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MOLGENIS moved to github
We are delighted to report that all code of MOLGENIS is now in GitHub?. See http://www.github.com/molgenis. For those not yet up to speed with github we prepared two tutorials: [https://docs.google.com/presentation/d/134WeHhs8bpWNaAO005QoYMLnnPgHCuR ...
xQTL workbench paper published
See http://bioinformatics.oxfordjournals.org/content/28/7/1042. QTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite ab ...
MOLGENIS at BOSC and ISMB 2010, Boston July 9-13
You can see us at BOSC2010 SIG on Saturday July 10, 14.40 - 15.00 hours, speak to us at posters Q01, E19, E15, P05 on Sunday, July 11: 12.40 - 14.30 and see us at the ISMB technology track, Tuesday, July 13: 12.15 - 12.40.
MOLGENIS and XGAP at BOSC/ISMB
MOLGENIS was at BOSC/DAM meeting and coffee-break demos at the NBIC booth. See BOSC 2009 schedule
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 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 (PANACEA), Danny Arends (RUG/GBIC), Andre de Vries (LifeLines), and Morris Swertz ([ttps://wiki.nbic.nl/index.php/Biobanking NBIC biobanking] and UMCG/GCC).
Uses of XGAP are to:
- Share experimental data with collaborators using the easy to create and parse file format.
- Manage and query your data using the downloadable, free and customizeable web portal (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 EU-PANACEA project
- GWAS workbench: for GWAS studies in human populations LifeLines and NBIC biobanking projects.
You can download XGAP for local use, checkout the source to customize XGAP using the open source MOLGENIS generator, or send an email to xgap-usersATgooglegroups.com to request a personal instance of XGAP on the xgap.org server. Please cite:
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
- 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 Installation
- XgapDownload - Get the XGAP program
- XgapInstall - Performing a regular installation
How to extend your XGAP for new data?
XGAP uses the 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@… or xgap-users@… for all questions, suggestions and discussions regarding XGAP.
