Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Core Unit Bioinformatics (CUBI), Berlin 10117 , Germany.
Gigascience. 2022 Dec 28;12. doi: 10.1093/gigascience/giad052. Epub 2023 Jul 27.
Scientists employing omics in life science studies face challenges such as the modeling of multiassay studies, recording of all relevant parameters, and managing many samples with their metadata. They must manage many large files that are the results of the assays or subsequent computation. Users with diverse backgrounds, ranging from computational scientists to wet-lab scientists, have dissimilar needs when it comes to data access, with programmatic interfaces being favored by the former and graphical ones by the latter. We introduce SODAR, the system for omics data access and retrieval. SODAR is a software package that addresses these challenges by providing a web-based graphical user interface for managing multiassay studies and describing them using the ISA (Investigation, Study, Assay) data model and the ISA-Tab file format. Data storage is handled using the iRODS data management system, which handles large quantities of files and substantial amounts of data. SODAR also offers programmable APIs and command-line access for metadata and file storage. SODAR supports complex omics integration studies and can be easily installed. The software is written in Python 3 and freely available at https://github.com/bihealth/sodar-server under the MIT license.
从事生命科学研究的科学家在使用组学方法时会面临一些挑战，例如多实验研究的建模、记录所有相关参数以及管理带有元数据的许多样本。他们必须管理许多大型文件，这些文件是实验或后续计算的结果。具有不同背景的用户，包括计算科学家和湿实验室科学家，在数据访问方面有不同的需求，前者更喜欢编程接口，后者更喜欢图形界面。我们引入了 SODAR，这是一个用于组学数据访问和检索的系统。SODAR 是一个软件包，通过提供基于 Web 的图形用户界面来管理多实验研究，并使用 ISA（Investigation、Study、Assay）数据模型和 ISA-Tab 文件格式对其进行描述，从而解决了这些挑战。数据存储由 iRODS 数据管理系统处理，该系统可以处理大量文件和大量数据。SODAR 还提供了用于元数据和文件存储的可编程 API 和命令行访问。SODAR 支持复杂的组学综合研究，并且易于安装。该软件是用 Python 3 编写的，可在 MIT 许可证下从 https://github.com/bihealth/sodar-server 获得。
