Changes between Version 9 and Version 10 of ProjectOverview


Ignore:
Timestamp:
Sep 5, 2010 8:44:24 PM (11 years ago)
Author:
Morris Swertz
Comment:

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  • ProjectOverview

    v9 v10  
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    2424·         __This project is strongly linked with leading international sister projects to avoid duplicated efforts __and efficiently achieve these aims by having project members participating in, or staying at, institutes like European Bioinformatics Institute (1KG, EGA, !ArrayExpress), Netherlands Bioinformatics Center (NGS, eScience, CWA), projects like EU-GEN2PHEN, EU-BIOSHARE, OMII-UK, ESFRI/ELIXIR, Parelsnoer, Mondriaan, CTMM, TIFN, NPC, NMC, P3G, Human Variome Project and open source collaborations like !ObiBa, MOLGENIS/XGAP, ABEL and Concept Web Alliance.
    25 
    26 == Model driven software ==
     25=== Model driven software ===
    2726Flexible model driven software development as described in Swertz & Jansen (2007) has proven to be an efficient method to rapidly produce harmonized software infrastructures for life scientists while sharing the best models, software and tools notwithstanding large variation in research aims. This project will build and extend upon open source implementations of these methods such as MOLGENIS and Galaxy focusing on:
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    29 ·        Implementing __extensible standard data models and software components__ developed internationally (we co-piloted data models for microarrays, QTLs, GWAS studies [Swertz 2010], and phenotypes in EU consortia like GEN2PHEN and EBI and participated in international GWAS and sequencing initiatives like the 1KG project).
     28 * Implementing __extensible standard data models and software components__ developed internationally (we co-piloted data models for microarrays, QTLs, GWAS studies [Swertz 2010], and phenotypes in EU consortia like GEN2PHEN and EBI and participated in international GWAS and sequencing initiatives like the 1KG project).
    3029
    31 ·        Making tools and protocols reusable in __a user-friendly catalog of bioinformatics tools and workflows __that captures all necessary inputs, outputs, optimization properties and user interactions in models to automatically incorporate existing tools (building or inspired on Taverna and Galaxy).
     30 * Making tools and protocols reusable in __a user-friendly catalog of bioinformatics tools and workflows __that captures all necessary inputs, outputs, optimization properties and user interactions in models to automatically incorporate existing tools (building or inspired on Taverna and Galaxy).
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    33 ·        __Generating automatically from these data and tool models the scalable back-ends and front-ends needed__. This automatic procedure ensures harmonized software results building on industry standard databases for metadata and innovative approaches like cloud computing activities at SARA/Amsterdam, CIT/Groningen and BigGRID/Rotterdam to connect to the scalable compute power and storage needed.
     32 * __Generating automatically from these data and tool models the scalable back-ends and front-ends needed__. This automatic procedure ensures harmonized software results building on industry standard databases for metadata and innovative approaches like cloud computing activities at SARA/Amsterdam, CIT/Groningen and BigGRID/Rotterdam to connect to the scalable compute power and storage needed.
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    35 ·        __Ease finding and integration of resources using semantic and ontology technologies__ such as developed at EBI and NBIC/Concept Web Alliance to build bridges between data and tools, tapping into existing ontologies for data (e.g. HPO for human phenotype ontology) and for analysis protocols to help user and systems developers to bring tools together.
     34 * __Ease finding and integration of resources using semantic and ontology technologies__ such as developed at EBI and NBIC/Concept Web Alliance to build bridges between data and tools, tapping into existing ontologies for data (e.g. HPO for human phenotype ontology) and for analysis protocols to help user and systems developers to bring tools together.
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    3736== Ready-to-use databases and tools ‘in-a-box’ that can federate into national resources ==