ABI Innovation: Wallace: a flexible platform for reproducible modeling of species niches and distributions built for community expansion

ABI 创新：Wallace：一个灵活的平台，用于为社区扩展而构建的物种生态位和分布的可重复建模

• 批准号: 1661510
• 负责人: Robert Anderson
• 金额: $ 59.34万
• 依托单位: CUNY City College
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2022-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1661510&HistoricalAwards=false
• 关键词: ABI; Innovation; Wallace; flexible; platform

The software to be produced in this project aims to provide analyses that estimate a species' environmental requirements (habitat) and geographic distribution (range). Scientific progress calls for software with several qualities rarely found together. Ideally, scientific software: 1) is open-source (providing the underlying code); 2) gives conceptual and methodological guidance (orienting the user and helping them make decisions); 3) is flexible (allowing many options); 4) is interactive (showing the results of each stage of the analysis as it is completed); 5) can be expanded/updated easily and quickly; and 6) provides explicit documentation of the analyses run (making it easy to reproduce the results). The software to be produced in this project responds directly to these needs. It will be an example of an innovative way to make new scientific methods accessible to a broad audience of researchers, far beyond the specialists of a particular subfield. It targets a large user base of biologists and natural resource managers, and also will be of interest to programmers, educators, and students. This software should lead to better estimates of species ranges, important to interests as diverse as conservation biology, the study of invasive species and diseases passed to humans from insects and wildlife. The project will train graduate and undergraduate students in computer coding. In addition to the software itself, the researchers will produce scientific publications and online webinars that document and explain its use.Specifically, the project will greatly expand the software Wallace for the burgeoning field of niche/distributional modeling and related fields. Such models estimate environmental suitability for a species, indicating their potential geographic distribution for a wide variety of scientific studies. Currently, researchers struggle to follow advances and achieve a nimble uptake of new ideas and techniques. To improve this situation, the Wallace software provides a modular platform offering customizable workflows through a Graphical User Interface (GUI). Taking advantage of the modular nature of Wallace, the researchers will coordinate with many external partners to add diverse cutting-edge functionalities. The project will: 1) produce a comprehensive framework for modeling based on occurrence data that document the presence of a species; 2) include techniques that take advantage of repeated sampling; 3) allow seamless user up/download and customizable workflows via online and local implementations; and 4) grow the user community. Eventually, this approach could be scaled-up, allowing high-quality modeling for thousands of species. Wallace also will serve as an example for the development of scientific software in other disciplines. The results of the project will be made available at: https://wallaceecomod.github.io/

该项目中开发的软件旨在提供分析，估计物种的环境要求（栖息地）和地理分布（范围）。科学的进步要求软件具有几种很少同时出现的品质。理想情况下，科学软件：（1）开源（提供基本代码）; 2）提供概念和方法指导（引导用户并帮助他们做出决策）; 3）灵活（允许多种选择）; 4）是交互式的（在分析完成时显示分析的每个阶段的结果）; 5）可以容易且快速地扩展/更新;和6）提供分析运行的明确文档（使得容易再现结果）。本项目将生产的软件直接响应这些需求。这将是一个创新方式的例子，使新的科学方法能够为广大研究人员所利用，而不仅仅是某一特定领域的专家。它的目标用户群是生物学家和自然资源管理人员，程序员、教育工作者和学生也会感兴趣。该软件将有助于更好地估计物种的分布范围，这对保护生物学、研究入侵物种以及昆虫和野生动物传播给人类的疾病等多种兴趣都很重要。该项目将对研究生和本科生进行计算机编码培训。除了软件本身，研究人员还将制作科学出版物和在线网络研讨会，记录和解释其使用。具体来说，该项目将大大扩展软件华莱士的新兴领域的利基/分布式建模和相关领域。这些模型估计一个物种的环境适应性，为各种科学研究表明其潜在的地理分布。目前，研究人员正在努力跟上进步，并实现对新思想和技术的灵活吸收。为了改善这种情况，Wallace软件提供了一个模块化平台，通过图形用户界面（GUI）提供可定制的工作流程。利用Wallace的模块化特性，研究人员将与许多外部合作伙伴协调，以增加各种尖端功能。该项目将：1）基于记录物种存在的发生数据生成用于建模的综合框架; 2）包括利用重复采样的技术; 3）允许无缝用户上传/下载以及通过在线和本地实现的可定制工作流;以及4）发展用户社区。最终，这种方法可以扩大规模，为数千个物种提供高质量的建模。华莱士还将成为其他学科科学软件开发的典范。该项目的结果将在以下网站公布：https://wallaceecomod.github.io/

项目成果

Curso modelado de nicho ecológico, version 1.0

Curso modelado de nicho ecológico，版本 1.0

• DOI: 10.17161/bi.v14i0.8189
• 发表时间: 2019
• 期刊: Biodiversity Informatics
• 影响因子: 6.5
• 作者: Peterson, A. Townsend;Anderson, Robert P;Cobos, Marlon E;Cuahutle, Martín;Cuervo-Robayo, Angela P;Escobar, Luis E;Fernández, Marc;Jiménez-García, Daniel;Lira-Noriega, Andrés;Lobo, Jorge M
• 通讯作者: Lobo, Jorge M

A Constraint-based model of Dynamic Island Biogeography: environmental history and species traits predict hysteresis in populations and communities

基于约束的动态岛屿生物地理学模型：环境历史和物种特征预测种群和群落的滞后现象

• DOI: 10.21425/f5fbg44383
• 发表时间: 2019
• 期刊: Frontiers of Biogeography
• 作者: Burger, Joseph R.;Anderson, Robert P.;Balk, Meghan A.;Fristoe, Trevor S.
• 通讯作者: Fristoe, Trevor S.

A checklist for maximizing reproducibility of ecological niche models

• DOI: 10.1038/s41559-019-0972-5
• 发表时间: 2019-10-01
• 期刊: NATURE ECOLOGY & EVOLUTION
• 影响因子: 16.8
• 作者: Feng, Xiao;Park, Daniel S.;Popes, Monica
• 通讯作者: Popes, Monica

ENM2020: A Free Online Course and Set of Resources on Modeling Species' Niches and Distributions

ENM2020：关于物种生态位和分布建模的免费在线课程和资源集

• DOI: 10.17161/bi.v17i.15016
• 发表时间: 2022
• 期刊: Biodiversity Informatics
• 影响因子: 6.5
• 作者: Peterson, A. Townsend;Aiello-Lammens, Matthew;Amatulli, Giuseppe;Anderson, Robert;Cobos, Marlon;Diniz-Filho, José Alexandre;Escobar, Luis;Feng, Xiao;Franklin, Janet;Gadelha, Luiz
• 通讯作者: Gadelha, Luiz

occCite: Tools for querying and managing large biodiversity occurrence datasets

occCite：用于查询和管理大型生物多样性发生数据集的工具

• DOI: 10.1111/ecog.05618
• 发表时间: 2021
• 期刊: Ecography
• 影响因子: 5.9
• 作者: Owens, Hannah L.;Merow, Cory;Maitner, Brian S.;Kass, Jamie M.;Barve, Vijay;Guralnick, Robert P.
• 通讯作者: Guralnick, Robert P.