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Generic database for modeling - QxDB: A generic database to support mathematical modeling in biology

By Benjamin Ribba, Philippe Tracqui, Jean-Laurent Boix, Jean-Pierre Boissel and S. Randall Thomas

Abstract

International audienceQxDB is a web-based generic database package designed especially to house quantitative and structural information. Its development was motivated by the need for centralised 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 customised by adapting the contents of the database table containing the descriptors that characterise 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

Topics: [SCCO.COMP]Cognitive science/Computer science, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-GT]Computer Science [cs]/Computer Science and Game Theory [cs.GT], [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], [SDV.MHEP.UN]Life Sciences [q-bio]/Human health and pathology/Urology and Nephrology, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB]
Publisher: 'The Royal Society'
Year: 2006
DOI identifier: 10.1098/rsta.2006.1784
OAI identifier: oai:HAL:hal-00339605v1
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