wiki:XgapStart

News

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 ...

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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 ...

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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 ( 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:

 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:

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

How to install XGAP locally?

XGAP is free to download and install on your own web server:

How to extend your XGAP for new data?

XGAP uses the MOLGENIS biosoftware generator to enable quick customization to your needs

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.