A framework for scientific data modeling and automated software development.

TitleA framework for scientific data modeling and automated software development.
Publication TypeJournal Article
Year of Publication2005
AuthorsFogh, R. H., W. Boucher, W. F. Vranken, A. Pajon, T. J. Stevens, T. N. Bhat, J. Westbrook, J. M. C. Ionides, and E. D. Laue
JournalBioinformatics
Volume21
Issue8
Pagination1678-84
Date Published2005 Apr 15
ISSN1367-4803
KeywordsBiopolymers, Computer Simulation, Database Management Systems, Documentation, Guidelines as Topic, Information Storage and Retrieval, Magnetic Resonance Spectroscopy, Models, Biological, Models, Chemical, Reference Standards, Science, Software, Unified Medical Language System
Abstract

MOTIVATION: The lack of standards for storage and exchange of data is a serious hindrance for the large-scale data deposition, data mining and program interoperability that is becoming increasingly important in bioinformatics. The problem lies not only in defining and maintaining the standards, but also in convincing scientists and application programmers with a wide variety of backgrounds and interests to adhere to them.RESULTS: We present a UML-based programming framework for the modeling of data and the automated production of software to manipulate that data. Our approach allows one to make an abstract description of the structure of the data used in a particular scientific field and then use it to generate fully functional computer code for data access and input/output routines for data storage, together with accompanying documentation. This code can be generated simultaneously for different programming languages from a single model, together with, for example for format descriptions and I/O libraries XML and various relational databases. The framework is entirely general and could be applied in any subject area. We have used this approach to generate a data exchange standard for structural biology and analysis software for macromolecular NMR spectroscopy.AVAILABILITY: The framework is available under the GPL license, the data exchange standard with generated subroutine libraries under the LGPL license. Both may be found at http://www.ccpn.ac.uk; http://sourceforge.net/projects/ccpnCONTACT: ccpn@mole.bio.cam.ac.uk.

DOI10.1093/bioinformatics/bti234
Alternate JournalBioinformatics
PubMed ID15613391
Grant ListBB/C512110/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/C512145/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
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