* This project was supported in part by an NIH grant R01CA68822.
 

  1. Introduction
  2. Publications
  3. Program Download
  4. News
  5. Contacts

1. Introduction

Use Summary

Registered users:1385LOGIN times:9824Software download:1737Data operating/analysis requests:15229
Arrays:7094Platforms:221Probes:15879244

WebArray

WebArray is a web platform for analysis of microarray data. Two-color data and Affymetrix data are supported. Click HERE for details.

WebArrayDB

WebArrayDB is a database system and online cross-platform analysis suite for analysis of microarray data. Click HERE for details.

Comparison of WebArray And WebArrayDB
WebArrayWebArrayDB
data file uploadyesyes
data file storage in databasenoyes
data file search by keywordsnoyes
MIAME compliancenoyes
microarray analysis:
data normalizationyesyes
comparisons between identical platformsyesyes
comparisons between different platformsnoyes
supported dataAffymetrix CEL files & two-color datadata of any number of channels(colors)
statistical algorithmst-test (implemented in LIMMA)t-test, SAM, ANOVA, non-parametric analysis
parallel computationnoyes

System Requirements

A user needs to register to obtain a user ID before using this program. A web browser with JavaScript and cookie support is also required. To upload big files, JMaster's "JumpLoader" might be helpful. As a Java applet, JumpLoader requires the browser's support for Java.
As our main web browser used for testing/debugging, Mozilla Firefox is strongly recommended for users to explore WebArray/WebArrayDB. We also tested the program with Opera, Flock, Microsoft Internet Explorer (IE), and Google Chrome.

Tutorial Movies

A brief tutorial vedio will should you how to upload files, deposit data into the database, browse or search data in the database, and analyze data across different microarray platforms. Click the button to watch it.

2. Publications

  1. Xia X, McClelland M, Wang Y. WebArray: an online platform for microarray data analysis. BMC Bioinformatics. 2005, 6(1): 306.     [Abstract] [Full Text] [PDF]

  2. The WebArray can be cited in Endnote format (download HERE), or in BibTex format:
    @Article{WEBARRAY,
      author = {XiaoQin Xia and Michael McClelland and Yipeng Wang},
      title = {WebArray: an online platform for microarray data analysis},
      journal = {BMC Bioinformatics},
      volume = {6},
      year = {2005},
      pages = {306},
      url = {http://www.biomedcentral.com/1471-2105/6/306}
    }
    
  3. Wang Y, McClelland M, Xia XQ. Analyzing microarray data using WebArray. Cold Spring Harbor Protocols. 2009(8): pdb.prot5260. doi:10.1101/pdb.prot5260.     [Abstract] [Full Text]

  4. Citation in BibTex format:
    @article{YipengWang08012009,
      author = {Wang, Yipeng and McClelland, Michael and Xia, Xiao-Qin},
      title = {{Analyzing Microarray Data Using WebArray}},
      journal = {Cold Spring Harbor Protocols},
      volume = {2009},
      number = {8},
      pages = {pdb.prot5260-},
      doi = {10.1101/pdb.prot5260},
      year = {2009},
      URL = {http://cshprotocols.cshlp.org/cgi/content/abstract/2009/8/pdb.prot5260}
    }
    
  5. Xia XQ, McClelland M, Porwollik S, Song W, Cong X, Wang Y. WebArrayDB: Cross-platform microarray data analysis and public data repository. Bioinformatics, 2009, doi:10.1093/bioinformatics/btp430.     [Abstract] [Full Text].

  6. Citation in BibTex format:
    @ARTICLE{Xia2009,
      author = {Xiao-Qin Xia and Michael McClelland and Steffen Porwollik and Wenzhi
    	Song and Xianling Cong and Yipeng Wang},
      title = {WebArrayDB: cross-platform microarray data analysis and public data
    	repository.},
      journal = {Bioinformatics},
      year = {2009},
      volume = {25},
      pages = {2425--2429},
      number = {18},
      month = {Sep},
      doi = {10.1093/bioinformatics/btp430},
      institution = {Vaccine Research Institute San Diego, San Diego, CA 92121, USA. xqxia70@gmail.com},
      keywords = {Computational Biology, methods; Information Storage and Retrieval,
    	methods; Internet; Microarray Analysis, methods; Software; Statistics
    	as Topic; User-Computer Interface},
      language = {eng},
      medline-pst = {ppublish},
      owner = {xxia},
      pii = {btp430},
      pmid = {19602526},
      timestamp = {2010.07.13},
      url = {http://dx.doi.org/10.1093/bioinformatics/btp430}
    }
    

3. Program Download

WebArray is under GNU GPL, you may download the WebArray source codes following the links below. WebArray is under maintaining actively and might be modified/upgraded frequently. This is revealed by the software's packing date since we intend to not change the version number too often. Please read the "README" file especially when you are upgrading from a old distribution.

Tutorials, data for demo, and README
WebArray-1.4 (with WebArrayDB): webarray-1.4.tar.gz (packed on 2011-02-22 14:21)
WebArray-1.3 (with WebArrayDB): webarray-1.3.tar.gz (packed on 2009-11-30 16:19)
WebArray-1.1: webarray-1.1.tar.gz and README (packed on 2008-08-08 17:31)

4. News
2008/3/17WebArrayDB (in BETA testing) - a cross-platform database system and analysis platform was integrated in. Any feedback is highly appreciated.
2007/08/18Microarray databases (WebArrayDB) were designed and are on testing.
2006/10/19R was upgraded to version 2.4.0. Accordingly Bioconductor was upgraded to version 1.9. More Affymetrix GeneChip types are supported.
2006/10/19The interface between python and R language was switch from Rpy to pipe offered by python. This permits R to run faster.
2006/02/03Gal file is no longer necessary for those data files with gene & grid information.
2006/02/03Source codes are available for downloading.

5. Contacts

For questions, please contact with Xiao-Qin Xia ( w e b a r r a y d b @ g m a i l . c o m


updated on 2013-01-24 19:23