| | 1 | [[BlogList(recent=5, max_size=250, format=float, heading=News)]] |
| | 2 | = Welcome to the eXtensible Genotype And Phenotype platform (XGAP) = |
| | 3 | |
| | 4 | XGAP is an open and flexible data platform for all your xQTL, GWL, GWA and mutagenisis data and analysis. Use XGAP to: |
| | 5 | |
| | 6 | 1. '''Share experimental data with collaborators''' using the [XgapFormatTutorial easy to create and parse file format]. |
| | 7 | 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]). |
| | 8 | 1. '''Connect your analysis tools''' using the scriptable bioinformatic interfaces to R, Taverna, and Java. |
| | 9 | |
| | 10 | 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. |
| | 11 | |
| | 12 | 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. |
| | 13 | |
| | 14 | = How to sharing data easily? = |
| | 15 | 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: |
| | 16 | * XgapFormatTutorial - how to create a set of XGAP tab delimited files to report your investigation |
| | 17 | * XgapFormatReference - complete reference of all XGAP tab delimited file types |
| | 18 | * XgapDataModel - overview of the XGAP data model underlying XGAPs exchange format |
| | 19 | * DataSets - examples of XGAP data sets |
| | 20 | * DataConversionSchema - how to import a non XGAP data file into XGAP model |
| | 21 | |
| | 22 | = How to manage and query data with the web portal? = |
| | 23 | XGAP has a web user interface that individuals, labs and consortia can use to manage, query and archive all their xQTL investigations: |
| | 24 | * UserInterface - manage and trace your data using the XGAP user interface |
| | 25 | * DataWizard - how to import a dataset of files in XGAP format |
| | 26 | * [wiki:DataArchiver] - how to export and import XGAP filesets from/to zip files |
| | 27 | |
| | 28 | = How to connect to analysis tools? = |
| | 29 | XGAP has scriptable interfaces for bioinformaticians to plug-in analysis tools |
| | 30 | * RprojectInterface - how to read/write your data from within R statistics |
| | 31 | * RqtlIntegration - how to use R/qtl to calculate QTLs for for your data |
| | 32 | * TavernaInterface - how to read/write your data from within Taverna |
| | 33 | * XgapExchange - How to convert XGAP format to/from external tools like dbGaP, PLINK, and Gene Network. |
| | 34 | * AddingUserInterfaces - How to create user interface plugins to add custom tools |
| | 35 | * XgapPluginsAvailable - Overview of user interface enhancements that you can add to your XGAP |
| | 36 | |
| | 37 | = How to install XGAP locally? = |
| | 38 | XGAP is free to download and install on your own web server: |
| | 39 | * XgapDownload - Get the XGAP program |
| | 40 | * XgapInstall - Performing a regular installation |
| | 41 | |
| | 42 | = How to extend your XGAP for new data? = |
| | 43 | XGAP uses the [http://www.molgenis.org MOLGENIS biosoftware generator] to enable quick customization to your needs |
| | 44 | * XgapDevelopment - Performing a development installation |
| | 45 | * XgapCustomization - How to customize XGAP using a development installation |
| | 46 | * AddingDataTypes - How to extend the XGAP core model with new data types |
| | 47 | * XgapSourceCode - An overview of the XGAP source code |
| | 48 | * TestProtocol - Regression test procedure to verify your XGAP functions properly |
| | 49 | |
| | 50 | 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. |
