LabKey Server: an open source platform for scientific data integration, analysis and collaboration.
LabKey Server: an open source platform for scientific data integration, analysis and collaboration.
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DOI：
10.1186/1471-2105-12-71
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发表时间：
2011-03-09
影响因子：
3
通讯作者：
Igra M
中科院分区：
文献类型：
--
作者：
Nelson EK;Piehler B;Eckels J;Rauch A;Bellew M;Hussey P;Ramsay S;Nathe C;Lum K;Krouse K;Stearns D;Connolly B;Skillman T;Igra M
广泛的合作在疾病研究人员中越来越普遍。例如，全球艾滋病毒事业联合了跨学科的联合体，通过跨机构、跨大陆和跨专业的协调研究，加快艾滋病毒疫苗的进展。新的端到端的数据和标本管理软件工具对于实现此类联盟的宏伟目标是必要的。这些工具必须使研究人员能够在发现过程的早期组织和集成异构数据，标准化流程，获得对池数据的新见解并安全地进行协作。为了满足这些需求，我们增强了LabKey服务器平台（以前称为CPAS）。这个免费的开源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样本请求（ii）以图形方式定义新的实验数据类型、元数据和数据收集向导（iii）将实验结果从多种电子表格转换为共享数据库中的自定义表格（iv）安全地组织、整合、分析、可视化和共享各种数据类型，从临床记录到标本再到复杂的测定（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）在内置的在R脚本环境中。不同的研究组织已经采用和调整LabKey Server，包括全球艾滋病毒企业内的联盟。Atlas是LabKey Server的一个安装，专门为这些联盟服务。它已投入生产使用，并展示了LabKey Server的核心功能。Atlas系统现有来自大约36个国家和350个组织的2 800多个活跃用户账户。它跟踪大约27，000次检测运行、860，000个样本瓶和1，300，000个小瓶转移。共享数据、分析工具和基础设施可以通过提高效率和实现新的见解来加快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许可证2.0下获得。
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.
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DOI：
10.1197/jamia.m1138
发表时间：
2002-11-01
影响因子：
6.4
作者：
Jakobovits, RM;Rosse, C;Brinkley, JF
通讯作者：
Brinkley, JF
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
3
作者：
Goddard, NH;Cannon, RC;Howell, FW
通讯作者：
Howell, FW
影响因子：
4.5
作者：
Goble, Carole;Stevens, Robert
通讯作者：
Stevens, Robert
科学软件开发不是矛盾的。
影响因子：
4.3
作者：
Baxter, Susan M.;Day, Steven W.;Fetrow, Jacquelyn S.;Reisinger, Stephanie J.
通讯作者：
Reisinger, Stephanie J.