Towards a complete covering of SBML functionalities

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Citations (Scopus)

Abstract

The complexity of biological systems is at times made worse by the diversity of ways in which they are described: the organic evolution of the science over many years has led to a myriad of conventions. This confusion is reflected by the in-silico representation of biological models, where many different computational paradigms and formalisms are used in a variety of software tools. The Systems Biology Markup Language (SBML) is an attempt to overcome this issue and aims to simplify the exchange of information by imposing a standardized way of representing models. The success of the idea is attested to by the fact that more than 110 software tools currently support SBML in one form or another. This work focuses on the translation of the Cyto-Sim simulation language (based on a discrete stochastic implementation of P systems) to SBML. We consider the issues both from the point of view of the employed software architecture and from that of the mapping between the features of the Cyto-Sim language and those of SBML.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages353-366
Number of pages14
Volume4860 LNCS
Publication statusPublished - 2007
Event8th International Workshop on Membrane Computing, WMC 2007 - Thessaloniki, Greece
Duration: Jun 25 2007Jun 28 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4860 LNCS
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other8th International Workshop on Membrane Computing, WMC 2007
CountryGreece
CityThessaloniki
Period6/25/076/28/07

Fingerprint

Markup languages
Systems Biology
Covering
Language
Software
Software Tools
Computer simulation languages
Software architecture
Biological systems
Biological Models
P Systems
Tool Support
Software Architecture
Biological Systems
Computer Simulation
Simplify
Paradigm
Simulation

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Mazza, T. (2007). Towards a complete covering of SBML functionalities. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 4860 LNCS, pp. 353-366). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4860 LNCS).

Towards a complete covering of SBML functionalities. / Mazza, Tommaso.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 4860 LNCS 2007. p. 353-366 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4860 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Mazza, T 2007, Towards a complete covering of SBML functionalities. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 4860 LNCS, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4860 LNCS, pp. 353-366, 8th International Workshop on Membrane Computing, WMC 2007, Thessaloniki, Greece, 6/25/07.
Mazza T. Towards a complete covering of SBML functionalities. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 4860 LNCS. 2007. p. 353-366. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
Mazza, Tommaso. / Towards a complete covering of SBML functionalities. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 4860 LNCS 2007. pp. 353-366 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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