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  • Alternative biological modeling languages
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BioPAX - http://www.biopax.org - standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data.

SBML - Systems Biology Markup Language (SBML; www.sbml.org) [Hucka et al., 2003] and many published models can be found in the BioModels Database (http://www.ebi.ac.uk/biomodels-main/)

CellML – Supports the exchange and storage of computer based mathematical models of biological systems [Nielsen and Halstead, 2004].

NeuroML – Supports the exchange and description of models “to describe the biophysics, anatomy and network architecture of neuronal systems at multiple scales”1 [Gleeson et al., 2010].

NineML – Describes neuronal networks in a “simulator independent language”2 that is design to in- teract with NeuroML [Gorchetchnikov et al., 2010].

SED-ML – Encodes simulation experiments of SBML and CellML models “to ensure exchangeability 5 and reproducibility of simulation experiments”3 [Waltemath et al., 2011]. 

PharmML - http://www.ddmore.eu - XML based language that will be able to encode models from NONMEM, MONOLIX, BUGS and related tools for Pharmacometricians

HELM - http://www.openhelm.org/ - Hierarchical Editing Language for Macromolecules, from the Pistoia Alliance. (Exchange syntax.)

BioTapestry - http://www.biotapestry.org/ - "is an interactive tool for building, visualizing, and simulating genetic regulatory networks." (Not quite a markup language, but can be exported to CSV.)

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