创建可用的生物信息学命令行软件的 10 项建议。
Ten recommendations for creating usable bioinformatics command line software.
机构信息
Victorian Bioinformatics Consortium, Building 76 Monash University Clayton, Clayton, VIC 3800, Australia.
出版信息
Gigascience. 2013 Nov 13;2(1):15. doi: 10.1186/2047-217X-2-15.
Abstract
Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten recommendations for command line software author's tools to follow, which I believe would greatly improve the uptake and usability of their products, waste less user's time, and improve the quality of scientific analyses.
摘要
生物信息学软件的质量差异很大。就可用性而言，命令行界面是用户首次体验工具的方式。不幸的是，这通常也是用户最后一次使用该工具。在这里，我提出了十个关于命令行软件作者工具的建议，我相信这些建议将极大地提高产品的采用率和可用性，减少用户的时间浪费，并提高科学分析的质量。
相似文献
1
Ten recommendations for creating usable bioinformatics command line software.创建可用的生物信息学命令行软件的 10 项建议。
Gigascience. 2013 Nov 13;2(1):15. doi: 10.1186/2047-217X-2-15.
2
Reusable Software Usability Specifications for mHealth Applications.可复用软件的移动医疗应用可用性规范
J Med Syst. 2018 Jan 25;42(3):45. doi: 10.1007/s10916-018-0902-0.
3
Dark Suite: a comprehensive toolbox for computer-aided drug design.Dark Suite：一个用于计算机辅助药物设计的综合工具箱。
EMBnet J. 2020;25. doi: 10.14806/ej.25.0.928. Epub 2020 Mar 13.
4
ORBIT: an integrated environment for user-customized bioinformatics tools.ORBIT：一个用于用户定制生物信息学工具的集成环境。
Bioinformatics. 1999 Oct;15(10):847-51. doi: 10.1093/bioinformatics/15.10.847.
5
Usability study of clinical exome analysis software: top lessons learned and recommendations.临床外显子组分析软件的可用性研究：汲取的主要经验教训与建议
J Biomed Inform. 2014 Oct;51:129-36. doi: 10.1016/j.jbi.2014.05.004. Epub 2014 May 24.
6
User experience integrated life-style cloud-based medical application.用户体验集成式基于生活方式的云端医疗应用程序。
Stud Health Technol Inform. 2015;210:642-6.
7
TabSQL: a MySQL tool to facilitate mapping user data to public databases.TabSQL：一个 MySQL 工具，用于方便将用户数据映射到公共数据库。
BMC Bioinformatics. 2010 Jun 23;11:342. doi: 10.1186/1471-2105-11-342.
8
On the usability of grid middleware and security mechanisms.网格中间件和安全机制的可用性。
Philos Trans A Math Phys Eng Sci. 2011 Aug 28;369(1949):3413-28. doi: 10.1098/rsta.2011.0131.
9
The contribution of apparent and inherent usability to a user's satisfaction in a searching and browsing task on the Web.在网络搜索和浏览任务中，表面可用性和内在可用性对用户满意度的贡献。
Ergonomics. 2002 May 15;45(6):415-24. doi: 10.1080/00140130110120033.
10
Mobyle: a new full web bioinformatics framework.Mobyle：一个全新的全网络生物信息学框架。
Bioinformatics. 2009 Nov 15;25(22):3005-11. doi: 10.1093/bioinformatics/btp493. Epub 2009 Aug 17.
引用本文的文献
1
Positive selection of efficient ethanol producers from xylose at 45 °C in the yeast Ogataea polymorpha.在45°C下从木糖中对多形汉逊酵母中的高效乙醇生产者进行正向选择。
Sci Rep. 2025 Jul 22;15(1):26530. doi: 10.1038/s41598-025-12204-2.
2
For long-term sustainable software in bioinformatics.用于生物信息学中的长期可持续软件。
PLoS Comput Biol. 2024 Mar 15;20(3):e1011920. doi: 10.1371/journal.pcbi.1011920. eCollection 2024 Mar.
3
Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software.使用研究软件的FAIR原则评估液相色谱-高分辨质谱代谢组学数据处理软件。
Metabolomics. 2023 Feb 6;19(2):11. doi: 10.1007/s11306-023-01974-3.
4
Ten simple rules and a template for creating workflows-as-applications.创建工作流即应用程序的十条简单规则及一个模板。
PLoS Comput Biol. 2022 Dec 15;18(12):e1010705. doi: 10.1371/journal.pcbi.1010705. eCollection 2022 Dec.
5
Ten simple rules for making a software tool workflow-ready.让软件工具适用于工作流程的十条简单规则。
PLoS Comput Biol. 2022 Mar 24;18(3):e1009823. doi: 10.1371/journal.pcbi.1009823. eCollection 2022 Mar.
6
UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs).UCEasy：一个用于自动化和简化超保守元件（UCEs）分析的软件包。
Biodivers Data J. 2021 Dec 10;9:e78132. doi: 10.3897/BDJ.9.e78132. eCollection 2021.
7
AI applications in functional genomics.人工智能在功能基因组学中的应用。
Comput Struct Biotechnol J. 2021 Oct 11;19:5762-5790. doi: 10.1016/j.csbj.2021.10.009. eCollection 2021.
8
DISCo-microbe: design of an identifiable synthetic community of microbes.DISCo-微生物：可识别的微生物合成群落的设计
PeerJ. 2020 Feb 27;8:e8534. doi: 10.7717/peerj.8534. eCollection 2020.
9
Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software.Bionitio：展示和促进生物信息学命令行软件的最佳实践。
Gigascience. 2019 Sep 1;8(9). doi: 10.1093/gigascience/giz109.
10
Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism.深海沉积物中的病毒基因组扩展了海洋巨型病毒组，并支持病毒巨型化的独立起源。
mBio. 2019 Mar 5;10(2):e02497-18. doi: 10.1128/mBio.02497-18.
Zotero 插件