Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.
Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.
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DOI：
10.1038/s41467-021-27222-7
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发表时间：
2021-11-29
影响因子：
16.6
通讯作者：
Bonneau R
中科院分区：
文献类型：
--
作者：
Koehler Leman J;Lyskov S;Lewis SM;Adolf-Bryfogle J;Alford RF;Barlow K;Ben-Aharon Z;Farrell D;Fell J;Hansen WA;Harmalkar A;Jeliazkov J;Kuenze G;Krys JD;Ljubetič A;Loshbaugh AL;Maguire J;Moretti R;Mulligan VK;Nance ML;Nguyen PT;Ó Conchúir S;Roy Burman SS;Samanta R;Smith ST;Teets F;Tiemann JKS;Watkins A;Woods H;Yachnin BJ;Bahl CD;Bailey-Kellogg C;Baker D;Das R;DiMaio F;Khare SD;Kortemme T;Labonte JW;Lindorff-Larsen K;Meiler J;Schief W;Schueler-Furman O;Siegel JB;Stein A;Yarov-Yarovoy V;Kuhlman B;Leaver-Fay A;Gront D;Gray JJ;Bonneau R
每年都有大量的国际资源浪费在不可复制的研究上。科学界在采用标准软件工程实践方面进展缓慢，尽管高维数据、工作流程复杂性和计算环境不断增加。在这里，我们展示了如何科学的软件应用程序可以创建一个可重复的方式时，简单的设计目标的可重复性得到满足。我们描述了一个测试服务器框架和40个科学基准的实现，涵盖了Rosetta生物大分子建模中的众多应用。高性能计算集群集成允许这些基准测试连续自动运行。详细的协议捕获对于Rosetta和其他大分子建模工具的开发人员和用户非常有用。这里提出的框架和设计概念对于任何类型的科学软件的开发人员和用户以及科学界创建可重现的方法都是有价值的。具体的例子突出了这个框架的实用性，全面的文档说明了在几个小时内添加新测试的方便性。计算方法正成为生物学研究中越来越重要的一部分。以Rosetta框架为例，作者演示了如何以可重复和可靠的方式完成社区驱动的计算方法开发。
Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework, and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours. Computational methods are becoming an increasingly important part of biological research. Using the Rosetta framework as an example, the authors demonstrate how community-driven development of computational methods can be done in a reproducible and reliable fashion.
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影响因子：
2.9
作者：
Haas J;Barbato A;Behringer D;Studer G;Roth S;Bertoni M;Mostaguir K;Gumienny R;Schwede T
通讯作者：
Schwede T
影响因子：
4.3
作者：
Alford RF;Koehler Leman J;Weitzner BD;Duran AM;Tilley DC;Elazar A;Gray JJ
通讯作者：
Gray JJ
影响因子：
3.9
作者：
Daneshjou R;Wang Y;Bromberg Y;Bovo S;Martelli PL;Babbi G;Lena PD;Casadio R;Edwards M;Gifford D;Jones DT;Sundaram L;Bhat RR;Li X;Pal LR;Kundu K;Yin Y;Moult J;Jiang Y;Pejaver V;Pagel KA;Li B;Mooney SD;Radivojac P;Shah S;Carraro M;Gasparini A;Leonardi E;Giollo M;Ferrari C;Tosatto SCE;Bachar E;Azaria JR;Ofran Y;Unger R;Niroula A;Vihinen M;Chang B;Wang MH;Franke A;Petersen BS;Pirooznia M;Zandi P;McCombie R;Potash JB;Altman RB;Klein TE;Hoskins RA;Repo S;Brenner SE;Morgan AA
通讯作者：
Morgan AA
影响因子：
64.8
作者：
Bhardwaj, Gaurav;Mulligan, Vikram Khipple;Bahl, Christopher D.;Gilmore, Jason M.;Harvey, Peta J.;Cheneval, Olivier;Buchko, Garry W.;Pulavarti, Surya V. S. R. K.;Kaas, Quentin;Eletsky, Alexander;Huang, Po-Ssu;Johnsen, William A.;Greisen, Per Jr;Rocklin, Gabriel J.;Song, Yifan;Linsky, Thomas W.;Watkins, Andrew;Rettie, Stephen A.;Xu, Xianzhong;Carter, Lauren P.;Bonneau, Richard;Olson, James M.;Coutsias, Evangelos;Correnti, Colin E.;Szyperski, Thomas;Craik, David J.;Baker, David
通讯作者：
Baker, David
影响因子：
5.5
作者：
Alford, Rebecca F.;Samanta, Rituparna;Gray, Jeffrey J.
通讯作者：
Gray, Jeffrey J.