一句话：通过实证研究揭示生物信息学工具配置选项缺乏文档、功能与性能多变且存在未检测故障，并提出自动化技术路线图。
生物信息学软件领域包含大量应用，用户从专业开发者到缺乏计算经验者不等。为满足需求，开发者提供众多配置选项以调整算法，但用户选择选项时缺乏自动化帮助来理解其后果。本文通过实际使用可配置生物信息学工具进行实证研究，考察选项组合、文档与帮助，并测试功能与性能变化。研究发现文档和帮助有限，功能与性能存在差异，并发现此前未检测到的故障。作者总结了一系列经验教训，并提出了创建自动化技术以与生物信息学软件交互的路线图，认为这些发现可推广到其他科学软件。
The bioinformatics software domain contains thousands of applications for automating tasks such as the pairwise alignment of DNA sequences, building and reasoning about metabolic models or simulating growth of an organism. Its end users range from sophisticated developers to those with little computational experience. In response to their needs, developers provide many options to customize the way their algorithms are tuned. Yet there is little or no automated help for the user in determining the consequences or impact of the options they choose. In this paper we describe our experience working with configurable bioinformatics tools. We find limited documentation and help for combining and selecting options along with variation in both functionality and performance. We also find previously undetected faults. We summarize our findings with a set of lessons learned, and present a roadmap for creating automated techniques to interact with bioinformatics software. We believe these will generalize to other types of scientific software.
@inproceedings{paperbot4766,
title = {Navigating the maze: the impact of configurability in bioinformatics software},
author = {Mikaela Cashman and Myra B. Cohen and Priya Ranjan and Robert W. Cottingham},
booktitle = {ASE},
year = {2018},
doi = {10.1145/3238147.3240466}
}