wiki:GccStart
Last modified 7 weeks ago

News

Observ-OM data model published

Observ-OM and Observ-TAB, the Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information, is published in  Human Mutation. Genetic and epidemiological resear ...

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CHD7 mutation database published

We are proud with another  MOLGENIS for the CHARGE syndrome using  Observ-OM published in  Human Mutation. CHD7 is a member of the chromodomain helicase DNA- ...

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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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GenomeNL variation database

The first version of the GenomeNL database is online. Now researchers can already sneak peak the GoNL variant data to verify whether variants observed in their own sample are unique against 25 million SNPs observed in the panel of 500 parents. By Ap ...

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OntoCAT easy ontology search

With so many ontocat papers published  NBIC has made a newsitem on OntoCAT! n annotating life sciences data, ontologies are quickly gaining im ...

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Welcome to the Genomics Coordination Centre

  • Analysis pipelines for NGS, GWA, GWL studies
  • Research portals for multi-omics laboratory, biobanks, consortia
  • Large data infrastructure in software and hardware

Organization

GCC is a growing team of 10 researchers, programmers and system managers headed by Dr. Morris Swertz (m.a.swertz@…) 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  ‘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,  Netherlands Bioinformatics Center, Netherlands Proteomics Center,  BigGrid,  EU-GEN2PHEN, EU-CASIMIR, EU-PANACEA and  BBMRI-NL. All GCC tools are collected in the open source  MOLGENIS software project.

Contact head Morris Swertz (m.a.swertz@…) for more information or check Internships or AboutGcc

Our team members: TeamMembers

Study Capturing and Sharing Applications

Analysis Applications

  •  Sequencing - Pipelines for NGS data analysis and annotation
  •  Imputation - Pipelines for imputation
  • R/QTL - R package QTL analysis
  •  OntoCAT - ontology toolkit
  • Design GG - experimental design of QTL experiments
  • Genomic Islands - genomic islands
  • PeakML format - file format for mass spectrometry data
  • MzMatch - pipeline for mass spectrometry experiments in the area of metabolomics

Shared Modules

Intranet

See GccIntranet for a complete overview

Collaborations & Projects

  •  GBIC - Groningen Bioinformatics Center, our method partner
  •  Genetics - UMCG genetics department hosts the GccTeam
  •  CIT - Groningen Center for Information Technology hosts our data and computations
  •  BBMRI.NL - Project lead of BBMRI-NL Bioinformatics
  •  NBIC - Lead Biobanking task force Netherlands BioInformatics Center
  •  LifeLines - Developing IT infrastructure for 30yr/165.000 people cohort study
  •  EBI - Visitor European Bioinformatics Institute
  •  EU-GEN2PHEN - Associated partner Genotype to Phenotype project
  •  CASIMIR - Invited partner Coordination and Sustainability of International Mouse Informatics Resources
  •  SYSGENET - European systems genetics network
  •  PANACEA - Pathway analysis in C. elegans