EAGER: DynaMo: A novel computational workflow for dynamic monographs and revisionary systematics

分类学专著联合收割机综合了关于生物体的外观、发生、系谱关系和分类的信息，并提供了鉴定它们的方法。 这些基线信息对于理解生命的多样性至关重要，并有助于为其他生物学研究问题提供信息。 目前的分类学专著遭受的是静态的文件，不提供一个有效的手段访问或分析的基础数据。该项目将开发一套连接的计算工具（DynaMo），以制作一个动态的专着，简化工作流程，整合基于XML的数据，并促进这些数据的分析。尽管还处于开发的早期阶段，但DynaMo显示出巨大的潜力，可以改变分类学专著的生成、分析和呈现方式。该项目将在系统生物学、生物信息学和软件开发方面培训一名博士后研究员和本科生，包括代表性不足的群体的成员。 关于动态专题论文和数量分类学的两个讲习班将有助于培训更广泛的系统学界。由此产生的DynaMo软件和项目产生的所有数据将通过公共数据库和储存库免费提供。虽然系统学的其他领域已经采用了现代方法，但分类学专著的制作一直受到阻碍，因为缺乏有效的计算工具来有效地整合和更新作为专题研究基础的大型数据集和复杂分析。该项目将开发数字基础设施（DynaMo），使系统学家能够记录并与制作专著所需的所有数据管理和分析工具进行交互，并帮助使专题方法和分析更加透明，可复制和可扩展。支撑这一工作流程的数字基础设施将是一个通用的关系数据库，存储所有主要的生物多样性数据以及中间资源，以便更快地检索。存储在数据库中的数据将通过模块化管道进行整合和分析。该数据库将随着新数据和结果的出现而不断更新，并且每当数据库中的基础数据发生变化时，分析管道将自动生成新结果。分析结果、交互式可视化、原始数据和文本将是机器可读的，并可通过动态专著访问，这是一个在线文档，由于它提供了一个与底层基于XML的数据库的接口，因此永远是最新的。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的知识价值和更广泛的影响审查标准进行评估来支持。

Taxonomic monographs combine information about the appearance, occurrence, genealogical relationships, and classification of organisms and provide methods for their identification. This baseline information is critical for understanding the diversity of life and helps inform other biological research questions. Current taxonomic monographs suffer from being static documents that do not provide an efficient means of accessing or analyzing the underlying data. This project will develop a linked set of computational tools (DynaMo) to produce a dynamic monograph that streamlines the workflow, integrates specimen-based data, and facilitates analysis of these data. Despite being in the early stages of development DynaMo shows immense potential to transform how taxonomic monographs are generated, analyzed and presented. The project will train a post-doctoral researcher and undergraduates, including members of underrepresented groups, in systematic biology, bioinformatics, and software development. Two workshops on dynamic monographs and quantitative taxonomy will help train the broader systematics community. The resulting DynaMo software, and all data generated by the project, will be made freely available through public databases and repositories.While other areas of systematics have adopted modern approaches, the production of taxonomic monographs has been hindered by the lack of efficient computational tools to efficiently integrate and update the large data sets and complex analyses that underly monographic research. This project will develop the digital infrastructure (DynaMo) to enable systematists to document and interact with all the data management and analysis tools needed to produce a monograph and help make monographic methods and analyses more transparent, reproducible, and extendable. The digital infrastructure underpinning this workflow will be a generic relational database that stores all primary biodiversity data as well as intermediate resources for faster retrieval. The data stored in the database will be integrated and analyzed via modular pipelines. This database will be continuously updated as new data and results become available and the analysis pipelines will automatically generate new results whenever the underlying data in the database change. The results of analyses, interactive visualizations, raw data, and text will be machine-readable and accessible via a dynamic monograph, an online document that is perpetually up-to-date because it provides an interface to the underlying specimen-based database.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.