Changes between Version 66 and Version 67 of WikiStart


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Timestamp:
Jun 6, 2013 10:44:28 AM (6 years ago)
Author:
mswertz
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  • WikiStart

    v66 v67  
    11[[BlogList(recent=5, max_size=250, format=float, heading=New blogs)]]
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    3 = Dynamic bioinformatics infrastructures for biobank enrichment (BBMRI-NL rainbow 2)=
    4 This is the wiki for the Dynamic bioinformatics infrastructures for biobank enrichment project of [http://www.bbmri.nl BBMRI-NL (rainbow project 2)] in collaboration with the Genome of the Netherlands project ([http://www.nlgenome.nl GoNL], BBMRI-NL rainbow project 1), UMCG, UMCU, VU, ErasmusMC, LUMC and NBIC.
     3= Projects =
    54
    6  * See MeetingMinutes - minutes of our Skype meetings (members only)
    7  * See ProjectOverview - description of the bioinformatics regenboog
    8  * See DataAnalysisPlan - description of the GvNL analysis objectives
    9  * See WorkPlan - description of the current planning
    10  * See ReadingMaterials - for recommended powerpoints and papers
    11  * See DataManagement - for Data Management strategy
    12  * See [wiki:BGIDatasets] - for information about BGI data
    13  * See [wiki:ComputeResources] - for information about the GoNL compute clusters
    14  * Join our [https://trac.nbic.nl/mailman/listinfo/biobanking-interest mailing list]
    15 = Projects and pipelines: =
    16  * '''Sequence analysis (WP1)'''
    17    * SchematicOverview - overview of the pipelines needed
    18    * SnpCallingPipeline - description of the variation analysis pipeline (UMCG)
    19    * DataConcordance - comparison of sequence data vs genotype chip data (UMCG)
    20    * CoverageAnalysisPipeline - description of the coverage analysis pipeline (AMC)
    21    * GwasQcPipeline - description of immunochip QC before ngs-chip comparison (UMCG)
    22    * ChipBasedQcPipeline - description of the chip data comparison QC pipeline (EMC)
    23    * MendelianQcPipeline - description of the mendelian check pipeline (EMC)
    24    * DeNovoVariationPipeline - finding de novo variations in the GvNL data (LUMC)
    25    * StructuralVariationPipeline - finding indels/inversions/CNV/translocations in the GvNL data (SV group)
    26    * TrioAwareVariantDiscoveryPipeline - Trio-aware variant discovery and genotype calling pipeline (UU)
    27    * GenomeViewer - view read and snp data in their genomic context, e.g. using IGV
    28    * [http://www.molgenis.org/wiki/NgsWorkbench Next Generation Sequence LIMS] - track and trace all GoNL samples and analysis (UMCG)
    29    * SequencingIntersection - Find shared variants among samples (UMCG)
    30  * '''Genotype analysis and imputation (WP2)'''
    31    * [wiki:Imputations] - Work group main page
    32    * [wiki:PhenotypeAnalysis] - Work group main page
    33    * TrioAwarePhasingPipeline - phasing the individuals using trio information (EMC)
    34    * SnpAnnotationPipeline - annotating SNPs with known functional information (LUMC,UMCG)
    35    * ImputationPipeline - description of the imputation pipeline (VU,UMCG)
    36    * [http://www.bbmriwiki.nl/wiki/Impute2Pipeline Impute2Pipeline] - description of the Impute2 pipeline (UMCG)
    37    * AlleleCounting - count alleles accross a set of sample.vcf
    38  * '''Catalogue and search of biobanks (WP3)'''
    39    * [http://www.phenoflow.org/wiki/BiobankCatalog Catalog of Dutch biobanks] - in collaboration with [https://wiki.nbic.nl/index.php/Biobanking NBIC biobanking task force]
    40    * [https://sites.google.com/a/nbiceng.net/hackathonii Connecting biobanks Hackaton] - in collaboration with [https://wiki.nbic.nl/index.php/Interoperability NBIC interoperability task force]
    41  * '''Genomic biobank IT infrastructure (WP4)'''
    42    * DataManagement - how we use MOLGENIS to track/trace data and tools (UMCG)
    43    * WorkflowTools - how to configure, manage and run pipelines (UMCG,AMC)
    44    * SequenceBIMS - to have report on samples, raw/intermediate/result data and processing pipelines run
    45    * GwasBIMS - to have report on samples, imputation runs and results
    46    * ApplyForDataTool - to provide researchers with a way to request access to BBMRI-NL data sets
    47    * BigStorage - how we store the NGS and GWAS data (UMCG,SARA,CIT)
    48    * BigCompute - how we will enable the pipelines on grids and clusters (UMCG,AMC,SARA,CIT)
     5* [GonlStart Dynamic bioinformatics infrastructures for biobank enrichment (BBMRI-NL rainbow 2)]
     6* [FGStart Functional genomics (BBMRI-NL rainbow 3)]
    497
    50 *Work organization based on regenboog project. Clearly there is much connection between all work.
     8
    519= Using this wiki =
    5210As all Wiki pages, this page is editable, this means that you can modify the contents of this page simply by using your web-browser. Simply click on the "Edit this page" link at the bottom of the page. WikiFormatting will give you a detailed description of available Wiki formatting commands.
     
    6018 * '''Subversion''' - Programmers can commit their code using SVN at http://gbic.target.rug.nl/bbmri/svn
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    62 = BBMRI bioinformatics and genome of the netherlands project are developed in collaboration with =
     20= BBMRI projects are developed in collaboration with =
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    6422[[Image(bbmri.gif)]] [[Image(nbic.png)]]