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