CellML and Related Efforts

Table of Contents

Software and Groups Using CellML

See the tools page for a detailed listing of current tools supporting the use of CellML. Some other related efforts are:

National Simulation Resource, led by Professor James Bassingthwaighte at the university of Washington. This group have developed JSim - a tool capable of running CellML models.
National resource for cell analysis and modeling. This group have developed The Virtual Cell, a general framework for the modelling and simulation of cell physiology.

National Biomedical Computation Resource. NBCR is responsible for the software development of Continuity, a multiscale problem solving environment.

Oxford Cardiac Electrophysiology Group, led by Professor Denis Noble. This group have developed Cellular Open Resource (COR) - a tool used for editing and running CellML models.
Computational Biology, Oxford University, led by Professor David Gavaghan.
Cell/Biodynamics Simulation Project, led by Professor Akinori Noma at Kyoto University.
Cardiac Mechanics Research Group, The University of California, San Diego. Led by Professor Andrew McCulloch.
Cardiac Systems Biology Laboratory, University of Virginia. In particular modelling work carried out by Jeff Saucerman.
Computational Bioengineering Laboratory, The National University of Singapore, led by Martin Buist.
KidneySim - a prototype repository for renal models. Led by Professor S. Randall Thomas.

Sheffield Epitheliome Project led by Professor 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. This project is being led by Professor Donald Bers.

University of New South Wales BME group led by Professor Nigel Lovell.
Fisiocomp: Laboratory of Computational Physiology at the Universidade Federal de Juiz de Fora, Brazil. Led by Professor Rodrigo Weber dos Santos.

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.