CellRex: Software platform for managing biological cell data

IF 2.4 4区计算机科学 Q2 COMPUTER SCIENCE, SOFTWARE ENGINEERING

SoftwareX Pub Date : 2025-08-13 DOI:10.1016/j.softx.2025.102284

Jan Hölter , Tim Rickmeyer , Christiane Thielemann

引用次数: 0

Abstract

This work introduces the software platform CellRex, a research data management system for laboratories capable of storing, searching, and enriching data with biological metadata. CellRex addresses data management challenges by storing data in an ontology-based directory structure within the filesystem, with metadata saved as JSON files and in a document-oriented SQLite database. The framework, deployed as container services in a software-as-a-service model, features a web-based GUI and API for user interaction and machine-readable access, providing functionalities such as duplicate detection, experiment grouping, and templating. CellRex improves research efficiency and facilitates data reuse, providing a targeted solution for laboratories focused on cell analysis research.

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CellRex：管理生物细胞数据的软件平台

这项工作介绍了CellRex软件平台，这是一个实验室研究数据管理系统，能够存储，搜索和丰富生物元数据。CellRex通过将数据存储在文件系统中基于本体的目录结构中，将元数据保存为JSON文件和面向文档的SQLite数据库，从而解决了数据管理方面的挑战。该框架在软件即服务模型中作为容器服务部署，具有基于web的GUI和API，用于用户交互和机器可读访问，提供重复检测、实验分组和模板等功能。CellRex提高了研究效率，促进了数据重用，为专注于细胞分析研究的实验室提供了有针对性的解决方案。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

SoftwareX COMPUTER SCIENCE, SOFTWARE ENGINEERING-

CiteScore

5.50

自引率

2.90%

发文量

184

审稿时长

9 weeks

期刊介绍： SoftwareX aims to acknowledge the impact of software on today''s research practice, and on new scientific discoveries in almost all research domains. SoftwareX also aims to stress the importance of the software developers who are, in part, responsible for this impact. To this end, SoftwareX aims to support publication of research software in such a way that: The software is given a stamp of scientific relevance, and provided with a peer-reviewed recognition of scientific impact; The software developers are given the credits they deserve; The software is citable, allowing traditional metrics of scientific excellence to apply; The academic career paths of software developers are supported rather than hindered; The software is publicly available for inspection, validation, and re-use. Above all, SoftwareX aims to inform researchers about software applications, tools and libraries with a (proven) potential to impact the process of scientific discovery in various domains. The journal is multidisciplinary and accepts submissions from within and across subject domains such as those represented within the broad thematic areas below: Mathematical and Physical Sciences; Environmental Sciences; Medical and Biological Sciences; Humanities, Arts and Social Sciences. Originating from these broad thematic areas, the journal also welcomes submissions of software that works in cross cutting thematic areas, such as citizen science, cybersecurity, digital economy, energy, global resource stewardship, health and wellbeing, etcetera. SoftwareX specifically aims to accept submissions representing domain-independent software that may impact more than one research domain.