A model diagram layout extension for SBML

Bioinformatics

Volumn 22, Issue 15, 2006, Pages 1879-1885

  Gauges, Ralph ^a   Rost, Ursula ^a   Sahle, Sven ^a   Wegner, Katja ^a  

^a EML Research   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHEMICAL REACTION; COMPUTER LANGUAGE; DATA ANALYSIS SOFTWARE; INFORMATION PROCESSING; INFORMATION STORAGE; MOLECULAR INTERACTION; MOLECULAR MODEL; PLOTS AND CURVES; PRIORITY JOURNAL; PROCESS DESIGN; PROCESS MODEL; REFERENCE DATABASE; SPECIES; SYSTEMS BIOLOGY;

EID: 33747825750     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl195     Document Type: Article

References (13)

1. Batik, Batik SVG Toolkit.
2. Hucka,M. et al. (2005) Systems Biology Markup Language (SBML) Level 1: Structures and Facilities for Basic Model Definitions.
3. Hucka,M. et al. (2003) The systems biology markup language (sbml): A medium for representation and exchange of biochemical network models. Bioinformatics, 1, 524-531.
4. Hucka,M. and Finney,A. (2003) Systems biology markup language: Level 2 and beyond. Biochem. Soc. Trans., 31, 1472-1473.
5. Karp,P.D. and Paley,S. (1994) Automated drawing of metabolic pathways. In Hunter,L., Searls,D. and Shavlik,J. (eds), Third International Conference on Bioinformatics and Genome Research, AAAI Press, pp. 207-215.
6. Kohn,K.W. et al. (2005) Molecular interaction maps of bioregulatory networks: A general rubric for systems biology. Mol. Biol. Cell, 17, 1-13.
7. Kitano,H. et al. (2005) Using process diagrams for the graphical representation of biological networks. Nat. Biotechnol., 23, 961-966.
8. libSBML. http://www.sbml.org/software/libsbml/, 2006.
9. SBML Layout Extension documentation. http://projects.villa-bosch.de/bcb/sbml/, 2005.
10. Schilling,C.H. et al. (1999) Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era.
11. Schreiber,F. (2002) High quality visualization of biochemical pathways in BioPath. In Silico Biol., 6, 59-73.
12. Sauro,H. (2006) JDesigner SBML Annotation.
13. Wegner,K. and Kummer,U. (2005) A new dynamical layout algorithm for complex biochemical reaction networks. BMC Bioinformatics, 6. http://www.biomedcentral.com/1417-2105/6/212.