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NYU Microarray Database (NYUMAD)

NYU Microarray Database (NYUMAD). Marc Rejali. Overview. Supports collaborative research Large data sets Extensible Analysis functionality Efficient and intuitive interface Flexible design Use of standards (MAGE-ML). Custom Web Pages. Java Applet. Web pages. Java Application. Custom

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NYU Microarray Database (NYUMAD)

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  1. NYU Microarray Database (NYUMAD) Marc Rejali

  2. Overview • Supports collaborative research • Large data sets • Extensible Analysis functionality • Efficient and intuitive interface • Flexible design • Use of standards (MAGE-ML)

  3. Custom Web Pages Java Applet Web pages Java Application Custom Application Clustering Modules Custom Calculation & clustering Modules Calculation Modules Java Servlets DB Relational DB Files Architecture/Design Front Tier XML ( MAGE-ML) Local C or C++ modules on user’s computer HTTP Middle Tier C++, C, Java, other languages Back Tier

  4. Data Sharing • Collaborative Data sharing • Controlled visibility/access • group-based read/write access • public/private data • Community access to public data • HTTP communication • XML and MAGE-ML standard • Easy data import/export • Can create customized data sets • Can filter and transform export data

  5. Array Definition Screen

  6. Experiment/Hybridization Data Screen

  7. Data Analysis 1 • Clustering analysis • Data filtering, normalization, transformation • New ‘shrinkage’ similarity measure • Gene and experiment cluster generation • Graphical display of clustering • Expression profile analysis • Find expression profiles correlated/anti-correlated to a given gene’s expression profile • Compare to a synthetic profile • Data filtering, normalization and transformation available

  8. Data Analysis 2 • Use of fast plug-in C/C++ analysis modules • Sophisticated new technique for normalization and differential expression

  9. Clustering Screen

  10. Data Content • Experiments • calculated and typed experimental factors • templates for factor input • Hybridization results • batch and regular import • Array Design • array feature annotations • User arrays • Protocols

  11. Software Engineering • Three-tier architecture ensures performance, scalability and flexibility • Client and Server caching ensure speed • Re-use demonstrated with NYUSIM

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