title: Standards and ontologies in computational systems biology.
abstract: With the growing importance of computational models in systems biology there has been much interest in recent years to develop standard model interchange languages that permit biologists to easily exchange models between different software tools. In the present chapter two chief model exchange standards, SBML (Systems Biology Markup Language) and CellML are described. In addition, other related features including visual layout initiatives, ontologies and best practices for model annotation are discussed. Software tools such as developer libraries and basic editing tools are also introduced, together with a discussion on the future of modelling languages and visualization tools in systems biology.
authors.affiliation: Department of Bioengineering, William H. Foege Building, Seattle, WA 98195-5061, U.S.A. hsauro@u.washington.edu
authors.forename: Herbert M
authors.initials: HM
authors.lastname: Sauro
authors.forename: Frank T
authors.initials: FT
authors.lastname: Bergmann
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000592:standards*; D011381:Programming Languages; D049490:Systems Biology / Q000592:standards*
references.citation: Prog Biophys Mol Biol. 2004 Jun-Jul;85(2-3):433-50
references.pmid: 15142756
references.citation: BMC Neurosci. 2006 Oct 30;7 Suppl 1:S11
references.pmid: 17118155
references.citation: OMICS. 2003 Winter;7(4):355-72
references.pmid: 14683609
references.citation: Comput Appl Biosci. 1993 Oct;9(5):563-71
references.pmid: 8293329
references.citation: Mol Syst Biol. 2006;2:51
references.pmid: 17016517
references.citation: Nat Biotechnol. 2005 Dec;23(12):1509-15
references.pmid: 16333295
references.citation: BMC Bioinformatics. 2007 Mar 06;8:79
references.pmid: 17341299
references.citation: Bioinformatics. 2006 Aug 1;22(15):1879-85
references.pmid: 16709586
references.citation: Bioinformatics. 2005 Feb 15;21(4):560-1
references.pmid: 15454409
references.citation: Bioinformatics. 2003 Mar 1;19(4):524-31
references.pmid: 12611808
references.citation: Mol Biol Cell. 1999 Aug;10(8):2703-34
references.pmid: 10436023
references.citation: J Theor Biol. 1998 May 7;192(1):117-28
references.pmid: 9628844
references.citation: Bioinformatics. 2006 Dec 1;22(23):2966-7
references.pmid: 17038346
references.citation: Bioinformatics. 1999 Jan;15(1):72-84
references.pmid: 10068694
references.citation: Nat Biotechnol. 2006 Jun;24(6):667-72
references.pmid: 16763599
references.citation: Nat Biotechnol. 2005 Jan;23(1):131-6
references.pmid: 15637632
references.citation: Biochem Soc Trans. 2003 Dec;31(Pt 6):1472-3
references.pmid: 14641091
references.citation: Nat Biotechnol. 2005 Aug;23(8):961-6
references.pmid: 16082367
references.citation: Comput Biomed Res. 1968 Aug;2(1):31-44
references.pmid: 5743538