ABI Sustaining: Maintenance of the XMA/ZMAPortal video data management systems and XMALab video motion analysis software for the comparative biomechanics community

ABI Sustaining：为比较生物力学界维护 XMA/ZMAPortal 视频数据管理系统和 XMALab 视频运动分析软件

• 批准号: 1661129
• 负责人: Elizabeth Brainerd
• 金额: $ 33.99万
• 依托单位: Brown University
• 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: 2017-08-15 至 2023-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1661129&HistoricalAwards=false
• 关键词: ABI; Sustaining; Maintenance; XMA; ZMAPortal

Comparative biomechanics is the field that studies the fundamental engineering rules governing how organisms move, frequently leading to practical applications as well as basic understanding. For example, by comparing the biomechanics of swimming in sharks, fish and whales, efficient swimming robots have been developed for undersea exploration and search and rescue. A wide array of instruments is used by different research groups to collect similar motion-capture data, and a wide array of methods is used to store and document the data, including both commercial software and locally-generated code as tools for data analysis, creating technical barriers to sharing and reusing both data and tools. Since progress in science is accelerated when scientists can share and reuse data and software, these technical barriers have hindered wide data sharing in the field of comparative biomechanics. The goal of this project is to maintain online data management and software analysis tools to accelerate research in comparative biomechanics. These tools, the Zoological Motion Analysis Portal (zmaportal.org), X-ray Motion Analysis Portal (xmaportal.org) and X-ray Motion Analysis Lab (XMALab client software) were developed with NSF support, and this project will provide routine maintenance of the open-source code base and server and storage space for hosting the online tools. These biological informatics tools are accelerating research in comparative biomechanics by enhancing data sharing and the ability to compare across species. From such comparisons, fundamental engineering concepts are discovered, that can then be applied to human engineering designs (biologically-inspired design and biomimetics). These advances promote US economic competiveness through technological innovation.New discoveries in the field of comparative biomechanics have often been driven by the introduction of new technologies. High-speed video imaging, X-ray imaging, XROMM and 3-D motion analysis are key components of this toolkit. A fundamental goal of comparative biomechanics is to compare species in a phylogenetic context, and thereby to extract robust relationships between phenotype (form) and biomechanical function. The tools to be maintained through this resource significantly increase the throughput of motion analysis, thereby increasing the number of species available for comparison. The XMAPortal and ZMAPortal are designed to standardize video data and metadata, thereby facilitating reproducibility and comparison among many studies of multiple species from data collected at multiple research sites. Together these products will increase the quality, quantity, reusability, and comparability of animal motion data available for comparative biomechanics research. This project will maintain valuable cyberinfrastructure tools for the study of animals in motion for comparative biomechanics research. It will support continued efforts to make these tools accessible to as wide a range of scientists and students as possible. Toward broad understanding and appreciation of science, animals in motion are inherently beautiful and fascinating to the general public. XROMM animations are visually compelling, and the xromm.org web site has received, and continues to receive, substantial interest from the lay press and television producers. The results of this project may be found at the following stable URLs: [xromm.org; xmaportal.org; zmaportal.org; bitbucket.org/xromm/xmalab/].

比较生物力学是研究生物体如何运动的基本工程规则的领域，经常导致实际应用和基本理解。 例如，通过比较鲨鱼、鱼类和鲸鱼游泳的生物力学，开发出了高效的游泳机器人，用于海底勘探和搜救。不同的研究小组使用各种各样的仪器来收集类似的运动捕捉数据，并使用各种各样的方法来存储和记录数据，包括商业软件和本地生成的代码作为数据分析工具，为共享和重用数据和工具创造了技术障碍。由于科学家可以共享和重用数据和软件，从而加速了科学的进步，因此这些技术障碍阻碍了比较生物力学领域的广泛数据共享。该项目的目标是维护在线数据管理和软件分析工具，以加速比较生物力学的研究。这些工具，动物运动分析门户网站（zmaportal.org），X射线运动分析门户网站（xmaportal.org）和X射线运动分析实验室（XMALab客户端软件）是在NSF的支持下开发的，该项目将提供开放源代码库和服务器的日常维护以及托管在线工具的存储空间。这些生物信息学工具通过加强数据共享和跨物种比较的能力，正在加速比较生物力学的研究。从这样的比较中，基本的工程概念被发现，然后可以应用于人类工程设计（生物启发的设计和仿生学）。这些进步通过技术创新促进了美国的经济竞争力。在比较生物力学领域的新发现往往是由新技术的引入所推动的。高速视频成像、X射线成像、XROMM和三维运动分析是该工具包的关键组成部分。比较生物力学的一个基本目标是在系统发育背景下比较物种，从而提取表型（形式）和生物力学功能之间的鲁棒关系。通过该资源维护的工具显著增加了运动分析的吞吐量，从而增加了可用于比较的物种数量。XMAPortal和ZMAPortal旨在标准化视频数据和元数据，从而促进多个研究站点收集的多个物种数据的重复性和比较。这些产品将提高动物运动数据的质量、数量、可重用性和可比性，可用于比较生物力学研究。该项目将为比较生物力学研究中的运动动物研究提供宝贵的网络基础设施工具。它将支持继续努力，使尽可能多的科学家和学生能够使用这些工具。为了对科学的广泛理解和欣赏，运动中的动物天生美丽，对公众来说是迷人的。XROMM动画在视觉上引人注目，xromm.org网站已经并将继续受到新闻界和电视制片人的极大兴趣。该项目的结果可在以下稳定URL中找到：[xromm.org; xmaportal.org; zmaportal.org; bitbucket.org/xromm/xmalab/]。

项目成果

Axial morphology and 3D neurocranial kinematics in suction-feeding fishes.

• DOI: 10.1242/bio.036335
• 发表时间: 2018-09-20
• 期刊: Biology open
• 影响因子: 2.4
• 作者: Jimenez YE;Camp AL;Grindall JD;Brainerd EL
• 通讯作者: Brainerd EL

Locomotor rib kinematics in two species of lizards and a new hypothesis for the evolution of aspiration breathing in amniotes

• DOI: 10.1038/s41598-020-64140-y
• 发表时间: 2020-05-12
• 期刊: SCIENTIFIC REPORTS
• 影响因子: 4.6
• 作者: Cieri, Robert L.;Hatch, Samuel T.;Brainerd, Elizabeth L.
• 通讯作者: Brainerd, Elizabeth L.

The opercular mouth-opening mechanism of largemouth bass functions as a 3D four-bar linkage with three degrees of freedom

• DOI: 10.1242/jeb.159079
• 发表时间: 2017-12-15
• 期刊: JOURNAL OF EXPERIMENTAL BIOLOGY
• 影响因子: 2.8
• 作者: Olsen, Aaron M.;Camp, Ariel L.;Brainerd, Elizabeth L.
• 通讯作者: Brainerd, Elizabeth L.

Royal knifefish generate powerful suction feeding through large neurocranial elevation and high epaxial muscle power

皇家刀鱼通过大的颅神经高度和高的轴外肌肉力量产生强大的吸食

• DOI: 10.1242/jeb.244294
• 发表时间: 2022
• 期刊: Journal of Experimental Biology
• 影响因子: 2.8
• 作者: Li, Ellen Y.;Kaczmarek, Elska B.;Olsen, Aaron M.;Brainerd, Elizabeth L.;Camp, Ariel L.
• 通讯作者: Camp, Ariel L.

Breathing with floating ribs: XROMM analysis of lung ventilation in savannah monitor lizards

• DOI: 10.1242/jeb.189449
• 发表时间: 2018-11-01
• 期刊: JOURNAL OF EXPERIMENTAL BIOLOGY
• 影响因子: 2.8
• 作者: Cieri, Robert L.;Moritz, Sabine;Brainerd, Elizabeth L.
• 通讯作者: Brainerd, Elizabeth L.