The Promise and Shortcomings of XML as an Interchange Format for Computational Models of Biology

Ivan Raikov, Erik De Schutter
2011 Neuroinformatics  
A number of XML-based (Extensible Markup Language 1 ) model description languages have been developed for representing models of dynamic biological processes independently of simulator platforms. NineML 2 is an effort that aims to provide an unambiguous description of large-scale neuronal network models. NeuroML 3 is a language for defining and exchanging descriptions of neuronal cell and network models. The Systems Biology Markup Language 4 (SBML) can represent cell signaling pathways,
more » ... ry networks, and other kinds of biochemical network models. CellML 5 aims for a wider scope of model description and is not specific to any one field of biology.
doi:10.1007/s12021-011-9136-8 pmid:22147428 fatcat:ob7yrujy4zbtlieufqtlgm27wa