Welcome to the Groningen Genomics Coordination Centre

Groningen Genomics Coordination Center is the bioinformatics hotel of University and University Medical Center. GCC functions as Data Coordination Center or Data Analysis Center for small and big data projects in genomics, clinic and biobanking. Services and tools include:

• Analysis pipelines for NGS, GWA, GWL, e.g. compute & pipelines
• Biobank catalogues, e.g. ​Lifelines and ​BBMRI-NL
• Research portals for multi-omics laboratory, biobanks, consortia, e.g. ​WormQTL
• Patient registries, rare disease, personalized medicine and mutation databases, e.g. ​DEB, ​CHD7
• Large data infrastructure, e.g. 2 Petabyte high-speed storage, 960 cpu cores
• Data Coordination Center and/or Data Analysis Center, e.g. ​Genome of the Netherlands

We are highly motivated to collaborate on these tools and to share all our software and best practices via the ​MOLGENIS project

We are part of the Groningen ​Systems Genetics Network

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 ​MOLGENIS - biosoftware toolkit ​XGAP - GWAS and GWL ​AnimalDB - animal observation ​MutationDB - mutations and patients ​Pheno - phenotype observations ​MAGE - microarray database	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 ​Systems Genetics - Software repository to analyze and process -omics data
Shared Modules Modules
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 GccIfolder - How to connect to our iFolder GccLogs - Logbooks of GCC people GccAttachments - Attach here your private stuff GccTargetStorage - directory structure on Target	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 ​BioSHaRE - BioSHaRE