Changes between Version 12 and Version 13 of ProjectOverview


Ignore:
Timestamp:
Sep 5, 2010 8:48:54 PM (11 years ago)
Author:
Morris Swertz
Comment:

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  • ProjectOverview

    v12 v13  
    4545
    4646 * preserving flexibility to go beyond standardization and accommodate specific local needs.
     47== Roadmap ==
     48Total duration 3 years
    4749
    48 = 8. Duration of project: =
    49 3 years
     50||Planning (matching GvNL planning where appropriate) ||||
     51||Short read archive                  ||                                                                       Month 0 – 8||
    5052
    51 Planning (matching GvNL planning where appropriate)
     53||Biobank catalog pilot                ||                                                                    Month 0 – 6||
    5254
    53 Short read archive                                                                                         Month 0 – 8
     55||Sequence analysis Phase 1 (GvNL)           ||                                             Month 4 – 16||
    5456
    55 Biobank catalog pilot                                                                                    Month 0 – 6
     57||Harmonized exchange formats                    ||                                                           Month 6 - 24||
    5658
    57 Sequence analysis Phase 1 (GvNL)                                                        Month 4 – 16
     59||Establish variation QC and analysis pipeline     ||                                  Month 8 – 20||
    5860
    59 Harmonized exchange formats                                                                               Month 6 - 24
     61||Sequence analysis Phase 2 (GvNL)                                                        Month 8 – 20||
    6062
    61 Establish variation QC and analysis pipeline                                       Month 8 – 20
     63||Variation catalog/Dutch !HapMap     ||                                                      Month 20||
    6264
    63 Sequence analysis Phase 2 (GvNL)                                                        Month 8 – 20
     65||GWAS data release server        ||                                                                Month 0 – 12||
    6466
    65 Variation catalog/Dutch !HapMap                                                           Month 20
     67||GWAS QC and imputation protocols     ||                                                Month 6 – 20||
    6668
    67 GWAS data release server                                                                        Month 0 – 12
     69||Dutch GWAS Control Cohort (DGCC)      ||                                              Month 12 –24||
    6870
    69 GWAS QC and imputation protocols                                                     Month 6 – 20
     71||Imputation of available GWA data (GvNL)  ||                                        Month 20 – 30||
    7072
    71 Dutch GWAS Control Cohort (DGCC)                                                    Month 12 –24
     73||Make sequence data available (GvNL)   ||                                               Month 12 – 30||
    7274
    73 Imputation of available GWA data (GvNL)                                          Month 20 – 30
     75||GWAS analysis tools catalog       ||                                                              Month 12 – 36||
    7476
    75 Make sequence data available (GvNL)                                                  Month 12 – 30
     77||Web access tools             ||                                                                              Month 22 – 30||
    7678
    77 GWAS analysis tools catalog                                                                     Month 12 – 36
     79||Integrated DCGG and Variation catalog web access tools ||           Month 24 – 36||
    7880
    79 Web access tools                                                                                           Month 22 – 30
     81== Deliverables ==
    8082
    81 Integrated DCGG and Variation catalog web access tools            Month 24 – 36
     83== WP1 Sequencing ==
    8284
    83 '''9. Deliverables'''
     85 * __Short Read Archive (GvNL)__ – a database and user interface to manage and trace next generation sequencing data, associated sample annotations (metadata) and intermediate- and end-results.
    8486
    85 D1 Sequencing
     87 * __Variation analysis and QC pipelines (GvNL)__ – harmonization and enrichment of available processing pipelines for quality control and variation analysis for (exome) re-sequencing projects.
    8688
    87 ·         __Short Read Archive (GvNL)__ – a database and user interface to manage and trace next generation sequencing data, associated sample annotations (metadata) and intermediate- and end-results.
     89 * __Variation catalog/Dutch !HapMap (GvNL) __– release of the enrichment results of variation analysis of the GvNL 1000 genomes as produced using above tools as imputation data source.
    8890
    89 ·         __Variation analysis and QC pipelines (GvNL)__ – harmonization and enrichment of available processing pipelines for quality control and variation analysis for (exome) re-sequencing projects.
     91WP2 Genome-wide association analysis
    9092
    91 ·         __Variation catalog/Dutch !HapMap (GvNL) __– release of the enrichment results of variation analysis of the GvNL 1000 genomes as produced using above tools as imputation data source.
     93 * __GWAS data release server__– database and user interfaces to manage and query GWAS data, in particular to create GWAS (control cohort imputation) data releases.
    9294
    93 D2 Genome-wide association analysis
     95 *  __GWAS CQ and imputation protocols__ – harmonization and enrichment of tools and pipelines to verify and clean GWAS data sets and produce data sets ready for analysis by the researcher.
    9496
    95 ·         __GWAS data release server__– database and user interfaces to manage and query GWAS data, in particular to create GWAS (control cohort imputation) data releases.
     97 * __GWAS data analysis __– a catalog of established protocols and bioinformatic pipeline implementations thereof for GWAS analysis.
    9698
    97 ·         __GWAS CQ and imputation protocols__ – harmonization and enrichment of tools and pipelines to verify and clean GWAS data sets and produce data sets ready for analysis by the researcher.
     99 *  __GWAS control cohort and DCGG (GvNL) __– collection of BBMRI-NL GWAS data into the DCGG database and release of imputed datasets  using variation catalog produced by GvNL
    98100
    99 ·         __GWAS data analysis __– a catalog of established protocols and bioinformatic pipeline implementations thereof for GWAS analysis.
     101=== WP3 Biobank (meta)data finding and exchange ===
    100102
    101 ·         __GWAS control cohort and DCGG (GvNL) __– collection of BBMRI-NL GWAS data into the DCGG database and release of imputed datasets  using variation catalog produced by GvNL
     103 *  __Biobank and biobankers catalogue __– central index of biobanks with aggregate metadata on biobank contents (protocols, features observed, optionally (aggregate) data) and semantic search functionality to enable researchers to find biobank(er)s and samples.
    102104
    103 D3 Biobank (meta)data finding and exchange
     105 * __Harmonized data exchange formats __– harmonization of syntaxes / file formats to transfer sample annotations, phenotypic data and molecular data between biobanks and/or central hubs.
    104106
    105 ·         __Biobank and biobankers catalogue __– central index of biobanks with aggregate metadata on biobank contents (protocols, features observed, optionally (aggregate) data) and semantic search functionality to enable researchers to find biobank(er)s and samples.
     107 *  __Pseudonimization system __– to ensure privacy of participants is protected and legal/ethical requirements are addressed (in collaboration with Parelsnoer).
    106108
    107 ·         __Harmonized data exchange formats __– harmonization of syntaxes / file formats to transfer sample annotations, phenotypic data and molecular data between biobanks and/or central hubs.
     109=== WP4 Core software platform (support of above to prevent reinvented wheels) ===
    108110
    109 ·         __Pseudonimization system __– to ensure privacy of participants is protected and legal/ethical requirements are addressed (in collaboration with Parelsnoer).
     111 * __Flexible ‘model-driven’ software platform__ – which allows to efficiently produce, configure and maintain all data models, databases, compute services and pipelines needed.
    110112
    111 D4 Core software platform (support of above to prevent reinvented wheels)
     113 * __Large data platform__ – to harmonize how to deal with the GWAS and NGS data within data archives (storage), algorithms (runtime) and data exchange (network)
    112114
    113 ·         __Flexible ‘model-driven’ software platform__ – which allows to efficiently produce, configure and maintain all data models, databases, compute services and pipelines needed.
     115 * __Flexible compute pipeline platform__ - to harmonize how to run large scale analyses without each pipeline having to bother about how difficult it is to run your algorithms on clusters, grids or clouds with suitable user interfaces
    114116
    115 ·         __Large data platform__ – to harmonize how to deal with the GWAS and NGS data within data archives (storage), algorithms (runtime) and data exchange (network)
    116 
    117 ·         __Flexible compute pipeline platform__ - to harmonize how to run large scale analyses without each pipeline having to bother about how difficult it is to run your algorithms on clusters, grids or clouds with suitable user interfaces
    118 
     117 * __Web access tools__ – harmonized user interfaces and programmers interfaces to provide a single point of access to all the resources developed in this project.
    119118·         __Web access tools__ – harmonized user interfaces and programmers interfaces to provide a single point of access to all the resources developed in this project.