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EarthCube Building Blocks: Collaborative Proposal: GeoTrust: Improving Sharing and Reproducibility of Geoscience Applications

EarthCube 构建模块：协作提案：GeoTrust：提高地球科学应用的共享性和可重复性

基本信息

批准号：
1639759
负责人：
Tanu Malik
金额：
$ 78.4万
依托单位：
DePaul University
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2016
资助国家：
美国
起止时间：
2016-09-01 至 2021-08-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1639759&HistoricalAwards=false
关键词：
EarthCube Building Blocks Collaborative Proposal

项目摘要

Scientific reproducibility -- the ability to independently verify the work of other scientists -- continues to be a critical barrier towards achieving the vision of cross-disciplinary science. Federal agencies and publishers increasingly mandate and incentivize scientists to, at a minimum, establish computational reproducibility of scientific experiments. To comply scientists must connect descriptions of scientific experiments in scholarly publications with the underlying data and code used to produce the published results and findings. However, in practice, computational reproducibility is hard to achieve since it entails isolating necessary and sufficient computational artifacts and then preserving those artifacts in a standard way for later re-execution. Both isolation and preservation present challenges in large part due to the complexity of existing software and systems as well as the implicit dependencies, resource distribution, and shifting compatibility of systems that evolve over time -- all of which conspire to break the reproducibility of an experiment. The goal of the GeoTrust project is to understand the research lifecycle of scientific experiments from conception to publication and establish a framework that will improve their reproducibility. GeoTrust will develop sandboxing-based systems and tools that help scientists effectively isolate computational artifacts associated with an experiment, use languages and semantics to preserve artifacts, and re-execute /reproduce experiments by deploying the artifacts, changing datasets, algorithms, models, environments, etc. This reproducible framework will be adopted by and integrated within community infrastructures of three geoscience sub-disciplines viz. Hydrology, Solid Earth, and Space Science. Using cross-disciplinary science uses cases from these sub-disciplines, and engaging independent evaluators, we will assess the effectiveness of the framework in achieving reproducibility of computational experiments. Finally, verified results will be associated with ?stamps of reproducibility?, establishing community recognition of computational experiments. The framework will be developed as an EarthCube capability, with software developed and released as per EarthCube requirements. Early adopters across other geoscience sub-disciplines will be continually sought.

科学可重复性-独立验证其他科学家工作的能力-仍然是实现跨学科科学愿景的一个关键障碍。联邦机构和出版商越来越多地要求和激励科学家至少建立科学实验的计算再现性。为了遵守这一规定，科学家必须将学术出版物中对科学实验的描述与用于产生出版结果和发现的基础数据和代码联系起来。然而，在实践中，计算再现性很难实现，因为它需要隔离必要和足够的计算工件，然后以标准方式保存这些工件以供以后重新执行。隔离和保存都面临挑战，这在很大程度上是由于现有软件和系统的复杂性，以及随着时间的推移而发展的系统的隐式依赖性，资源分布和变化的兼容性-所有这些都共同破坏了实验的可重复性。GeoTrust项目的目标是了解科学实验从概念到出版的研究生命周期，并建立一个框架，以提高其可重复性。GeoTrust将开发基于沙箱的系统和工具，帮助科学家有效地隔离与实验相关的计算工件，使用语言和语义来保存工件，并通过部署工件，更改数据集，算法，模型，环境等重新执行/复制实验。固体地球和空间科学。使用跨学科科学使用这些子学科的案例，并聘请独立评估人员，我们将评估该框架在实现计算实验的可重复性方面的有效性。最后，验证的结果将与？可重复性的印记？建立社区对计算实验的认可。该框架将作为EarthCube的一项能力加以开发，并根据EarthCube的要求开发和发布软件。将继续寻求其他地球科学子学科的早期采用者。

项目成果

期刊论文数量（9）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Efficient Provenance Alignment in Reproduced Executions

复制执行中的高效出处对齐

DOI：
发表时间：
2020
期刊：
USENIX Theory and Practice of Provenance
影响因子：
0
作者：
Y. Nakamura, T. Malik
通讯作者：
Y. Nakamura, T. Malik

SciInc: A Container Runtime for Incremental Recomputation

SciInc：用于增量重新计算的容器运行时

DOI：
10.1109/escience.2019.00040
发表时间：
2019
期刊：
IEEE 15th International Conference on eScience
影响因子：
0
作者：
A. Youngdahl, D.H. Ton
通讯作者：
A. Youngdahl, D.H. Ton

Utilizing Provenance in Reusable Research Objects

利用可重复使用的研究对象的来源

DOI：
10.3390/informatics5010014
发表时间：
2018
期刊：
Informatics
影响因子：
0
作者：
Yuan, Zhihao;Ton That, Dai;Kothari, Siddhant;Fils, Gabriel;Malik, Tanu
通讯作者：
Malik, Tanu

Sciunits: Reusable Research Objects

Sciunits：可重复使用的研究对象

DOI：
10.1109/escience.2017.51
发表时间：
2017
期刊：
IEEE 13th International Conference on e-Science (e-Science
影响因子：
0
作者：
Ton That, Dai Hai;Fils, Gabriel;Yuan, Zhihao;Malik, Tanu
通讯作者：
Malik, Tanu

Integrating scientific cyberinfrastructures to improve reproducibility in computational hydrology: Example for HydroShare and GeoTrust

集成科学网络基础设施以提高计算水文学的可重复性：HydroShare 和 GeoTrust 示例

DOI：
10.1016/j.envsoft.2018.03.025
发表时间：
2018
期刊：
Environmental Modelling & Software
影响因子：
4.9
作者：
Essawy, Bakinam T.;Goodall, Jonathan L.;Zell, Wesley;Voce, Daniel;Morsy, Mohamed M.;Sadler, Jeffrey;Yuan, Zhihao;Malik, Tanu
通讯作者：
Malik, Tanu