CellDesigner

CellDesigner is a structured diagram editor for gene-regulatory and biochemical reaction networks, and, by extension, the name of the file format it produces. It was developed by Akira Funahashi, Hiroaki Kitano, and colleagues at The Systems Biology Institute in Tokyo. Rather than defining a new container, CellDesigner stores models in standard format:sbml-l3v2-family SBML (historically SBML Level 2), so the files remain valid to any SBML-aware tool. What distinguishes the "CellDesigner format" is a set of proprietary extensions carried inside SBML <annotation> elements under the namespace http://www.sbml.org/2001/ns/celldesigner.

These annotations serve two purposes. First, they add graphical layout information—coordinates, sizes, colours, compartment boundaries, and reaction link routing—which plain SBML omits, effectively covering the ground of the later SBML Layout and Render packages. Second, they enrich the biological semantics: species are typed (protein, gene, RNA, ion, complex, and so on), residues and state transitions are recorded, and reactions carry modifier arcs such as catalysis, inhibition, and physical stimulation. The visual vocabulary follows Kitano's process-diagram notation, an ancestor of the Systems Biology Graphical Notation embodied today in format:sbgn-ml-0.3.

CellDesigner is widely used to draft and curate signalling and metabolic pathway maps, to browse and edit SBML models with database cross-references, and to run or export models for kinetic simulation via SBW, COPASI, and SBML ODE solvers. Large curated disease maps are frequently authored and distributed in this format.

The format's chief limitation is that its layout and semantic extensions are specific to CellDesigner and are not equivalent to either SBGN-ML or the standard SBML Layout/Render packages; lossless round-tripping between them is generally not possible. Interoperability therefore relies on dedicated converters—cd2sbgnml for bidirectional CellDesigner-to-format:sbgn-ml-0.3 translation, and editors such as tool:newt and libraries like tool:libsbgn. Because the files are still ordinary SBML XML, general SBML libraries such as libSBML and importers like tool:cy3sbml in tool:cytoscape can read the model layer even when they ignore the CellDesigner-specific glyph details.