Collaborative Research: OpenDendro - Advanced Open-source Tools for Paleoenvironmental Reconstruction

合作研究：OpenDendro - 用于古环境重建的先进开源工具

• 批准号: 2054515
• 负责人: Edward Cook
• 金额: $ 7.35万
• 依托单位: Columbia University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-06-01 至 2023-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2054515&HistoricalAwards=false
• 关键词: Collaborative; Research; OpenDendro; Advanced; Open

The research team aims to create openDendro as an open-source framework of the base analytic software tools used in dendrochronology in both the R and Python programming languages. The research goal is to create and curate a unified set of critical tools in open-source environments that will provide the necessary baseline for researchers using tree-ring data to adopt open-science practices and increase both rigor and transparency in dendrochronology.Much of the software used in dendrochronology are in legacy programming languages and have been maintained by a small number of volunteers for decades. The codes are at risk of becoming inoperable or incompatible as advances in computing architecture accelerate. The techniques and tools adversely impacted include specialized data input and output, detrending, cross-dating, chronology building, spectral modeling, descriptive statistics, and other common data-handling and data-processing tasks. The research team argues that this situation could be addressed by incorporating these legacy programs into a modern open-source and open-science framework. While some of this work has been completed in the R package dplR, many of the tools most needed by the broader research community are still not widely available in R (including signal free standardization) and virtually none are implemented in the Python ecosystem. The potential Broader Impacts include creating a modern open-source software base that will be immediately usable by paleoclimatologists using tree-ring data for paleoclimate research. Modernizing and enhancing this software will also extend both their reach and utility beyond the dendrochronology community and allow integration into related initiatives in the atmospheric and earth sciences including LinkedEarth and Pangeo. Making these tools open source will also facilitate further collaborative development, broaden the responsibility for collective maintenance and enhancement of this software, and ensure the persistence of these unique tools. This project provides training opportunities for the next generation of paleoenvironmental scientists with a coding `bootcamp' on the openDendro toolkit and broadly models the application of open-science concepts and practices within dendrochronology.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

研究团队的目标是创建 openDendro 作为 R 和 Python 编程语言中用于树木年代学的基本分析软件工具的开源框架。 研究目标是在开源环境中创建和管理一套统一的关键工具，为使用树木年轮数据的研究人员采用开放科学实践并提高树木年代学的严谨性和透明度提供必要的基线。树木年代学中使用的软件采用传统编程语言，几十年来一直由少数志愿者维护。 随着计算架构的进步加速，这些代码面临着无法运行或不兼容的风险。受到不利影响的技术和工具包括专门的数据输入和输出、去趋势、交叉日期、年代学构建、频谱建模、描述性统计以及其他常见的数据处理和数据处理任务。研究团队认为，可以通过将这些遗留项目纳入现代开源和开放科学框架来解决这种情况。 虽然其中一些工作已经在 R 包 dplR 中完成，但更广泛的研究社区最需要的许多工具在 R 中仍然没有广泛使用（包括无信号标准化），并且几乎没有在 Python 生态系统中实现。潜在的更广泛影响包括创建一个现代开源软件库，古气候学家可以立即使用该库使用树木年轮数据进行古气候研究。 该软件的现代化和增强还将其范围和实用性扩展到树木年代学领域之外，并允许集成到大气和地球科学的相关计划中，包括 LinkedEarth 和 Pangeo。 将这些工具开源还将促进进一步的协作开发，扩大集体维护和增强该软件的责任，并确保这些独特工具的持久性。该项目通过 openDendro 工具包上的编码“训练营”为下一代古环境科学家提供培训机会，并广泛模拟开放科学概念和树年代学中实践的应用。该奖项反映了 NSF 的法定使命，并被认为值得支持通过使用基金会的智力优点和更广泛的影响审查标准进行评估。