The Stanford Microarray Database accommodates additional microarray platforms and data formats.
The Stanford Microarray Database accommodates additional microarray platforms and data formats.
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DOI：
10.1093/nar/gki006
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发表时间：
2005-01-01
影响因子：
14.9
通讯作者：
Sherlock G
中科院分区：
文献类型：
--
作者：
Ball CA;Awad IA;Demeter J;Gollub J;Hebert JM;Hernandez-Boussard T;Jin H;Matese JC;Nitzberg M;Wymore F;Zachariah ZK;Brown PO;Sherlock G
斯坦福大学微阵列数据库（SMD）（http：smd.stanford.edu）是数百名斯坦福大学研究人员及其合作者的研究工具。此外，SMD作为整个生物研究社区的资源，通过提供对SMD用户发布的微阵列数据的不受限制的访问和传播其源代码。除了存储GenePix（Axon Instruments）和ScanAlyze从点样微阵列输出，SMD最近增加了存储、检索、显示和分析由几个额外的微阵列平台和图像分析软件包产生的完整原始数据的能力，因此我们现在也可以接受来自AffysseGeneChips的数据。（MAS 5/GCOS或dChip）、Agilent Catalog或Custom阵列（使用Agilent的Feature Extraction软件）或由SpotReader（奈尔斯Scientific）创建的数据。我们已经实现了软件，使我们能够接受来自阵列制造商的MAGE-ML文件，并将符合MIAME-ML格式的数据直接提交给ArrayExpress和GEO，大大增加了SMD数据发布的便利性，并符合公认的标准，也增加了公众对已发布的微阵列数据的可访问性。我们引入了一个新工具，以促进用户之间的数据共享，以便在数据分析完成期间，之前或之后共享数据集。完整数据库软件包的最新版本源代码于2004年11月发布（http：//smd.stanford.edu/download/），使世界各地的研究人员能够部署他们自己的SMD安装。
The Stanford Microarray Database (SMD) (http://smd.stanford.edu) is a research tool for hundreds of Stanford researchers and their collaborators. In addition, SMD functions as a resource for the entire biological research community by providing unrestricted access to microarray data published by SMD users and by disseminating its source code. In addition to storing GenePix (Axon Instruments) and ScanAlyze output from spotted microarrays, SMD has recently added the ability to store, retrieve, display and analyze the complete raw data produced by several additional microarray platforms and image analysis software packages, so that we can also now accept data from Affymetrix GeneChips (MAS5/GCOS or dChip), Agilent Catalog or Custom arrays (using Agilent's Feature Extraction software) or data created by SpotReader (Niles Scientific). We have implemented software that allows us to accept MAGE-ML documents from array manufacturers and to submit MIAME-compliant data in MAGE-ML format directly to ArrayExpress and GEO, greatly increasing the ease with which data from SMD can be published adhering to accepted standards and also increasing the accessibility of published microarray data to the general public. We have introduced a new tool to facilitate data sharing among our users, so that datasets can be shared during, before or after the completion of data analysis. The latest version of the source code for the complete database package was released in November 2004 (http://smd.stanford.edu/download/), allowing researchers around the world to deploy their own installations of SMD.