Newt

Newt is a free, open-source, web-based viewer and editor for biological pathway maps, developed and maintained by the i-Vis (Information Visualization) Research Lab at Bilkent University, with support from the LCSB at the University of Luxembourg and past contributions from OHSU's Demir Lab and EISBM. It was introduced in a 2021 Bioinformatics paper and is distributed under the GNU LGPL, with source code hosted on GitHub. It runs entirely in the browser without installation, building on the earlier SBGNViz viewer to add full editing capabilities.

Newt is organized around the Systems Biology Graphical Notation (SBGN), rendering pathway models in both the Process Description (PD) and Activity Flow (AF) sublanguages. Its native interchange format is SBGN-ML (format:sbgn-ml-0.3), and it imports and exports several adjacent standards, including SBML (format:sbml-l3v2), the Simple Interaction Format (format:sif), CellDesigner (format:celldesigner), and WikiPathways GPML (format:gpml); some of these conversions are delegated to external services such as MINERVA. This makes Newt a practical bridge between the visual-diagram world of SBGN and the machine-readable model world of SBML.

Technically, Newt is written as a stack of libraries and extensions on top of Cytoscape.js, the same graph-rendering engine used by tool:cytoscape-js and the desktop tool:cytoscape platform. It uses Konva for canvas drawing, Backbone and Bootstrap for the UI, and a Node/Express backend to host conversion services. Automatic layout leans on i-Vis's compound-graph algorithms (the CoSE-Bilkent family), which handle SBGN's nested structures such as complexes, compartments, and submaps.

Distinctive features include semantic validation of SBGN-PD maps with guided fixes, first-class support for compound (nested) nodes, complexity management via hide/show and collapse/expand, experiment-data overlays, alignment guides, and remote model loading by URL. It integrates with pathway databases such as Pathway Commons, Reactome, and WikiPathways, and links out to annotation resources like GeneCards and ChEBI. Compared with editors such as tool:sbgn-ed (a VANTED plug-in) or tool:cytoscape proper, Newt's strengths are zero-install accessibility and strong SBGN conformance. Its main limitations follow from that focus: it is specialized for biological pathway notations rather than general graph formats, and complex conversions depend on backend services, so it is not a general-purpose graph-format converter.