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BioDCV - Features

BioDCV - Features. Application for analysis of microarray and proteomic data with Support Vector Machine (SVM) classifiers A grid application in production since Spring 2005 SQLite database flat files used to manage data/results on grid elements

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BioDCV - Features

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  1. BioDCV - Features • Application for analysis of microarray and proteomic data with Support Vector Machine (SVM)classifiers • A grid application in production since Spring 2005 • SQLite database flat files used to manage data/results on grid elements • BioDCV is written in C language without external libraries or services • Possibility to use LCG2 MPI grid sites • 193 CPU days of scalability and footprint tests on microarray data on the INFN – Egrid VO grid infrastructure • Maldi-TOF proteomics experiments on about 150 grid sites, 220 jobs, 2% failure, on Egee Biomed VO ITC-irst for NA4 biomed meeting at EGEE conference: Ginevra 2006

  2. Grid implementation The BioDCV system • Standard LCG user interface commands • grid-url-copy/lcg-cp db (from local to SE) • edg-job-submit BioDCV.jdl (jdl file) • grid-url-copy/lcg-cp db(from SE to local) In: 2-50 MB Out: 50-400 MB scp grid-ftp scp grid-ftp grid-ftp Grid infrastructure grid-ftp ITC-irst for NA4 biomed meeting at EGEE conference: Ginevra 2006

  3. BioDCV – Gui and Webservice • A Graphics user interface for MS Windows and Linux system (Aug06) • Next steps for GUI: • create JDL file • link to an LCG2/gLite user interface through a webservice Webservice: How? • Apache, mod_python and Zolera SOAP Infrastructure (ZSI) Why? • Use new gLite middleware services • Connect BioDCV to other available bioinformatic applications/tools (first application in: Cannataro M, Barla A, Gallo A, Paoli S, Jurman G, Merler S, Veltri P, Furlanello C. Workflows, ontologies and standards for unbiased prediction in high-throughput proteomics, MGED9, Seattle, Sept 2006) ITC-irst for NA4 biomed meeting at EGEE conference: Ginevra 2006

  4. BioDCV - Availability • SUBVersion repository: http://biodcv.itc.it • A production application for predictive profiling on high-throughput technologies • Computational procedures forcomplete validation • Control Selection Bias and Overfitting • Stability analysis of Biomarker Lists • Applications in molecular oncology • Microarrays: predictive classification • Mass spectrometry (SELDI-TOF, MALDI-TOF) • Contact: Cesare Furlanello (furlan@itc.it) ITC-irst for NA4 biomed meeting at EGEE conference: Ginevra 2006

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