CSB model representations

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Systems Model Representations


This page is a placeholder, or under current development; it is here principally to establish the logical framework of the site. The material on this page is correct, but incomplete.


As in any other applied computational discipline, systems models require their own computable abstractions and - hopefully - standards for data- and results exchange.


 

Introductory reading

Kohl (2011) Standards, databases, and modeling tools in systems biology. Methods Mol Biol 696:413-27. (pmid: 21063963)

PubMed ] [ DOI ]


 

Contents

  • Abstractions and Standards
  • SBML
  • CellML

   

Further reading and resources

Krause et al. (2011) Sustainable model building the role of standards and biological semantics. Meth Enzymol 500:371-95. (pmid: 21943907)

PubMed ] [ DOI ]


SBML The systems Biology Markup Language
Hucka et al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19:524-31. (pmid: 12611808)

PubMed ] [ DOI ]


CellML The CellML project at the Auckland Bioengineering Institute
Lloyd et al. (2004) CellML: its future, present and past. Prog Biophys Mol Biol 85:433-50. (pmid: 15142756)

PubMed ] [ DOI ]


BioPAX - Biological Pathway Exchange - a pathway description standard engineered for compatibility with SBML and CellML in areas where the descriptions overlap.
Demir et al. (2010) The BioPAX community standard for pathway data sharing. Nat Biotechnol 28:935-42. (pmid: 20829833)

PubMed ] [ DOI ]