LabKey Software, Seattle, WA 98102, USA.
BMC Bioinformatics. 2011 Mar 9;12:71. doi: 10.1186/1471-2105-12-71.
Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely.
To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment. Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350 organizations. It tracks roughly 27,000 assay runs, 860,000 specimen vials and 1,300,000 vial transfers.
Sharing data, analysis tools and infrastructure can speed the efforts of large research consortia by enhancing efficiency and enabling new insights. The Atlas installation of LabKey Server demonstrates the utility of the LabKey platform for collaborative research. Stable, supported builds of LabKey Server are freely available for download at http://www.labkey.org. Documentation and source code are available under the Apache License 2.0.
在疾病研究人员中，广泛的合作变得越来越普遍。例如，全球艾滋病毒企业通过在机构、大陆和专业之间协调研究，联合跨学科联盟，加速艾滋病毒疫苗的研究进展。新的、端到端的数据和标本管理软件工具对于实现这些联盟的雄心勃勃的目标是必要的。这些工具必须使研究人员能够在发现过程的早期组织和整合异构数据，标准化流程，深入了解汇集数据，并安全地进行协作。
为了满足这些需求，我们增强了 LabKey Server 平台，该平台以前称为 CPAS。这个免费的、开源的软件由专业工程师维护，他们使用商业上经过验证的软件开发和维护实践。最近的增强功能支持：（i）在合作组织之间提交标本请求（ii）图形定义新的实验数据类型、元数据和数据收集向导（iii）将来自多个电子表格的实验结果转换为共享数据库中的自定义表（iv）安全地组织、集成、分析、可视化和共享来自临床记录到标本到复杂检测的各种数据类型（v）与外部数据源动态交互（vi）随时间跟踪研究参与者和队列（vii）使用客户端库开发自定义界面（viii）在内置的 R 脚本环境中编写自定义可视化效果。各种研究组织已经采用和适应了 LabKey Server，包括全球艾滋病毒企业内部的联盟。Atlas 是一个专门为服务于这些联盟而定制的 LabKey Server 安装。它正在生产中使用，并展示了 LabKey Server 的核心功能。Atlas 现在拥有超过 2800 个来自大约 36 个国家和 350 个组织的活跃用户帐户。它跟踪大约 27000 次检测运行、860000 个标本小瓶和 1300000 个小瓶转移。
通过提高效率和提供新的见解，共享数据、分析工具和基础设施可以加速大型研究联盟的工作。LabKey Server 的 Atlas 安装展示了 LabKey 平台在协作研究中的实用性。LabKey Server 的稳定、受支持的版本可在 http://www.labkey.org 免费下载。文档和源代码可在 Apache License 2.0 下获得。
