Implementation of GenePattern within the Stanford Microarray Database.
Implementation of GenePattern within the Stanford Microarray Database.
复制标题
DOI：
10.1093/nar/gkn786
复制
发表时间：
2009-01
影响因子：
14.9
通讯作者：
Ball CA
中科院分区：
文献类型：
--
作者：
Hubble J;Demeter J;Jin H;Mao M;Nitzberg M;Reddy TB;Wymore F;Zachariah ZK;Sherlock G;Ball CA
全世界数百名研究人员使用Stanford MicroArray数据库（SMD； http://smd.stanford.edu/）存储，注释，查看，分析和共享微阵列数据。除了在斯坦福大学访问自己的数据的访问权限外，SMD还向世界任何地方的任何公共用户提供了对这些数据分析这些数据的访问权限。以前，将新的微阵列数据分析工具添加到SMD中受到可用工程资源的限制，此外，现有的工具套件并未提供一种简单的方法来设计，执行和共享分析管道，或记录此类管道的信息出版的目的。为了解决这个问题，我们将Genepattern软件包直接纳入了SMD，提供了对许多新分析工具的访问权限，以及插入式架构，该插入式体系结构允许用户直接通过SMD集成和共享其他工具。在本文中，我们将Genepattern微阵列分析软件包的实现描述为SMD代码库。 SMD源代码可以在开源许可下完全可以自由地使用SMD源代码，使其他组能够创建具有丰富数据分析能力的SMD的本地安装。
Hundreds of researchers across the world use the Stanford Microarray Database (SMD; http://smd.stanford.edu/) to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, SMD also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to SMD has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the GenePattern software package directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.
斯坦福微阵列数据库：新分析工具的实现和软件的开源发布。
影响因子：
14.9
作者：
Demeter, Janos;Beauheim, Catherine;Gollub, Jeremy;Hernandez-Boussard, Tina;Jin, Heng;Maier, Donald;Matese, John C.;Nitzberg, Michael;Wymore, Farrell;Zachariah, Zachariah K.;Brown, Patrick O.;Sherlock, Gavin;Ball, Catherine A.
通讯作者：
Ball, Catherine A.
影响因子：
14.9
作者：
Wheeler, David L.;Barrett, Tanya;Yaschenko, Eugene
通讯作者：
Yaschenko, Eugene
ArrayExpress-一个微阵列实验和基因表达曲线的公共数据库。
影响因子：
14.9
作者：
Parkinson, H;Kapushesky, M;Shojatalab, M;Abeygunawardena, N;Coulson, R;Farne, A;Holloway, E;Kolesnykov, N;Lilja, P;Lukk, M;Mani, R;Rayner, T;Sharma, A;William, E;Sarkans, U;Brazma, A
通讯作者：
Brazma, A