README.txt

* What is ArrayExpress Gene Expression Atlas

The ArrayExpress Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics
over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well
as broader exploratory searches for biologically interesting genes/samples.

To cite the Atlas in your research or to learn more about it, please refer to Kapushesky M et al. (2010), "Gene
Expression Atlas at the European Bioinformatics Institute", Nucleic Acids Research Database Issue 2010,
http://nar.oxfordjournals.org/cgi/content/full/gkp936?ijkey=zMCQ9oPVLrhe7zk&keytype=ref.

The EBI Gene Expression Atlas is running at http://www.ebi.ac.uk/gxa.

* Features of ArrayExpress Gene Expression Atlas

  + Standalone: only an Oracle RDBMS, R/Bioconductor and a Java Web App server required
  + Import your MAGE-TAB (http://www.mged.org/mage-tab) formatted data directly
  + Public curated EBI Gene Expression Atlas available in monthly releases on FTP
  + Statistical meta-analysis using R/Bioconductor
  + Semantic enrichment with the Experimental Factor Ontology (EFO, http://www.ebi.ac.uk/efo)
  + Powerful search and visualization interface

The ArrayExpress Gene Expression Atlas project is hosted at the EBI at:

* Getting Gene Expression Atlas

You can get the source code and read the installation instructions at our GitHub Repository at:

 http://github.com/gxa/gxa.

The EBI data dumps are available at ftp://aexpress:aexpress@ftp1.ebi.ac.uk/atlas2.

You can subscribe to our mailing list and email your questions, feedback and suggestions at:

  arrayexpress-atlas@ebi.ac.uk for further information.

* How to install

You will need an Oracle database, an R/Bioconductor installation and a web server that can run Java Web Applications,
e.g., Apache Tomcat. For more detail, read the instructions at:

  http://wiki.github.com/gxa/gxa/installation

* Authors

Project Leader:    Misha Kapushesky (ostolop@ebi.ac.uk)
Development Team:  Robert Petryszak, Olga Melnichuk, Nataliya Sklyar
Former Developers: Tony Burdett, Pavel Kurnosov, Andrey Zorin, Nikolay Pultsin, Alexey Filippov

* License and Copyright

Licensed under the Apache License, Version 2.0. 

Copyright 2008-2012 Microarray Informatics Team, EMBL-European Bioinformatics Institute.