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QxDB: a generic database to support mathematical modelling in biology.

Benjamin Ribba 1 Philippe Tracqui 2 Jean-Laurent Boix 1 Jean-Pierre Boissel 1 S Randall Thomas 3 
2 DynaCell
TIMC-IMAG - Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525
Abstract : QxDB (quantitative x-modelling database) is a web-based generic database package designed especially to house quantitative and structural information. Its development was motivated by the need for centralized access to such results for development of mathematical models, but its usefulness extends to the general research community of both modellers and experimentalists. Written in PHP (Hyper Preprocessor) and MYSQL, the database is easily adapted to new fields of research and ported to Apache-based web servers. Unlike most existing databases, experimental and observational results curated in QxDB are supplemented by comments from the experts who contribute input to the database, giving their evaluations of experimental techniques, breadth of validity of results, experimental conditions, and the like, thus providing the visitor with a basis for gauging the quality (or appropriateness) of each item for his/her needs. QxDB can be easily customized by adapting the contents of the database table containing the descriptors that characterize each data record according to an informal ontology of the research domain. We will illustrate this adaptability of QxDB by presenting two examples, the first dealing with modelling in oncology and the second with mechanical properties of cells and tissues.
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Submitted on : Thursday, November 22, 2012 - 7:31:26 PM
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Benjamin Ribba, Philippe Tracqui, Jean-Laurent Boix, Jean-Pierre Boissel, S Randall Thomas. QxDB: a generic database to support mathematical modelling in biology.. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 2006, 364 (1843), pp.1517-32. ⟨10.1098/rsta.2006.1784⟩. ⟨hal-00756364⟩



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