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Enlighten Your Research Global Award: Virtual Machine Images for Life Science Research
Denver (USA) 18 November 2013 – One of the four prestigious "Enlighten Your Research Global" has been awarded to an idea developed by an ELIXIR working group for the sharing of virtual machines over research and education networks.
MOLGENIS/compute at IWSG-2013
MOLGENIS/compute was presented at 5th International Workshop on Science Gateways, IWSG 2013, Zurich, Switzerland
Visual Analytics for Bio-Workflows at NBIC-2013
Towards visual analytics of bio-workflows presentation was given at the NBIC-2013 conference, Lunteren, Netherlands
Visual Analytics for Bio-Workflows at BIOINFORMATICS-2013
"Visualization of bioinformatics workflows for ease of understanding and design activities" paper will be presented at the BIOSTEC-BIOINFORMATICS-2013 conference, on February 11th, 2013, Bercelona, Spain. [http://www.molgenis.org/raw-attachment/blog ...
MOLGENIS/compute workshop at BioAssist meeting
MOLGENIS/compute workshop took place at the NBIC Bio Assist meeting, in Utrect, Oct.12, 2012
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. Use XGAP 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.
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:
- 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:
- 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.
