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Project #2267
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#2267 : Systems Biology Data Management and Analysis Platform (SYSMAP)
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Name of Applicant : Benno Schwikowski
Date of application : 23-07-2015
Unit : Systems Biology
Location : Laveran Building, 1st floor
Phone : 0145688620
@ Mail : benno@pasteur.fr

Project context and summary :

Most of the national and international projects performed between our lab and the GFMI unit (Anavaj Sakuntabhai) are driven by data collected at different (molecular/cellular/clinical) levels. The increased use/reuse of multiple data sources, large-scale technologies and increasing cohort sizes make state-of-the-art data management and analysis on a project-by-project basis very labor-intensive. To ensure efficiency and quality of our data-rich research, we propose the creation of a Systems Biology data management and analysis platform that provides [a] extensible storage and retrieval of different linked datasets, [b] a standardized workflow system for documentation and efficient generation of reproducible results, [c] versioning of input data, intermediate and end results, software, and parameters. A good Driving Project to guide development and implementation is a LabEx IBEID-funded thesis project in which we apply novel regression algorithms to discover biomolecules associated with the severity of dengue infection. Once successful for the Driving Project, we plan to successively extend the platform to other joint projects. Other necessary features beyond extensions of [a]–[c] are [d] support for visualization of intermediate and end results, [e] a Web-based interface for usability by non-expert users, [f] support of provenance tracking. This project will significantly boost speed and quality of our joint research between experimentation and modeling, and will provide a model for other laboratories involved in data-rich integrative biology. "The development of tools and software platforms that allow the integration of large-scale, diverse data sets into complex models that can then be operated upon and refined by experimentalists in an iterative fashion is perhaps the most critical milestone we must reach in the biological sciences if large-scale data and results are to impact on biological research routinely at all levels." (Eric Schadt 2009, Nature 461, p 218)


Related team publications :
Grange L, Bureau F, Nikolayeva I, Paul R, Van Steen K, *Schwikowski B, *Sakuntabhai A (2015) Filter-free exhaustive odds ratio-based genome-wide interaction approach pinpoints evidence for interaction in the HLA region. BMC Genetics 16(11) doi: 10.1186/s12863-015-0174-3
Shannon P, Markiel A, Ozier O, Baliga N, Amin N, Ramage D, *Schwikowski B, *Ideker T (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res\' 13(11): 2498-2504.
Service Delivery
Project Manager : mdillies@pasteur.fr
Status : Declined


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