Changes between Version 12 and Version 13 of ProjectOverview
- Timestamp:
- Sep 5, 2010 8:48:54 PM (14 years ago)
Legend:
- Unmodified
- Added
- Removed
- Modified
-
ProjectOverview
v12 v13 45 45 46 46 * preserving flexibility to go beyond standardization and accommodate specific local needs. 47 == Roadmap == 48 Total duration 3 years 47 49 48 = 8. Duration of project: = 49 3 years 50 ||Planning (matching GvNL planning where appropriate) |||| 51 ||Short read archive || Month 0 – 8|| 50 52 51 Planning (matching GvNL planning where appropriate) 53 ||Biobank catalog pilot || Month 0 – 6|| 52 54 53 Short read archive Month 0 – 8 55 ||Sequence analysis Phase 1 (GvNL) || Month 4 – 16|| 54 56 55 Biobank catalog pilot Month 0 – 6 57 ||Harmonized exchange formats || Month 6 - 24|| 56 58 57 Sequence analysis Phase 1 (GvNL) Month 4 – 16 59 ||Establish variation QC and analysis pipeline || Month 8 – 20|| 58 60 59 Harmonized exchange formats Month 6 - 24 61 ||Sequence analysis Phase 2 (GvNL) Month 8 – 20|| 60 62 61 Establish variation QC and analysis pipeline Month 8 – 20 63 ||Variation catalog/Dutch !HapMap || Month 20|| 62 64 63 Sequence analysis Phase 2 (GvNL) Month 8 – 20 65 ||GWAS data release server || Month 0 – 12|| 64 66 65 Variation catalog/Dutch !HapMap Month 20 67 ||GWAS QC and imputation protocols || Month 6 – 20|| 66 68 67 GWAS data release server Month 0 – 12 69 ||Dutch GWAS Control Cohort (DGCC) || Month 12 –24|| 68 70 69 GWAS QC and imputation protocols Month 6 – 20 71 ||Imputation of available GWA data (GvNL) || Month 20 – 30|| 70 72 71 Dutch GWAS Control Cohort (DGCC) Month 12 –24 73 ||Make sequence data available (GvNL) || Month 12 – 30|| 72 74 73 Imputation of available GWA data (GvNL) Month 20 – 30 75 ||GWAS analysis tools catalog || Month 12 – 36|| 74 76 75 Make sequence data available (GvNL) Month 12 – 30 77 ||Web access tools || Month 22 – 30|| 76 78 77 GWAS analysis tools catalog Month 12 – 36 79 ||Integrated DCGG and Variation catalog web access tools || Month 24 – 36|| 78 80 79 Web access tools Month 22 – 30 81 == Deliverables == 80 82 81 Integrated DCGG and Variation catalog web access tools Month 24 – 36 83 == WP1 Sequencing == 82 84 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. 84 86 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. 86 88 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. 88 90 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. 91 WP2 Genome-wide association analysis 90 92 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. 92 94 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. 94 96 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. 96 98 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 98 100 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 === 100 102 101 · __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. 102 104 103 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. 104 106 105 · __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). 106 108 107 · __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) === 108 110 109 · __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. 110 112 111 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) 112 114 113 · __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 114 116 115 · __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. 119 118 · __Web access tools__ – harmonized user interfaces and programmers interfaces to provide a single point of access to all the resources developed in this project.
