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FruitBreedomics KOM 29-03-2011 9 WP7 presentation
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  • The general objective of this wp is to collect and make available genetic genomic and phenotypic information produced within and outside the èroject to partners and eventually to stakeholders. As you’ll notice I did reorganized a little the objective and more is probably needed since comprehensive banks for many of the data we deals with in this project have been produced in previous and concurrent project, mostly by people in the audience. And of course we must account for this.
  • And of course, during the time between the development of the project and ita approval, sequencing and annotation project have come to a good point. We therefore need to relate our phenotypic and genotipic information to genome and annotation info produce by this project.
  • CDM = conceptual Data Model LDM = Logical Data Model Probabilmente sarebbe meglio appoggiarsi alla struttura del db di AppleBreed (mantenere le stesse chiavi per le interconnessioni fra tabelle/database) ed integrare i dati del GDR. Poi per interrogazione e visualizzazione potremmo strutturare una nostra interfaccia utilizzando i moduli già pronti in AppleBreed (PHP) ed integrandoli dove serve, appoggiando poi il tutto ad un nostro gbrowse come trait d’union fra i marcatori ed i QTL con relativa analisi. Resterebbero da implementare le parti dell’introduzione dati da parte degli utenti, l’analisi dei QTL (retrieval dei geni, analisi delle ontologie, identificazione di pathway coinvolti) e le interfacce mancanti per l’interrogazione e la visualizzazione dei risultati (da aggiungere a quelle già esistenti di AppleBreed)
  • Le parti in rosso sono quelle da implementare, in verde da integrare. Questo considerando di tenere la struttura di AppleBreed come centrale e di integrarla con dati e funzionalità accessorie.

FruitBreedomics KOM 29-03-2011 9 WP7 presentation FruitBreedomics KOM 29-03-2011 9 WP7 presentation Presentation Transcript

  • WP7: Tools and data management WP Alessandra Stella PTP, Italy
  • Objectives
    • To store and manage phenotypic data
        • Characterized genetic material
          • From Fruitbreedomics
          • From other projects and public data banks
    • To store and manage genotypic data
        • At gene, QTL, haplotype level
        • Integration of sequence and annotation information
    • To facilitate data input and retrieval for PBA/LD/MBA studies
        • Standardization – data format
        • Data and tools integration
  • Objectives
    • To improve collaboration among apple/peach genome studies
      • Networking with existing DBs and tools
    • To develop and use novel tools for structural and functional genomic analysis of model traits
        • ‘ Explain’ observed genotype, haplotype / trait association
          • Ascertain novel candidates
          • Phenotype prediction
    • To allow stakeholder to speed up breeding decisions and procedures
  • Approach / Methodology
    • Building the Fruitbreedomics DB
      • T 7.1 Structuring / mirroring of a consensus db
          • Integration and complementation of existing DB
          • Genome Database for Rosacee (GDR)
          • Applebreed DB
      • T 7.2 Construction of a relational DB of phenotypic data for targeted traits
          • User friendly interface
          • Tools for pre-processing and editing
      • T 7.3 Development of pipelines of analysis and storage of detected genomic variation
          • Pipeline for check –editing
          • Use of GDR structure
          • Link to in-house Genome Browser
    B I M S Breeding Information Management System
  • Approach / Methodology
    • Functional and structural analysis of identified genome variation
        • Identified linked/associated variation
        • Candidate regions
      • T 7.4 Meta – analysis
        • Data from PBA and GW studies
        • Development of statistical tools
      • T 7.5 Tools for functional and comparative analysis
  • Expected results / outcomes
    • Fruitbreedomics DB: an integrated informatic structure for apple and peach genetics and breeding
      • Interaction with other DBs management
        • Agreements for structure share/mirroring
      • Fruitbreedomics DB frame set: D7.1 (M12)
      • Phenotypic and genotypic data processing and storing constructed: D7.2 (M24)
      • Tools for functional and comparative analysis developed: D7.3 (M48)
      • DB completion – complete integration of tools D7.4 (M54)
  • Interactions planned with other WPs
    • WP1
      • Information to build the breeder interface
    • WP1, WP2
      • Breeding: input and query of data
    • WP3
      • PBA and QTL: input and query of data
      • Diversity: data input
    • WP4
      • Diversity: input and query of genotype data
      • CC characterization: Input of phenotypic data
    • WP5
      • Phenotyping: input and query of data
  • Partners involved
    • PTP
      • DB hosting
        • Server characteristics
      • DB and interface structuring and building
      • DB management
      • Functional and meta analysis
    • CRA-W
      • DB integration
      • Content evaluation, decision making
      • DB and interface structuring and building
    • DLO
      • DB integration
      • Content evaluation, decision making
      • DB and interface structuring and building
    • All partners
      • Data submission / analysis / query
  • Available DBs and tools Fruit Breedomics DB
    • GDR framework
    • GDR data:
      • markers
      • traits
      • SNPs
      • maps
    AppleBreed DB
    • AppleBreed structure for data management (CDM + LDM)
    • AppleBreed data:
      • genotype
      • phenotype
      • molecular data
      • growthsite
      • organization
  • Fruit Breedomics DB
    • additional interfaces for:
      • user-friendly queries
      • output visualization
      • output download
    • genome data integration:
    • genome browser
    • QTL analysis
    • gene-centered information (ontologies, pathways, etc)
    AppleBreed DB GDR data data input interface
  • Fruit Breedomics DB
      • A shared Linux cluster of 280 Opteron AMD cores 275 at 2.2 GHz is available at PTP. The system is composed by ten chassis of six blades diskless, each one equipped with an Infiniband 4X network card and 8GB of RAM (total 480GB RAM). Storage facilities consist of more than 20TB of disk space, which can be accessed through a dedicated fiber channel network. Database and web interfaces are located on virtual servers, obtained through hardware virtualization of Linux systems. These servers' resources can be reshaped "real-time", on the base of specific requirements and according to the hardware availability, which consist of a server equipped with two Core 2 Quad processors, 32 GB of RAM and 18 TB of disk space, with a RAID6 software for data security ensurance.