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= Welcome to the eXtensible Genotype And Phenotype platform (XGAP) =

XGAP is an open and flexible data platform for all your xQTL, GWL, GWA and mutagenisis data and analysis. XGAP was originally born out of the Groningen Bionformatics Center, the EU-CASIMIR projet and EU-GEN2PHEN. Currently new XGAP extensions are being developed for 
* xQTL studies in model organism C. elegans experiments in the [http://www.panaceaproject.eu/ EU-PANACEA] project 
* GWAS studies in human populations [http://www.lifelines.org LifeLines] and [https://wiki.nbic.nl/index.php/Biobanking NBIC biobanking] projects.

Use XGAP to:

 1. '''Share experimental data with collaborators''' using the [XgapFormatTutorial easy to create and parse file format].                                                            
 1. '''Manage and query your data''' using the downloadable, free and customizeable web portal                                                         ([http://gbic.target.rug.nl:8080/xgap_1_2_demo/molgenis.do demo]).
 1. '''Connect your analysis tools''' using the scriptable bioinformatic interfaces to R, Taverna, and Java.

You can download XGAP for local use, checkout the source to customize XGAP using the open source [http://www.molgenis.org MOLGENIS] generator, or send an email to xgap-usersATgooglegroups.com to request a personal instance of XGAP on the xgap.org server.

Please cite '''[http://genomebiology.com/2010/11/3/R27 Swertz et al (2010) XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. Genome Biology 9;11(3):R27]''' on use.

= How to sharing data easily? =
XGAP has a simple format to exchange all your genetic, transcript, metabolite and protein data and natural and model organism populations annotations in one folder:
 * XgapFormatTutorial - how to create a set of XGAP tab delimited files to report your investigation
 * XgapFormatReference - complete reference of all XGAP tab delimited file types
 * XgapDataModel - overview of the XGAP data model underlying XGAPs exchange format
 * DataSets - examples of XGAP data sets
 * DataConversionSchema - how to import a non XGAP data file into XGAP model

= How to manage and query data with the web portal? =
XGAP has a web user interface that individuals, labs and consortia can use to manage, query and archive all their xQTL investigations:
 * UserInterface - manage and trace your data using the XGAP user interface
 * DataWizard - how to import a dataset of files in XGAP format
 * [wiki:DataArchiver] - how to export and import XGAP filesets from/to zip files

= How to connect to analysis tools? =
XGAP has scriptable interfaces for bioinformaticians to plug-in analysis tools
 * RprojectInterface - how to read/write your data from within R statistics
 * RqtlIntegration - how to use R/qtl to calculate QTLs for for your data
 * TavernaInterface - how to read/write your data from within Taverna
 * XgapExchange - How to convert XGAP format to/from external tools like dbGaP, PLINK, and Gene Network.
 * AddingUserInterfaces - How to create user interface plugins to add custom tools
 * XgapPluginsAvailable - Overview of user interface enhancements that you can add to your XGAP

= How to install XGAP locally? =
XGAP is free to download and install on your own web server:
 * '''NEW: Installation of the XGAP 1.4 development version at [http://www.xgap.org/wiki/Installation Installation]'''
 * XgapDownload - Get the XGAP program
 * XgapInstall - Performing a regular installation

= How to extend your XGAP for new data? =
XGAP uses the [http://www.molgenis.org MOLGENIS biosoftware generator] to enable quick customization to your needs
 * XgapDevelopment - Performing a development installation 
 * XgapCustomization - How to customize XGAP using a development installation
 * AddingDataTypes - How to extend the XGAP core model with new data types
 * XgapSourceCode - An overview of the XGAP source code
 * TestProtocol - Regression test procedure to verify your XGAP functions properly

We are happy to host your customizations and plugins in the www.xgap.org/svn repository. Also post ideas on XgapEnhancements. Please email m.a.swertz@rug.nl or xgap-users@googlegroups.com for all questions, suggestions and discussions regarding XGAP.