Introduction

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.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.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/ccpnccpn@mole.bio.cam.ac.uk.

Publications

  1. A framework for scientific data modeling and automated software development.
    Cite this
    Fogh RH, Boucher W, Vranken WF, Pajon A, Stevens TJ, Bhat TN, Westbrook J, Ionides JM, Laue ED, 2005-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Rasmus H Fogh
    Developer

    Department of Biochemistry, University of Cambridge

  2. Wayne Boucher
    Developer

  3. Wim F Vranken
    Developer

  4. Anne Pajon
    Developer

  5. Tim J Stevens
    Developer

  6. T N Bhat
    Developer

  7. John Westbrook
    Developer

  8. John M C Ionides
    Developer

  9. Ernest D Laue
    Investigator

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Summary
AccessionBT002419
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++
User InterfaceTerminal Command Line
Download Count0
Submitted ByErnest D Laue