May 6th 2011.
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XML4MAT: Inter-conversion between MatlabTM
structured variables and the markup language MbML
Jonas S Almeida*, Shuyuan Wu, Eberhard O. Voit
Department of Biometry & Epidemiology, Medical University of South Carolina
135 Cannon Street, Suite 303, P.O. Box 250835, Charleston, SC 29425, USA
* corresponding author, almeidaj@musc.edu

Abstract
The MatlabTM programming environment and related public license environments
such as Octave are gaining in popularity for the identification of algorithms and the
rapid prototyping of applications in bioinformatics. At the same time, there is a
strong push to standardize the identification of extended modelling languages (XML)
and their underlying ontologies, to facilitate bioinformatic integration of data and
methods. We hereby introduce a new m-file library, XML4MAT, that supports the
inter-conversion between any MatlabTM structured variable and a specialized extended
markup language (XML), designated as MbML. The library developed also includes
functions to import non-MbML compliant XML structures. The functionality
described is achieved without object-oriented programming, which makes it ideal for
inclusion in declarative programming and implicitly turns m-structures into generalpurpose
object models for data structures. The new library is made freely available at
http://bioinformatics.musc.edu/xml4mat. It is ideally suited for 1) computation of
XML structures in Matlab programming environments and 2) its inter-conversion to
and from a specialized markup language, MbML. This also enables using Matlab
structures as a format to identify new markup languages that are MbML compliant,
with the corresponding gain in clarity and computability for bioinformatic
applications in that environment.

Keywords
XML, Matlab, data structures, ontology, XML4MAT, MbML