CellML and Related Efforts

Table of Contents

Other Markup Languages

Systems Biology Markup Language (SBML) — SBML is CellML's closest cousin. The main difference between the two languages is the scope: CellML is intended to describe the mathematics behind any biological model while SBML is a 'format for representing models of biochemical reaction networks' (from the SBML.org website).

aMAZE Project — 'A WorkBench for the representation, management, annotation and analysis of information on networks of cellular processes.' Of particular interest for us is the aMAZE Data Model.

Biological Pathways Exchange (BioPAX) — The BioPAX interest group is still in the process of developing a 'data exchange format for biological pathways.'

Digital Anatomist Project — meant to 'represent anatomy in a comprehensive and consistent way.' They use a knowledge base that is useful as either a model or for interaction with our developing ontologies.

Kyoto Encyclopedia of Genes and Genomes (KEGG) Database — composed of three pathway, gene, and ligand databases and several gene catalogs.

TAMBIS — compiling biological information sources with a single web interface. TAMBIS uses an ontology of molecular biology and bioinformatics concepts of interest.

BioUML — a 'Java framework for systems biology. It spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization and simulations.' Will eventually import and export CellML pathway models.

Cellular Open Resource (COR) — 'an environment for cellular and multi-cellular modelling'. Imports and exports CellML electrophsyiological models.

Cell Electrophysiology Simulation Environment (CESE) — 'a comprehensive framework specifically designed to perform computational electrophysiological simulations, for example, simulations of cardiac myocyte electrical activity. CESE is useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations.' Imports CellML electrophsyiological models.

Sheffield Epitheliome Project led by Dawn Walker and Rod Smallwood — using CellML to model the interaction of epithelial cells.

LabHEART — a teaching tool that lets you alter simulation parameters of a contemporary cardiac calcium regulation model.

Virtual Cell (VCell) Modeling and Simulation Framework — capable of importing and exporting CellML files. 'This new technology associates biochemical and electrophysiological data describing individual reactions with experimental microscopic image data describing their subcellular locations. Cell physiological events can then be simulated within the empirically derived geometries, thus facilitating the direct comparison of model predictions with experiment.'