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

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