Cisar Petr, Soloviov Dmytro, Barta Antonin, Urban Jan, Stys Dalibor
Faculty of Fisheries and Protection of Waters, Institute of Complex Systems, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zámek 136, 37333, Nove Hrady, Czech Republic.
Biomed Eng Online. 2016 Jul 15;15 Suppl 1(Suppl 1):74. doi: 10.1186/s12938-016-0188-8.
One of the main challenges in modern science is the amount of data produced by the experimental work; it is difficult to store, organize and share the scientific data and to extract the wealth of knowledge. Experimental method descriptions in scientific publications are often incomplete, which complicates experimental reproducibility. The proposed system was created in order to address these issues. It provides a solution for management of the experimental data and metadata to support the reproducibility.
The system is implemented as a repository for experiment descriptions and experimental data. It has three main entry points: desktop application for protocol design and data processing, web interface dedicated for protocol and data management, and web-based interface for mobile devices suitable for the field experiments. The functionality of desktop client can be extended using the custom plug-ins for data extraction and data processing. The system provides several methods to support experimental reproducibility: standardized terminology support, data and metadata at a single location, standardized protocol design or protocol evolution.
The system was tested in the framework of international infrastructure project AQUAEXCEL with five pilot installations at different institutes. The general testing in Tissue culture certified laboratory, Institute of complex systems and IFREMER verified the usability under different research infrastructures. The specific testing focused on the data processing modules and plug-ins demonstrated the modularity of the system for the specific conditions. The BioWes system represents experimental data as black box and therefore can handle any data type so as to provide broad usability for a variety of experiments and provide the data management infrastructure to improve the reproducibility and data sharing.
The proposed system provides the tools for standard data management operations and extends the support by the standardization possibilities, protocol evolution with visualization features and modularity based on the data processing modules and device communication plug-ins. The software can be used at different organization levels: from a single researcher (to improve data organization) to research consortium through the central protocols management repository. Support from the protocol design until being shared with the standardization features helps to improve the reproducibility of research work. The platform provides support from experimental protocol design to cooperation using simple sharing.
现代科学的主要挑战之一是实验工作产生的数据量；存储、组织和共享科学数据以及提取丰富的知识都很困难。科学出版物中的实验方法描述往往不完整，这使得实验的可重复性变得复杂。为了解决这些问题，创建了所提出的系统。它为实验数据和元数据的管理提供了一个解决方案，以支持可重复性。
该系统被实现为一个用于实验描述和实验数据的存储库。它有三个主要入口点：用于协议设计和数据处理的桌面应用程序、专门用于协议和数据管理的网页界面以及适用于野外实验的移动设备的基于网页的界面。桌面客户端的功能可以使用用于数据提取和数据处理的自定义插件进行扩展。该系统提供了几种支持实验可重复性的方法：标准化术语支持、数据和元数据集中存储、标准化协议设计或协议演进。
该系统在国际基础设施项目AQUAEXCEL的框架内进行了测试，在不同机构有五个试点装置。在组织培养认证实验室、复杂系统研究所和法国海洋开发研究院进行的总体测试验证了在不同研究基础设施下的可用性。针对数据处理模块和插件的具体测试证明了该系统在特定条件下的模块化。BioWes系统将实验数据表示为黑箱，因此可以处理任何数据类型，从而为各种实验提供广泛的可用性，并提供数据管理基础设施以提高可重复性和数据共享。
所提出的系统提供了标准数据管理操作的工具，并通过标准化可能性、具有可视化功能的协议演进以及基于数据处理模块和设备通信插件的模块化来扩展支持。该软件可以在不同的组织层面使用：从单个研究人员（以改善数据组织）到通过中央协议管理存储库的研究联盟。从协议设计到通过标准化功能进行共享的支持有助于提高研究工作的可重复性。该平台提供从实验协议设计到使用简单共享进行合作的支持。
