State-of-the-Art Data Management: Improving the Reproducibility, Consistency, and Traceability of Structural Biology and in Vitro Biochemical Experiments.
State-of-the-Art Data Management: Improving the Reproducibility, Consistency, and Traceability of Structural Biology and in Vitro Biochemical Experiments.
复制标题
DOI：
10.1007/978-1-0716-0892-0_13
复制
发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Minor W
中科院分区：
文献类型：
--
作者：
Cooper DR;Grabowski M;Zimmerman MD;Porebski PJ;Shabalin IG;Woinska M;Domagalski MJ;Zheng H;Sroka P;Cymborowski M;Czub MP;Niedzialkowska E;Venkataramany BS;Osinski T;Fratczak Z;Bajor J;Gonera J;MacLean E;Wojciechowska K;Konina K;Wajerowicz W;Chruszcz M;Minor W
高效而全面的数据管理是现代科学研究不可或缺的组成部分，除了最琐碎的实验外，所有实验都需要有效的工具。LabDB系统的开发和使用，在我们的实验室最初的目的是跟踪结构确定管道在几个大型美国国立卫生研究院（NIH）项目的进展。虽然最初设计用于结构生物学实验，但其模块化性质使其易于应用于许多实验领域的各种规模的实验室。多年来，LabDB已经转变为一个集成了一系列生物化学，生物物理和晶体学实验数据的复杂系统，该系统直接从实验室仪器和通过Web界面人工输入获取数据。该系统的核心模块处理多种类型的通用实验室管理数据，如实验室人员、化学品库存、存储位置和定制库存解决方案。LabDB还跟踪各种生化实验，包括分光光度和荧光分析，热位移分析，等温滴定量热实验等。LabDB已被用于管理实验数据，导致超过1200个存款到蛋白质数据库（PDB）;该系统目前由传染病结构基因组学中心（CSGID）和几个大型实验室使用。本章还提供了数据挖掘分析的示例，以及对不完整和不一致的实验数据的警告。这些功能，连同其详细跟踪、分析和审计实验数据的能力，使得所描述的系统特别适合于检查生命科学研究中的不可再现性的潜在来源。
Efficient and comprehensive data management is an indispensable component of modern scientific research and requires effective tools for all but the most trivial experiments. The LabDB system developed and used in our laboratory was originally designed to track the progress of a structure determination pipeline in several large National Institutes of Health (NIH) projects. While initially designed for structural biology experiments, its modular nature makes it easily applied in laboratories of various sizes in many experimental fields. Over many years, LabDB has transformed into a sophisticated system integrating a range of biochemical, biophysical, and crystallographic experimental data, which harvests data both directly from laboratory instruments and through human input via a web interface. The core module of the system handles many types of universal laboratory management data, such as laboratory personnel, chemical inventories, storage locations, and custom stock solutions. LabDB also tracks various biochemical experiments, including spectrophotometric and fluorescent assays, thermal shift assays, isothermal titration calorimetry experiments, and more. LabDB has been used to manage data for experiments that resulted in over 1200 deposits to the Protein Data Bank (PDB); the system is currently used by the Center for Structural Genomics of Infectious Diseases (CSGID) and several large laboratories. This chapter also provides examples of data mining analyses and warnings about incomplete and inconsistent experimental data. These features, together with its capabilities for detailed tracking, analysis, and auditing of experimental data, make the described system uniquely suited to inspect potential sources of irreproducibility in life sciences research.