于2008年成立,作为乳头瘤病毒研究的关键生物信息资源.
- 随着时间的推移,最初的PaVE基础设施变得过时,需要全面升级以满足当前的科学需求.
研究的目的:
- 重新开发和现代化PaVE资源,确保其继续作为研究乳头瘤病毒的研究人员和临床医生的基本工具.
- 为PaVE实施一个可扩展和强大的技术基础,促进未来的改进和更广泛的可访问性.
主要方法:
- 使用亚马逊网络服务 (AWS) 重建了PaVE 2.0基础设施,包括云存储 (S3),集装箱 (ECS) 和自动部署管道.
- 关键软件组件进行了更新,包括将数据库从MySQL切换到Neo4j,采用Python Flask与JavaScript/JINJA前端,并实施Swagger API.
- 主要的分析工具得到了现代化,例如用MAFFT取代COBALT用于多个序列对齐,以及用Mol*取代Jmol用于蛋白质结构可视化.
主要成果:
- 现在PaVE 2.0具有在AWS上托管的完全升级和重建的软件基础架构,确保增强性能和可扩展性.
- 对核心工具进行了显著的改进,包括BLAST,L1类型,基因组位置查看器,家族遗传树生成器,多个序列对齐和蛋白质结构查看器.
- 新架构通过Celery队列支持更长时间的任务,并通过Swagger API提供程序化数据访问,从而实现高级研究应用.
结论:
- PaVE 2.0 代表了实质性的进步,为乳头瘤病毒研究社区提供了必不可少的现代化资源.
- PaVE 2.0的开源框架和更新的基础设施可以作为开发其他病毒类似数据库的模板.
- PaVE 2.0的增强功能将支持更多的用户,并促进乳头瘤病毒研究中的更复杂的分析.
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