Changes between Version 54 and Version 55 of GccStart


Ignore:
Timestamp:
2017-02-07T12:43:14+01:00 (3 months ago)
Author:
mswertz
Comment:

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  • GccStart

    v54 v55  
    1515== Organization ==
    1616
    17 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.
     17GCC is a growing team of 25 researchers, programmers and system managers headed by Prof.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 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 BBMRI-NL, NFU Data4Lifesciences, DTL, BBMRI-ERIC, RD-connect, CORBEL, EXCELERATE, European Bioinformatics Institute. All GCC tools are collected in the open source [http://www.molgenis.org MOLGENIS] software project.
    1818
    19 Contact head Morris Swertz (m.a.swertz@rug.nl) for more information or check [[Internships]] or AboutGcc
     19Contact head Morris Swertz (m.a.swertz@rug.nl) for more information or AboutGcc
    2020
    21 Our team members: TeamMembers
    22 
    23 {{{#!td valign="top"
    24 
    25 = Study Capturing and Sharing Applications =
    26 * [http://www.molgenis.org MOLGENIS] - biosoftware toolkit
    27 * [http://www.xgap.org XGAP] - GWAS and GWL
    28 * [http://www.animaldb.org AnimalDB] - animal observation
    29 * [http://gbic.target.rug.nl/trac/lsdb MutationDB] - mutations and patients
    30 * [http://www.phenoflow.org Pheno] - phenotype observations
    31 * [http://gbic.target.rug.nl/trac/mage MAGE] - microarray database
    32 }}}
    33 {{{#!td
    34 
    35 = Analysis Applications =
    36  * [http://www.bbmriwiki.nl Sequencing] - Pipelines for NGS data analysis and annotation
    37  * [http://www.bbmriwiki.nl Imputation] - Pipelines for imputation
    38  * [RqtlPackage R/QTL] - R package QTL analysis
    39  * [http://www.ontocat.org OntoCAT] - ontology toolkit
    40  * [DesignGg Design GG] - experimental design of QTL experiments
    41  * [GenomicIslandsAnalysis Genomic Islands] - genomic islands
    42  * [wiki:PeakML] format - file format for mass spectrometry data
    43  * MzMatch - pipeline for mass spectrometry experiments in the area of metabolomics
    44  * [http://www.molgenis.org/systemsgenetics Systems Genetics] - Software repository to analyze and process -omics data
    45 }}}
    46 |-------------------
    47 {{{#!td valign="top" colspan="2"
    48 
    49 = Shared Modules =
    50 * [wiki:Modules]
    51 
    52 }}}
    53 |-------------------
    54 {{{#!td
    55 
    56 = Intranet =
    57 See GccIntranet for a complete overview
    5821
    5922 * GccGettingStarted - overview for new GCC participants
     
    7134 * GccTargetStorage - directory structure on Target
    7235
    73 }}}
    74 {{{#!td valign="top"
    75 
    76 = Collaborations & Projects=
    77 * [http://gbic.biol.rug.nl GBIC] - Groningen Bioinformatics Center, our method partner
    78 * [http://www.geneticsgroningen.nl Genetics] - UMCG genetics department hosts the GccTeam
    79 * [http://www.rug.nl/cit/index CIT] - Groningen Center for Information Technology hosts our data and computations
    80 * [http://www.bbmriwiki.org BBMRI.NL] - Project lead of BBMRI-NL Bioinformatics
    81 * [http://wiki.nbic.nl NBIC] - Lead Biobanking task force Netherlands BioInformatics Center
    82 * [http://www.lifelines.nl LifeLines] - Developing IT infrastructure for 30yr/165.000 people cohort study
    83 * [http://www.ebi.ac.uk EBI] - Visitor European Bioinformatics Institute
    84 * [http://www.gen2phen.org EU-GEN2PHEN] - Associated partner Genotype to Phenotype project
    85 * [http://www.casimir.ac.uk CASIMIR] - Invited partner Coordination and Sustainability of International Mouse Informatics Resources
    86 * [http://www.helmholtz-hzi.de/en/research/host_resistance_and_susceptibility/infection_genetics/externally_funded_projects/sysgenet/ SYSGENET] -  European systems genetics network
    87 * [http://www.panaceaproject.eu/ PANACEA] - Pathway analysis in C. elegans
    88 * [https://www.bioshare.eu/ BioSHaRE] - BioSHaRE
    89 }}}