XML Representation of Metabolic P Systems

Author

Manca, Vincenzo ; Marchetti, Luca

Author_Institution

Dept. of Comput. Sci., Univ. of Verona, Verona

fYear

2009

Firstpage

3103

Lastpage

3110

Abstract

Metabolic P systems (MP systems) are a special class of P systems introduced for expressing biological metabolic phenomena. The graphical formalism of MP graphs represents, in a simple and intuitive way, the structure of these systems. However, there are some cases in which they would be better specified by semi-structured textual documents, especially for information exchanging between different computational tools elaborating on different biological aspects. The aim of this paper is to define such a way of exportation from MP graphs to XML documents. It turns out that all properties which guarantee the correctness of MP graphs can be formally described by means of logical formulae on trees, and completely expressed as XML constraints in XSD (XML Schema Definition), a W3C standard for XML validation.

Keywords

XML; biocomputing; trees (mathematics); MP graph; W3C standard; XML representation; XML schema definition; biological metabolic P system; information exchange; logical formulae; semi structured textual document; trees; Biological systems; Biology computing; Chemical processes; Differential equations; Evolution (biology); Immune system; Recruitment; Tree graphs; White blood cells; XML;

fLanguage

English

Publisher

ieee

Conference_Titel

Evolutionary Computation, 2009. CEC '09. IEEE Congress on

Conference_Location

Trondheim

Print_ISBN

978-1-4244-2958-5

Electronic_ISBN

978-1-4244-2959-2

Type

conf

DOI

10.1109/CEC.2009.4983336

Filename

4983336