[[BlogList(recent=5, max_size=250, format=float, heading=News, category=xgap)]] = 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 based on [http://www.molgenis.org MOLGENIS]. XGAP was originally born out of the Groningen Bionformatics Center, the EU-CASIMIR projet and EU-GEN2PHEN. Active contributors include Joeri van der Velde ([http://www.panaceaproject.eu PANACEA]), Danny Arends ([http://gbic.biol.rug.nl RUG/GBIC]), Andre de Vries ([http://www.lifelines.nl LifeLines]), and Morris Swertz ([ttps://wiki.nbic.nl/index.php/Biobanking NBIC biobanking] and [http://wiki.gcc.rug.nl UMCG/GCC]). Uses of XGAP are to: * '''Share experimental data with collaborators''' using the [XgapFormatTutorial easy to create and parse file format]. * '''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]). * '''Connect your analysis tools''' using the scriptable bioinformatic interfaces to R, Taverna, and Java. * '''Manage analysis''' - NEW! under development for xqtl/C. elegans and gwas imputation Currently new XGAP extensions are being developed for * '''xQTL workbench''': for xQTL studies in model organism C. elegans experiments in the [http://www.panaceaproject.eu/ EU-PANACEA] project * '''GWAS workbench''': for GWAS studies in human populations [http://www.lifelines.org LifeLines] and [https://wiki.nbic.nl/index.php/Biobanking NBIC biobanking] projects. 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.