wiki:XgapStart

Version 1 (modified by mswertz, 10 years ago) (diff)

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News

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.

  • Posted: 2015-04-03 15:06 (Updated: 2015-04-03 15:07)
  • Author: george
  • Categories: MCF
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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

  • Posted: 2013-06-04 10:01 (Updated: 2013-06-04 10:05)
  • Author: george
  • Categories: MCF
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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 ...

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  • Posted: 2013-01-31 10:57 (Updated: 2013-01-31 10:59)
  • Author: george
  • Categories: MCF
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MOLGENIS/compute workshop at BioAssist meeting

MOLGENIS/compute workshop took place at the NBIC Bio Assist meeting, in Utrect, Oct.12, 2012

  • Posted: 2012-11-22 13:41 (Updated: 2012-11-22 13:42)
  • Author: george
  • Categories: MCF
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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:

  1. Share experimental data with collaborators using the easy to create and parse file format.
  2. Manage and query your data using the downloadable, free and customizeable web portal (demo).
  3. 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:

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.