Silva Luis Bastiao, Jimenez Rafael C, Blomberg Niklas, Luis Oliveira José
BMD Software, Aveiro, Portugal.
ELIXIR Hub, Wellcome Trust Genome Campus, Hinxton, UK.
F1000Res. 2017 Mar 15;6:273. doi: 10.12688/f1000research.10750.2. eCollection 2017.
Most bioinformatics tools available today were not written by professional software developers, but by people that wanted to solve their own problems, using computational solutions and spending the minimum time and effort possible, since these were just the means to an end. Consequently, a vast number of software applications are currently available, hindering the task of identifying the utility and quality of each. At the same time, this situation has hindered regular adoption of these tools in clinical practice. Typically, they are not sufficiently developed to be used by most clinical researchers and practitioners. To address these issues, it is necessary to re-think how biomedical applications are built and adopt new strategies that ensure quality, efficiency, robustness, correctness and reusability of software components. We also need to engage end-users during the development process to ensure that applications fit their needs. In this review, we present a set of guidelines to support biomedical software development, with an explanation of how they can be implemented and what kind of open-source tools can be used for each specific topic.
当今可用的大多数生物信息学工具并非由专业软件开发人员编写，而是由那些希望解决自身问题的人编写，他们采用计算解决方案并尽可能少地投入时间和精力，因为这些仅仅是达到目的的手段。因此，目前有大量的软件应用程序，这妨碍了识别每个应用程序的效用和质量的任务。与此同时，这种情况阻碍了这些工具在临床实践中的常规应用。通常，它们的开发程度不足以供大多数临床研究人员和从业者使用。为了解决这些问题，有必要重新思考生物医学应用程序的构建方式，并采用新的策略来确保软件组件的质量、效率、稳健性、正确性和可重用性。我们还需要在开发过程中让最终用户参与进来，以确保应用程序符合他们的需求。在本综述中，我们提出了一套支持生物医学软件开发的指南，并解释了如何实施这些指南以及针对每个特定主题可以使用哪些开源工具。
