XML4MAT: Inter-conversion between MatlabTM structured variables and the markup language MbML

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Almeida, Jonas S.
Wu, Shuyuan
Voit, Eberhard O.
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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.
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