Publishing repeatable and reproducible computational models is a crucial aspect of the scientific method in computational biology and one that is often forgotten in the rush to publish. The pressures of academic life and the lack of any reward system at institutions, granting agencies and journals means that publishing reproducible science is often either non-existent or, at best, presented in the form of an incomplete description. In the article, we will focus on repeatability and reproducibility in the systems biology field where a great many published models cannot be reproduced and in many cases even repeated. This review describes the current landscape of software tooling, model repositories, model standards and best practices for publishing repeatable and reproducible kinetic models. The review also discusses possible future remedies including working more closely with journals to help reviewers and editors ensure that published kinetic models are at minimum, repeatable. Contact: hsauro@uw.edu

中文翻译：

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发布可重复的动态动力学模型。


发布可重复和可再现的计算模型是计算生物学科学方法的一个重要方面，但在急于发布的过程中经常被遗忘。学术生活的压力以及机构、资助机构和期刊缺乏任何奖励制度意味着出版可重复的科学往往要么不存在，要么充其量以不完整描述的形式呈现。在本文中，我们将重点讨论系统生物学领域的重复性和再现性，其中许多已发表的模型无法再现，在许多情况下甚至可以重复。这篇评论描述了软件工具、模型存储库、模型标准以及发布可重复和可再现动力学模型的最佳实践的当前状况。该评论还讨论了未来可能的补救措施，包括与期刊更密切地合作，以帮助审稿人和编辑确保已发表的动力学模型至少具有可重复性。联系方式： hsauro@uw.edu