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= Welcome to the Genomics Coordination Centre =

GCC is a growing team of 10 researchers, programmers and system managers headed by Dr. Morris Swertz (m.a.swertz@rug.nl) set up to develop, manage and exploit new bioinformatics models, software and tools to enable and support the next generation of GWA, GWL and NGS experiments. In the past two years GCC is organized as a bridge between the UMCG Department of Genetics providing bioinformatics support for the next generation sequencing facility (Prof. C. Wijmenga), the RuG Centre for Information Technology building towards [http://www.rug.nl/target/index ‘petabyte’ scale storage and compute infrastructure], and the Groningen Bioinformatics developing new bioinformatics method for high-throughput data (Prof. R.C. Jansen). Moreover, GCC is strongly rooted in national and international including the European Bioinformatics Institute, [http://www.nbic.nl Netherlands Bioinformatics Center], Netherlands Proteomics Center, [http://www.ebiogrid.nl BigGrid], [http://www.gen2phen.org EU-GEN2PHEN], EU-CASIMIR, EU-PANACEA and [http://www.bbmri.nl BBMRI-NL]. All GCC tools are collected in the open source [http://www.molgenis.org MOLGENIS] software project.

Contact head Morris Swertz (m.a.swertz@rug.nl) for more information or check [[Internships]] or AboutGcc

Our team members: TeamMembers

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= Study Capturing and Sharing Applications =
* [http://www.molgenis.org MOLGENIS] - biosoftware toolkit
* [http://www.xgap.org XGAP] - GWAS and GWL
* [http://www.animaldb.org AnimalDB] - animal observation
* [http://gbic.target.rug.nl/trac/lsdb MutationDB] - mutations and patients
* [http://www.phenoflow.org Pheno] - phenotype observations
* [http://gbic.target.rug.nl/trac/mage MAGE] - microarray database
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= Analysis Applications =
 * [http://www.bbmriwiki.nl Sequencing] - Pipelines for NGS data analysis and annotation
 * [http://www.bbmriwiki.nl Imputation] - Pipelines for imputation
 * [RqtlPackage R/QTL] - R package QTL analysis
 * [http://www.ontocat.org OntoCAT] - ontology toolkit
 * [DesignGg Design GG] - experimental design of QTL experiments
 * [GenomicIslandsAnalysis Genomic Islands] - genomic islands
 * [wiki:PeakML] format - file format for mass spectrometry data
 * MzMatch - pipeline for mass spectrometry experiments in the area of metabolomics
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= Shared Modules =
* [wiki:Modules]

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= Intranet =
See GccIntranet for a complete overview

 * GccGettingStarted - overview for new GCC participants
 * GccMeetings - Notes on our work meetings
 * MolgenisScrum - Our SCRUM project management pages
 * GccManuals - How to use the software and servers that we have
 * GccLinks - Hyperlinks to papers and websites of interest
 * GccTeam - Members of the group
 * GccCalendar - Meetings, etc.
 * GccEventSchedule - Conferences, courses, workshops, etc.
 * GccGroup - Our mailing list and group discussion site
 * GccServers - How to connect to our servers
 * GccIfolder - How to connect to our iFolder
 * GccLogs - Logbooks of GCC people
 * GccAttachments - Attach here your private stuff
 * DataSharing/DataStorage on sftp.gcc.rug.nl
 * GccTargetStorage - directory structure on Target

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= Collaborations & Projects=
* [http://gbic.biol.rug.nl GBIC] - Groningen Bioinformatics Center, our method partner
* [http://www.geneticsgroningen.nl Genetics] - UMCG genetics department hosts the GccTeam
* [http://www.rug.nl/cit/index CIT] - Groningen Center for Information Technology hosts our data and computations
* [http://www.bbmriwiki.org BBMRI.NL] - Project lead of BBMRI-NL Bioinformatics
* [http://wiki.nbic.nl NBIC] - Lead Biobanking task force Netherlands BioInformatics Center
* [http://www.lifelines.nl LifeLines] - Developing IT infrastructure for 30yr/165.000 people cohort study
* [http://www.ebi.ac.uk EBI] - Visitor European Bioinformatics Institute
* [http://www.gen2phen.org EU-GEN2PHEN] - Associated partner Genotype to Phenotype project
* [http://www.casimir.ac.uk CASIMIR] - Invited partner Coordination and Sustainability of International Mouse Informatics Resources
* [http://www.helmholtz-hzi.de/en/research/host_resistance_and_susceptibility/infection_genetics/externally_funded_projects/sysgenet/ SYSGENET] -  European systems genetics network
* [http://http://www.panaceaproject.eu/ PANACEA] - Pathway analysis in C. elegans
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