A comprehensive analysis of the usability and archival stability of omics computational tools and resources
A comprehensive analysis of the usability and archival stability of omics computational tools and resources
复制标题
组学计算工具和资源的可用性和存档稳定性的全面分析
DOI：
10.1101/452532
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发表时间：
2018
期刊：
影响因子：
--
通讯作者：
R. Blekhman
中科院分区：
文献类型：
--
作者：
S. Mangul;T. Mosqueiro;Dat Q. Duong;Keith Mitchell;V. Sarwal;Brian Hill;J. Brito;R. Littman;Benjamin Statz;Angela Ka;Gargi Dayama;Laura E. Grieneisen;Lana S. Martin;Jonathan Flint;E. Eskin;R. Blekhman
开发用于分析大规模生物数据的新软件工具是推进计算和数据支持研究的关键组成部分。科学复制发表的研究结果需要运行计算工具的数据产生的研究，但很少注意目前分配到封装为计算软件工具的计算机代码的可用性和存档稳定性。科学期刊要求数据和代码共享，但目前没有一个要求作者保证新发布工具的软件可用性和长期存档稳定性。我们通过对2000年至2017年出版的24，490个组学软件资源的可用性和存档稳定性进行实证分析，对计算生物学软件工具的可访问性进行了准确的估计。我们发现，26%的omics软件资源目前无法通过论文中发布的URL访问。在我们选择进行全面和系统的可用性测试的工具中，49%被认为“难以安装”，28%的工具由于实现问题而无法安装。此外，对于介绍新软件的论文，我们发现，当作者为已发布的软件提供简单的安装过程时，引用的数量显着增加。我们提出了纳入期刊政策的几个实际的解决方案，以增加广泛的可用性和已发表的生物信息学软件的存档稳定性。
Developing new software tools for analysis of large-scale, biological data is a key component of advancing computational, data-enabled research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the usability and archival stability of computer code encapsulated as computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee software usability and long-term archival stability of newly published tools. We developed an accurate estimation of the accessibility of computational biology software tools by performing an empirical analysis of usability and archival stability of 24,490 omics software resources published from 2000 to 2017. We found that 26% of all omics software resources are currently not accessible through URLs published in the paper. Among the tools selected for our comprehensive and systematic usability test, 49% were deemed “difficult to install,” and 28% of the tools failed to be installed due to problems in the implementation. Moreover, for papers introducing new software, we found that the number of citations significantly increased when authors provided an easy installation process for published software. We propose for incorporation into journal policy several practical solutions for increasing the widespread usability and archival stability of published bioinformatics software.
影响因子：
9.8
作者：
Stephens ZD;Lee SY;Faghri F;Campbell RH;Zhai C;Efron MJ;Iyer R;Schatz MC;Sinha S;Robinson GE
通讯作者：
Robinson GE