EMAAS: an extensible grid-based rich internet application for microarray data analysis and management.
EMAAS: an extensible grid-based rich internet application for microarray data analysis and management.
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DOI：
10.1186/1471-2105-9-493
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发表时间：
2008-11-25
影响因子：
3
通讯作者：
Butcher SA
中科院分区：
文献类型：
--
作者：
Barton G;Abbott J;Chiba N;Huang DW;Huang Y;Krznaric M;Mack-Smith J;Saleem A;Sherman BT;Tiwari B;Tomlinson C;Aitman T;Darlington J;Game L;Sternberg MJ;Butcher SA
微阵列实验需要应用复杂的分析方法以及使用非平凡的计算机技术来管理由此产生的大型数据集。这一点，再加上微阵列数据分析工具和技术的激增，使得实验室科学家跟上这一领域的最新发展非常具有挑战性。我们的目标是为微阵列数据分析和管理开发一个分布式电子支持系统。EMAAS（可扩展微阵列分析系统）是一个多用户富互联网应用程序（RIA），为微阵列数据存储和分析提供简单，强大的访问最新资源，并结合集成工具优化实时用户支持和培训。该系统利用分布式计算的能力来执行微阵列分析，并提供对位于各种远程设施的资源的无缝访问。EMAAS框架允许用户从多个来源导入微阵列数据到底层数据库，进行预处理，质量评估和分析数据，执行功能分析，并跟踪数据分析步骤，所有这些都通过一个易于使用的web门户。该界面以视频教程的形式和使用网络会议工具EVO的实时屏幕馈送为用户提供远程支持。包括R-Bioconductor和Affymetrix Power Tools在内的许多分析包已经集成在服务器端，可以通过postgresg - plr库或网格计算集群以编程方式使用。集成的分布式资源包括功能注释工具DAVID、GeneCards和微阵列数据存储库GEO、CELSIUS和MiMiR。EMAAS目前支持Affymetrix 3’和外显子表达阵列的分析，并且该系统可扩展以满足其他微阵列和转录组学平台的需求。EMAAS使用户能够通过一个简单易用的web应用程序跟踪和执行微阵列数据管理和分析任务。系统架构灵活且可扩展，允许相对容易地添加新的数组类型、分析算法和工具，并应对数据量的大量增加。
Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management. EMAAS (Extensible MicroArray Analysis System) is a multi-user rich internet application (RIA) providing simple, robust access to up-to-date resources for microarray data storage and analysis, combined with integrated tools to optimise real time user support and training. The system leverages the power of distributed computing to perform microarray analyses, and provides seamless access to resources located at various remote facilities. The EMAAS framework allows users to import microarray data from several sources to an underlying database, to pre-process, quality assess and analyse the data, to perform functional analyses, and to track data analysis steps, all through a single easy to use web portal. This interface offers distance support to users both in the form of video tutorials and via live screen feeds using the web conferencing tool EVO. A number of analysis packages, including R-Bioconductor and Affymetrix Power Tools have been integrated on the server side and are available programmatically through the Postgres-PLR library or on grid compute clusters. Integrated distributed resources include the functional annotation tool DAVID, GeneCards and the microarray data repositories GEO, CELSIUS and MiMiR. EMAAS currently supports analysis of Affymetrix 3' and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms. EMAAS enables users to track and perform microarray data management and analysis tasks through a single easy-to-use web application. The system architecture is flexible and scalable to allow new array types, analysis algorithms and tools to be added with relative ease and to cope with large increases in data volume.
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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：
3
作者：
Theilhaber J;Ulyanov A;Malanthara A;Cole J;Xu D;Nahf R;Heuer M;Brockel C;Bushnell S
通讯作者：
Bushnell S
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：
5.8
作者：
Hubbell, E;Liu, WM;Mei, R
通讯作者：
Mei, R
影响因子：
14.9
作者：
Hull D;Wolstencroft K;Stevens R;Goble C;Pocock MR;Li P;Oinn T
通讯作者：
Oinn T