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MEMOPS: Data modelling and automatic code generation

Fogh, Rasmus H. ; Boucher, Wayne ; Ionides, John M. C. ; Vranken, Wim F. ; Stevens, Tim J. ; Laue, Ernest D.

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
In recent years the amount of biological data has exploded to the point where much useful information can only be extracted by complex computational analyses. Such analyses are greatly facilitated by metadata standards, both in terms of the ability to compare data originating from different sources, and in terms of exchanging data in standard forms, e.g. when running processes on a distributed computing infrastructure. However, standards thrive on stability whereas science tends to constantly move, with new methods being developed and old ones modified. Therefore maintaining both metadata standards, and all the code that is required to make them useful, is a non-trivial problem. Memops is a framework that uses an abstract definition of the metadata (described in UML) to generate internal data structures and subroutine libraries for data access (application programming interfaces - APIs - currently in Python, C and Java) and data storage (in XML files or databases). For the individual project these libraries obviate the need for writing code for input parsing, validity checking or output. Memops also ensures that the code is always internally consistent, massively reducing the need for code reorganisation. Across a scientific domain a Memops-supported data model makes it easier to support complex standards that can capture all the data produced in a scientific area, share them among all programs in a complex software pipeline, and carry them forward to deposition in an archive. The principles behind the Memops generation code will be presented, along with example applications in Nuclear Magnetic Resonance (NMR) spectroscopy and structural biology.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
MEMOPS: Data modelling and automatic code generation. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 7(3), 2010

Online-Journal: http://journal.imbio.de/article.php?aid=123
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2010/5023



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