Commentary on the integration of model sharing and reproducibility analysis to scholarly publishing workflow in computational biomechanics.
Commentary on the integration of model sharing and reproducibility analysis to scholarly publishing workflow in computational biomechanics.
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DOI：
10.1109/tbme.2016.2602760
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发表时间：
2016-10
期刊：
影响因子：
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通讯作者：
Halloran JP
中科院分区：
文献类型：
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作者：
Erdemir A;Guess TM;Halloran JP;Modenese L;Reinbolt JA;Thelen DG;Umberger BR;Erdemir A;Guess TM;Halloran JP;Modenese L;Reinbolt JA;Thelen DG;Umberger BR;Umberger BR;Erdemir A;Thelen DG;Guess TM;Reinbolt JA;Modenese L;Halloran JP
本文件的总体目标是证明模型的传播和评估模拟结果的可重复性的分析可以纳入生物力学的科学审查过程。作为IEEE生物医学工程学报中关于模型共享和可重复性的特刊的一部分，提交了两篇关于计算生物力学的手稿：A。Rajagopal等人，IEEE生物医学学报工程师：2016年，A. Schmitz和D. Piovesan，IEEE Trans. Biomed.工程师：2016.这些研究中使用的模型与科学评论员和公众共享。除了对手稿进行标准审查外，审查人员还下载了模型并进行了模拟，重现了研究中报告的结果。作者的模拟结果与评论者的模拟结果基本一致。在必要的翻修期间解决了不一致性。根据评审员的反馈，更新了手稿和下载和模拟说明;如果在评审过程中没有进行明确的模型共享和模拟再现性分析，则可能会错过这些变更。注意到作者和审查人员为促进模型共享和重复模拟而增加的负担。当计算生物力学研究的作者提供访问模型和数据的权限时，科学评审员可以下载并彻底探索模型，执行模拟，并在传统的仅限手稿的评审过程之外评估模拟的可重复性。学术出版中的模型共享和再现性分析将导致更严格的审查过程，这将提高建模和模拟研究的质量，并为计算模型的未来用户提供信息。
The overall goal of this document is to demonstrate that dissemination of models and analyses for assessing the reproducibility of simulation results can be incorporated in the scientific review process in biomechanics. As part of a special issue on model sharing and reproducibility in IEEE Transactions on Biomedical Engineering, two manuscripts on computational biomechanics were submitted: A. Rajagopal et al., IEEE Trans. Biomed. Eng., 2016 and A. Schmitz and D. Piovesan, IEEE Trans. Biomed. Eng., 2016. Models used in these studies were shared with the scientific reviewers and the public. In addition to the standard review of the manuscripts, the reviewers downloaded the models and performed simulations that reproduced results reported in the studies. There was general agreement between simulation results of the authors and those of the reviewers. Discrepancies were resolved during the necessary revisions. The manuscripts and instructions for download and simulation were updated in response to the reviewers’ feedback; changes that may otherwise have been missed if explicit model sharing and simulation reproducibility analysis were not conducted in the review process. Increased burden on the authors and the reviewers, to facilitate model sharing and to repeat simulations, were noted. When the authors of computational biomechanics studies provide access to models and data, the scientific reviewers can download and thoroughly explore the model, perform simulations, and evaluate simulation reproducibility beyond the traditional manuscript-only review process. Model sharing and reproducibility analysis in scholarly publishing will result in a more rigorous review process, which will enhance the quality of modeling and simulation studies and inform future users of computational models.